From bernd.jagla@pasteur.fr Fri Mar 02 08:38:10 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S3N44-000860-Be>; Fri, 02 Mar 2012 08:38:08 +0100 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S3N44-0000Do-0p>; Fri, 02 Mar 2012 08:38:08 +0100 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 6A2C838104F for ; Fri, 2 Mar 2012 08:38:07 +0100 (CET) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 29C18381044 for ; Fri, 2 Mar 2012 08:38:07 +0100 (CET) Message-ID: <4F5078DD.4060502@pasteur.fr> Date: Fri, 02 Mar 2012 08:38:05 +0100 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:10.0.2) Gecko/20120216 Thunderbird/10.0.2 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/mixed; boundary="------------090708030003070701020107" X-Originating-IP: 157.99.64.82 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1330673888-000018DE-FAA3FC4C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.251668, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST Subject: [Seqan-dev] problem installing seqan X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 02 Mar 2012 07:38:10 -0000 This is a multi-part message in MIME format. --------------090708030003070701020107 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi, I think I have installed seqan correctly, but the make is coming up with some error messages.... Here is what I have done: svn update seqsan-svn/ cd seqsan-svn/ mkdir -p build/Debug cd build/Debug/ cmake ../../ -DCMAKE_BUILD_TYPE=Debug gmake => see gmake.err Could you please have a look and enlighten me what I am doing wrong? Thanks a lot for your kind help, Bernd --------------090708030003070701020107 Content-Type: text/plain; name="gmake.err" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="gmake.err" [ 0%] Generating ../../../core/include/seqan/basic/basic_generated_forwa= rds.h, ../../../core/include/seqan/chaining/chaining_generated_forwards.h= , ../../../core/include/seqan/consensus/consensus_generated_forwards.h, .= =2E/../../core/include/seqan/file/file_generated_forwards.h, ../../../cor= e/include/seqan/find/find_generated_forwards.h, ../../../core/include/seq= an/graph_algorithms/graph_algorithms_generated_forwards.h, ../../../core/= include/seqan/graph_align/graph_align_generated_forwards.h, ../../../core= /include/seqan/graph_msa/graph_msa_generated_forwards.h, ../../../core/in= clude/seqan/graph_types/graph_types_generated_forwards.h, ../../../core/i= nclude/seqan/index/index_generated_forwards.h, ../../../core/include/seqa= n/map/map_generated_forwards.h, ../../../core/include/seqan/misc/misc_gen= erated_forwards.h, ../../../core/include/seqan/modifier/modifier_generate= d_forwards.h, ../../../core/include/seqan/parallel/parallel_generated_for= wards.h, ../../../core/include/seqan/pipe/pipe_generated_forwards.h, ../.= =2E/../core/include/seqan/platform/platform_generated_forwards.h, ../../.= =2E/core/include/seqan/random/random_generated_forwards.h, ../../../core/= include/seqan/refinement/refinement_generated_forwards.h, ../../../core/i= nclude/seqan/score/score_generated_forwards.h, ../../../core/include/seqa= n/seeds/seeds_generated_forwards.h, ../../../core/include/seqan/seeds2/se= eds2_generated_forwards.h, ../../../core/include/seqan/sequence/sequence_= generated_forwards.h, ../../../core/include/seqan/sequence_journaled/sequ= ence_journaled_generated_forwards.h, ../../../core/include/seqan/store/st= ore_generated_forwards.h, ../../../core/include/seqan/system/system_gener= ated_forwards.h, include/seqan/align/align_generated_forwards.h, include/= seqan/basic/basic_generated_forwards.h, include/seqan/chaining/chaining_g= enerated_forwards.h, include/seqan/consensus/consensus_generated_forwards= =2Eh, include/seqan/file/file_generated_forwards.h, include/seqan/find/fi= nd_generated_forwards.h, include/seqan/graph_algorithms/graph_algorithms_= generated_forwards.h, include/seqan/graph_align/graph_align_generated_for= wards.h, include/seqan/graph_msa/graph_msa_generated_forwards.h, include/= seqan/graph_types/graph_types_generated_forwards.h, include/seqan/index/i= ndex_generated_forwards.h, include/seqan/map/map_generated_forwards.h, in= clude/seqan/misc/misc_generated_forwards.h, include/seqan/modifier/modifi= er_generated_forwards.h, include/seqan/parallel/parallel_generated_forwar= ds.h, include/seqan/pipe/pipe_generated_forwards.h, include/seqan/platfor= m/platform_generated_forwards.h, include/seqan/random/random_generated_fo= rwards.h, include/seqan/refinement/refinement_generated_forwards.h, inclu= de/seqan/score/score_generated_forwards.h, include/seqan/seeds/seeds_gene= rated_forwards.h, include/seqan/seeds2/seeds2_generated_forwards.h, inclu= de/seqan/sequence/sequence_generated_forwards.h, include/seqan/sequence_j= ournaled/sequence_journaled_generated_forwards.h, include/seqan/store/sto= re_generated_forwards.h, include/seqan/system/system_generated_forwards.h= create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/graph_types =2E . . . . . . . . . . . . . . . . . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/misc =2E . - - . . . . . . . . . . . . . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/sequence_journaled =2E . . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/find =2E . . . . . . . . . . . . . . . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/score =2E . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/store =2E . . . . . . . . . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/file - . . . . . . . . . . . . . . . . . - . . . - . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/graph_align =2E . . . . . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/align =2E . . . . . . . . . . . . - . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/graph_msa =2E . . . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/platform - - - - - create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/chaining =2E . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .= . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/parallel =2E . - - create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/system - - - - - - - - - . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/basic =2E . - . . . . . . - . - . . . . . . . - - . . . - - . . . . . . . . . .= - - . . . . . . . . . . . . . . . . . - . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/graph_algorithms =2E . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/pipe =2E . . . . . . . . . . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/seeds =2E . . . . . - . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/modifier =2E . . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/sequence =2E - . - . . . . . . . . . . . . . . . . . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/random =2E . . . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/refinement =2E . . . . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/seeds2 =2E . . . . . . . . . . . . . . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/map =2E . . . . - . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/index =2E . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .= . . . - . . - . . . . . . create forwards for /pasteur/solexa2/solexa_travail/PF2/programs/seqan/se= qsan-svn/core/include/seqan/consensus =2E . . . [ 0%] Built target SeqAnCore [ 0%] Building CXX object core/tests/index/CMakeFiles/test_index_creatio= n.dir/test_index_creation.cpp.o /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:1215: error: type/value mi= smatch at argument 1 in template parameter list for 'template struct seqan::EnableIf' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:1215: error: expected a = type, got 'seqan::IsCharType::VALUE' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:1215: error: invalid type = in declaration before ';' token /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:1216: error: type/value mi= smatch at argument 1 in template parameter list for 'template struct seqan::EnableIf' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:1216: error: expected a = type, got 'seqan::IsCharType::VALUE' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:1216: error: invalid type = in declaration before ';' token /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/modifier/modifier_functors.h: In member function 'seqan::DnaQ seq= an::FunctorComplement >::o= perator()(seqan::DnaQ) const': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/modifier/modifier_functors.h:207: error: call of overloaded 'ordV= alue(seqan::Dna)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:229: note: candidates are: typename seqa= n::ValueSize::Type seqan::ordValue(const TValue&) [with TValue =3D seq= an::Dna] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:236: note: typename seqa= n::ValueSize >::Type seqan::= ordValue(const seqan::SimpleType&) [with TValu= e =3D unsigned char, TSpec =3D seqan::Dna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:850: note: = unsigned int seqan::ordValue(const TValue&) [with TValue =3D seqan::Dna]= /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:851: note: = unsigned int seqan::ordValue(const seqan::SimpleType&) [with TValue =3D unsigned char, TSpec =3D seqan::Dna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/modifier/modifier_functors.h: In member function 'seqan::Dna5Q se= qan::FunctorComplement >:= :operator()(seqan::Dna5Q) const': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/modifier/modifier_functors.h:220: error: call of overloaded 'ordV= alue(seqan::Dna5)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:229: note: candidates are: typename seqa= n::ValueSize::Type seqan::ordValue(const TValue&) [with TValue =3D seq= an::Dna5] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:236: note: typename seqa= n::ValueSize >::Type seqan::= ordValue(const seqan::SimpleType&) [with TValu= e =3D unsigned char, TSpec =3D seqan::Dna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:850: note: = unsigned int seqan::ordValue(const TValue&) [with TValue =3D seqan::Dna5= ] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:851: note: = unsigned int seqan::ordValue(const seqan::SimpleType&) [with TValue =3D unsigned char, TSpec =3D seqan::Dna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h: In destructor 'seqan::FiniteOrderedAlph= abetConcept::~FiniteOrderedAlphabetConcept() [with TValue =3D seq= an::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::FiniteOrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:109: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:290: error: call of overloaded 'ordValue= (seqan::SimpleType&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:229: note: candidates are: typename seqa= n::ValueSize::Type seqan::ordValue(const TValue&) [with TValue =3D seq= an::Dna] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:236: note: typename seqa= n::ValueSize >::Type seqan::= ordValue(const seqan::SimpleType&) [with TValu= e =3D unsigned char, TSpec =3D seqan::Dna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:851: note: = unsigned int seqan::ordValue(const seqan::SimpleType&) [with TValue =3D unsigned char, TSpec =3D seqan::Dna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:850: note: = unsigned int seqan::ordValue(const TValue&) [with TValue =3D seqan::Dna]= /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h: In destructor 'seqan::FiniteOrderedAlph= abetConcept::~FiniteOrderedAlphabetConcept() [with TValue =3D seq= an::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::FiniteOrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:110: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:290: error: call of overloaded 'ordValue= (seqan::SimpleType&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:229: note: candidates are: typename seqa= n::ValueSize::Type seqan::ordValue(const TValue&) [with TValue =3D seq= an::Dna5] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:236: note: typename seqa= n::ValueSize >::Type seqan::= ordValue(const seqan::SimpleType&) [with TValu= e =3D unsigned char, TSpec =3D seqan::Dna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:851: note: = unsigned int seqan::ordValue(const seqan::SimpleType&) [with TValue =3D unsigned char, TSpec =3D seqan::Dna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:850: note: = unsigned int seqan::ordValue(const TValue&) [with TValue =3D seqan::Dna5= ] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h: In destructor 'seqan::FiniteOrderedAlph= abetConcept::~FiniteOrderedAlphabetConcept() [with TValue =3D seq= an::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::FiniteOrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:111: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:290: error: call of overloaded 'ordValue= (seqan::SimpleType&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:229: note: candidates are: typename seqa= n::ValueSize::Type seqan::ordValue(const TValue&) [with TValue =3D seq= an::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:236: note: typename seqa= n::ValueSize >::Type seqan::= ordValue(const seqan::SimpleType&) [with TValu= e =3D unsigned char, TSpec =3D seqan::DnaQ_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:851: note: = unsigned int seqan::ordValue(const seqan::SimpleType&) [with TValue =3D unsigned char, TSpec =3D seqan::DnaQ_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:850: note: = unsigned int seqan::ordValue(const TValue&) [with TValue =3D seqan::Simp= leType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h: In destructor 'seqan::FiniteOrderedAlph= abetConcept::~FiniteOrderedAlphabetConcept() [with TValue =3D seq= an::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::FiniteOrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:112: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:290: error: call of overloaded 'ordValue= (seqan::SimpleType&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:229: note: candidates are: typename seqa= n::ValueSize::Type seqan::ordValue(const TValue&) [with TValue =3D seq= an::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:236: note: typename seqa= n::ValueSize >::Type seqan::= ordValue(const seqan::SimpleType&) [with TValu= e =3D unsigned char, TSpec =3D seqan::Dna5Q_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:851: note: = unsigned int seqan::ordValue(const seqan::SimpleType&) [with TValue =3D unsigned char, TSpec =3D seqan::Dna5Q_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:850: note: = unsigned int seqan::ordValue(const TValue&) [with TValue =3D seqan::Simp= leType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h: In destructor 'seqan::FiniteOrderedAlph= abetConcept::~FiniteOrderedAlphabetConcept() [with TValue =3D seq= an::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::FiniteOrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:113: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:290: error: call of overloaded 'ordValue= (seqan::SimpleType&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:229: note: candidates are: typename seqa= n::ValueSize::Type seqan::ordValue(const TValue&) [with TValue =3D seq= an::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:236: note: typename seqa= n::ValueSize >::Type seqan::= ordValue(const seqan::SimpleType&) [with TValu= e =3D unsigned char, TSpec =3D seqan::Rna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:851: note: = unsigned int seqan::ordValue(const seqan::SimpleType&) [with TValue =3D unsigned char, TSpec =3D seqan::Rna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:850: note: = unsigned int seqan::ordValue(const TValue&) [with TValue =3D seqan::Simp= leType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h: In destructor 'seqan::FiniteOrderedAlph= abetConcept::~FiniteOrderedAlphabetConcept() [with TValue =3D seq= an::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::FiniteOrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:114: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:290: error: call of overloaded 'ordValue= (seqan::SimpleType&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:229: note: candidates are: typename seqa= n::ValueSize::Type seqan::ordValue(const TValue&) [with TValue =3D seq= an::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:236: note: typename seqa= n::ValueSize >::Type seqan::= ordValue(const seqan::SimpleType&) [with TValu= e =3D unsigned char, TSpec =3D seqan::Rna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:851: note: = unsigned int seqan::ordValue(const seqan::SimpleType&) [with TValue =3D unsigned char, TSpec =3D seqan::Rna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:850: note: = unsigned int seqan::ordValue(const TValue&) [with TValue =3D seqan::Simp= leType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h: In destructor 'seqan::FiniteOrderedAlph= abetConcept::~FiniteOrderedAlphabetConcept() [with TValue =3D seq= an::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::FiniteOrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:115: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:290: error: call of overloaded 'ordValue= (seqan::SimpleType&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:229: note: candidates are: typename seqa= n::ValueSize::Type seqan::ordValue(const TValue&) [with TValue =3D seq= an::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:236: note: typename seqa= n::ValueSize >::Type seqan::= ordValue(const seqan::SimpleType&) [with TValu= e =3D unsigned char, TSpec =3D seqan::Iupac_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:851: note: = unsigned int seqan::ordValue(const seqan::SimpleType&) [with TValue =3D unsigned char, TSpec =3D seqan::Iupac_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:850: note: = unsigned int seqan::ordValue(const TValue&) [with TValue =3D seqan::Simp= leType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h: In destructor 'seqan::FiniteOrderedAlph= abetConcept::~FiniteOrderedAlphabetConcept() [with TValue =3D seq= an::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::FiniteOrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:116: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:290: error: call of overloaded 'ordValue= (seqan::SimpleType&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:229: note: candidates are: typename seqa= n::ValueSize::Type seqan::ordValue(const TValue&) [with TValue =3D seq= an::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_storage.h:236: note: typename seqa= n::ValueSize >::Type seqan::= ordValue(const seqan::SimpleType&) [with TValu= e =3D unsigned char, TSpec =3D seqan::AminoAcid_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:851: note: = unsigned int seqan::ordValue(const seqan::SimpleType&) [with TValue =3D unsigned char, TSpec =3D seqan::AminoAcid_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/sequence/sequence_generated_forwards.h:850: note: = unsigned int seqan::ordValue(const TValue&) [with TValue =3D seqan::Simp= leType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:203: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:88: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:215: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::Dna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::Dna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:204: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:88: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:206: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::Dna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::Dna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:206: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:88: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:189: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::Dna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::Dna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:207: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:88: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:180: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::Dna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::Dna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:203: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:89: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:215: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::Dna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::Dna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:204: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:89: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:206: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::Dna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::Dna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:206: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:89: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:189: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::Dna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::Dna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:207: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:89: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:180: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::Dna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::Dna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:203: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:90: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:215: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::DnaQ_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::DnaQ_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:204: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:90: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:206: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::DnaQ_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::DnaQ_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:206: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:90: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:189: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::DnaQ_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::DnaQ_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:207: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:90: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:180: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::DnaQ_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::DnaQ_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:203: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:91: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:215: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::Dna5Q_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::Dna5Q_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:204: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:91: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:206: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::Dna5Q_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::Dna5Q_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:206: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:91: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:189: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::Dna5Q_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::Dna5Q_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:207: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:91: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:180: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::Dna5Q_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::Dna5Q_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:203: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:92: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:215: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::Rna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::Rna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:204: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:92: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:206: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::Rna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::Rna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:206: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:92: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:189: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::Rna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::Rna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:207: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:92: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:180: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::Rna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::Rna_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:203: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:93: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:215: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::Rna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::Rna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:204: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:93: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:206: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::Rna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::Rna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:206: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:93: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:189: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::Rna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::Rna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:207: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:93: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:180: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::Rna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::Rna5_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:203: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:94: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:215: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::Iupac_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::Iupac_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:204: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:94: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:206: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::Iupac_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::Iupac_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:206: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:94: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:189: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::Iupac_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::Iupac_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:207: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:94: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:180: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguous /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::Iupac_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::Iupac_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:203: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:95: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:215: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguou= s /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::AminoAcid_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::AminoAcid_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::minValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:204: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:95: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:206: error: call of overloaded 'infimumValu= eImpl(seqan::SimpleType*&)' is ambiguou= s /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:1927: note: candidates are: seqa= n::SimpleType seqan::infimumValueImpl(seqan::S= impleType*) [with TValue =3D unsigned char, TS= pec =3D seqan::AminoAcid_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:230: note: const = T& seqan::infimumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:264: note: const seqan::S= impleType& seqan::infimumValueImpl(seqan::Simp= leType*) [with TValue =3D unsigned char, TSpec= =3D seqan::AminoAcid_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue(T) [= with T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:206: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:95: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:189: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguo= us /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::AminoAcid_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::AminoAcid_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h: In function 'const T& seqan::maxValue() [w= ith T =3D seqan::SimpleType]': /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_concept.h:207: instantiated from 'seqan::Ordered= AlphabetConcept::~OrderedAlphabetConcept() [with TValue =3D seqan= ::SimpleType]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/concept_checking.h:355: instantiated from 'static void se= qan::requirement::failed()= [with Model =3D seqan::OrderedAlphabetConcept >]' /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_test_concepts.h:95: instantiated from here /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_math.h:180: error: call of overloaded 'supremumVal= ueImpl(seqan::SimpleType*&)' is ambiguo= us /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/basic_generated_forwards.h:2410: note: candidates are: seqa= n::SimpleType seqan::supremumValueImpl(seqan::= SimpleType*) [with TValue =3D unsigned char, T= Spec =3D seqan::AminoAcid_] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_adapt_builtins.h:182: note: const = T& seqan::supremumValueImpl(T*) [with T =3D seqan::SimpleType] /pasteur/solexa2/solexa_travail/PF2/programs/seqan/seqsan-svn/core/includ= e/seqan/basic/alphabet_simple.h:285: note: const seqan::S= impleType& seqan::supremumValueImpl(seqan::Sim= pleType*) [with TValue =3D unsigned char, TSpe= c =3D seqan::AminoAcid_] gmake[2]: *** [core/tests/index/CMakeFiles/test_index_creation.dir/test_i= ndex_creation.cpp.o] Error 1 gmake[1]: *** [core/tests/index/CMakeFiles/test_index_creation.dir/all] E= rror 2 gmake: *** [all] Error 2 --------------090708030003070701020107-- From manuel.holtgrewe@fu-berlin.de Fri Mar 02 09:00:17 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S3NPU-0000Lk-8n>; Fri, 02 Mar 2012 09:00:16 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S3NPU-0005yF-6d>; Fri, 02 Mar 2012 09:00:16 +0100 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.101]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1S3NPU-0007pP-40>; Fri, 02 Mar 2012 09:00:16 +0100 Message-ID: <4F507E0F.5070908@fu-berlin.de> Date: Fri, 02 Mar 2012 09:00:15 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:10.0.2) Gecko/20120216 Thunderbird/10.0.2 MIME-Version: 1.0 To: SeqAn Development References: <4F5078DD.4060502@pasteur.fr> In-Reply-To: <4F5078DD.4060502@pasteur.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1330675216-000018DE-10E0CFFE/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] problem installing seqan X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 02 Mar 2012 08:00:17 -0000 Bernd, that appears to be a bug in SeqAn. Can you give a minimal example source code on how you triggered this? Manuel On 03/02/2012 08:38 AM, Bernd Jagla wrote: > Hi, > > I think I have installed seqan correctly, but the make is coming up with > some error messages.... > > Here is what I have done: > > svn update seqsan-svn/ > cd seqsan-svn/ > mkdir -p build/Debug > cd build/Debug/ > cmake ../../ -DCMAKE_BUILD_TYPE=Debug > gmake > > => see gmake.err > > Could you please have a look and enlighten me what I am doing wrong? > > Thanks a lot for your kind help, > > Bernd > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From manuel.holtgrewe@fu-berlin.de Fri Mar 02 09:06:17 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S3NVI-0000Wm-O5>; Fri, 02 Mar 2012 09:06:16 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S3NVI-0006ss-Ls>; Fri, 02 Mar 2012 09:06:16 +0100 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.101]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1S3NVI-0008AI-JL>; Fri, 02 Mar 2012 09:06:16 +0100 Message-ID: <4F507F78.4010309@fu-berlin.de> Date: Fri, 02 Mar 2012 09:06:16 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:10.0.2) Gecko/20120216 Thunderbird/10.0.2 MIME-Version: 1.0 To: SeqAn Development References: <4F5078DD.4060502@pasteur.fr> In-Reply-To: <4F5078DD.4060502@pasteur.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1330675576-000018DE-4E1F4D08/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] problem installing seqan X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 02 Mar 2012 08:06:17 -0000 Sorry, I misread your email, this is generated in unchanged SeqAn sources, right? What is the version of the G++ program in your MinGW (I assume) install? You can generate it with c:\MinGW\g++.exe --version or c:\MinGW\mingw32-g++.exe --version. *m On 03/02/2012 08:38 AM, Bernd Jagla wrote: > Hi, > > I think I have installed seqan correctly, but the make is coming up with > some error messages.... > > Here is what I have done: > > svn update seqsan-svn/ > cd seqsan-svn/ > mkdir -p build/Debug > cd build/Debug/ > cmake ../../ -DCMAKE_BUILD_TYPE=Debug > gmake > > => see gmake.err > > Could you please have a look and enlighten me what I am doing wrong? > > Thanks a lot for your kind help, > > Bernd > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From bernd.jagla@pasteur.fr Fri Mar 02 09:38:10 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S3O07-0001Za-Eo>; Fri, 02 Mar 2012 09:38:07 +0100 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S3O07-0006LP-BO>; Fri, 02 Mar 2012 09:38:07 +0100 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id E4711381050 for ; Fri, 2 Mar 2012 09:38:06 +0100 (CET) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id C1114381044 for ; Fri, 2 Mar 2012 09:38:06 +0100 (CET) Message-ID: <4F5086ED.4050000@pasteur.fr> Date: Fri, 02 Mar 2012 09:38:05 +0100 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:10.0.2) Gecko/20120216 Thunderbird/10.0.2 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: <4F5078DD.4060502@pasteur.fr> <4F507F78.4010309@fu-berlin.de> In-Reply-To: <4F507F78.4010309@fu-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 157.99.64.82 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1330677487-000018DE-15AFDBE7/3532917630-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: xx X-Spam-Status: No, score=2.4 required=5.0 tests=DNS_FROM_RFC_POST, FU_XPURGATE_SUSP Subject: Re: [Seqan-dev] problem installing seqan X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 02 Mar 2012 08:38:10 -0000 Hi Manuel, I have started from scratch now (new fresh check out) and it seems to be working... Thanks for your help... Bernd On 3/2/2012 9:06 AM, Manuel Holtgrewe wrote: > Sorry, I misread your email, this is generated in unchanged SeqAn > sources, right? > > What is the version of the G++ program in your MinGW (I assume) > install? You can generate it with c:\MinGW\g++.exe --version or > c:\MinGW\mingw32-g++.exe --version. > > *m > > On 03/02/2012 08:38 AM, Bernd Jagla wrote: >> Hi, >> >> I think I have installed seqan correctly, but the make is coming up with >> some error messages.... >> >> Here is what I have done: >> >> svn update seqsan-svn/ >> cd seqsan-svn/ >> mkdir -p build/Debug >> cd build/Debug/ >> cmake ../../ -DCMAKE_BUILD_TYPE=Debug >> gmake >> >> => see gmake.err >> >> Could you please have a look and enlighten me what I am doing wrong? >> >> Thanks a lot for your kind help, >> >> Bernd >> >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > From bernd.jagla@pasteur.fr Wed Mar 07 11:35:18 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5EDF-00044J-7X>; Wed, 07 Mar 2012 11:35:17 +0100 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5EDF-0001BS-49>; Wed, 07 Mar 2012 11:35:17 +0100 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 80EBD381057 for ; Wed, 7 Mar 2012 11:35:16 +0100 (CET) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 37635381056 for ; Wed, 7 Mar 2012 11:35:16 +0100 (CET) Message-ID: <4F5739DB.5060409@pasteur.fr> Date: Wed, 07 Mar 2012 11:35:07 +0100 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:10.0.2) Gecko/20120216 Thunderbird/10.0.2 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: <1323956442.11617.4.camel@IR0912.bgbm.fu-berlin.de> <4EE9FBA6.6000306@fu-berlin.de> In-Reply-To: <4EE9FBA6.6000306@fu-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 157.99.64.82 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1331116517-000018DE-A5FA2DAC/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST Subject: [Seqan-dev] newbie question X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 07 Mar 2012 10:35:18 -0000 Hi, I am not very familiar with C++, nor templates etc so sorry for my ignorance... Since I am not using Eclipse at the moment I am relying on the trac pages and tutorials to give me the information I am looking for. Unfortunately this is not working as expected. I would like to write a simple record reader for a fastq file. There is an example for a fasta file and it shouldn't be that difficult to translate this into a fastq reader. But when I search for fastq in the track pages (http://docs.seqan.de/seqan/dev/) I don't get any results. I can't even find function Fasta() that is mentioned in the tutorial (http://trac.seqan.de/wiki/Tutorial/ReadingSequenceFiles)... Could you please enlighten me on what I am doing wrong? Thanks a lot, Bernd From bernd.jagla@pasteur.fr Wed Mar 07 15:32:42 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5Huz-0003Qo-O4>; Wed, 07 Mar 2012 15:32:41 +0100 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5Huz-0008DL-Kl>; Wed, 07 Mar 2012 15:32:41 +0100 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 70D42381060 for ; Wed, 7 Mar 2012 15:32:40 +0100 (CET) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 7984B38105F for ; Wed, 7 Mar 2012 15:32:37 +0100 (CET) Message-ID: <4F577183.3010200@pasteur.fr> Date: Wed, 07 Mar 2012 15:32:35 +0100 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:10.0.2) Gecko/20120216 Thunderbird/10.0.2 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 157.99.64.82 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1331130761-000018DE-7ED31A27/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST Subject: [Seqan-dev] comparison to python X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 07 Mar 2012 14:32:42 -0000 Hi, this is just to warn you that there WILL be more questions coming... ;) I just got the results back from a comparison between a simple seqan fastq reader and python version of such and it turns out that seqan is almost 100% faster : 13:38 min vs. 6:55 with the same CPU load and system resources being used... Thanks for this nice tool.... Looking forward, Bernd From manuel.holtgrewe@fu-berlin.de Wed Mar 07 18:09:20 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5KMZ-00005u-NC>; Wed, 07 Mar 2012 18:09:19 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5KMZ-0007jm-Kf>; Wed, 07 Mar 2012 18:09:19 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5KMZ-00081r-EX>; Wed, 07 Mar 2012 18:09:19 +0100 Received: from EX02A.campus.fu-berlin.de ([169.254.1.147]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.02.0283.003; Wed, 7 Mar 2012 18:09:19 +0100 From: "Holtgrewe, Manuel" To: 'SeqAn Development' Thread-Topic: [Seqan-dev] newbie question Thread-Index: AQHM/E4Dp9Xhz1csw0W0zS/ZJVwVtpZfD8Dg Date: Wed, 7 Mar 2012 17:09:18 +0000 Message-ID: References: <1323956442.11617.4.camel@IR0912.bgbm.fu-berlin.de> <4EE9FBA6.6000306@fu-berlin.de> <4F5739DB.5060409@pasteur.fr> In-Reply-To: <4F5739DB.5060409@pasteur.fr> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 130.133.170.202 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1331140159-000018DE-C2EBE29C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.0 required=5.0 tests=none Subject: Re: [Seqan-dev] newbie question X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 07 Mar 2012 17:09:21 -0000 Bernd, You have just discovered tag-based dispatch. Actually, Fasta and Fastq are = types in the seqan namespace. When using a class name as an expression (as you are in the readRecord() fu= nction call, using "KlassName()" creates a new object. Now, there are vario= us different template functions with the same name and slightly different s= ignatures, similar to: template int readRecord(TString & target, Fasta const &)= { ... } template int readRecord(TString & target, Fastq const &) = { ... } When you use the tag Fasta() then the first overload is used, with Fastq() = the second one is used. I assume that you could solve the original question from your other email. Cheers, HTH! Manuel -----Original Message----- From: Bernd Jagla [mailto:bernd.jagla@pasteur.fr]=20 Sent: Mittwoch, 7. M=E4rz 2012 11:35 To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] newbie question Hi, I am not very familiar with C++, nor templates etc so sorry for my ignoranc= e... Since I am not using Eclipse at the moment I am relying on the trac pages a= nd tutorials to give me the information I am looking for.=20 Unfortunately this is not working as expected. I would like to write a simple record reader for a fastq file. There is an = example for a fasta file and it shouldn't be that difficult to translate th= is into a fastq reader. But when I search for fastq in the track pages (htt= p://docs.seqan.de/seqan/dev/) I don't get any results. I can't even find fu= nction Fasta() that is mentioned in the tutorial (http://trac.seqan.de/wiki= /Tutorial/ReadingSequenceFiles)... Could you please enlighten me on what I am doing wrong? Thanks a lot, Bernd _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev From fheeger@mi.fu-berlin.de Thu Mar 08 16:51:22 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5fcf-0001Zn-5a>; Thu, 08 Mar 2012 16:51:21 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5fcf-00040I-32>; Thu, 08 Mar 2012 16:51:21 +0100 Received: from bgbm6.bgbm.fu-berlin.de ([160.45.63.17] helo=[192.168.2.164]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1S5fcf-0004Hh-0N>; Thu, 08 Mar 2012 16:51:21 +0100 From: Felix Heeger To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset="UTF-8" Date: Thu, 08 Mar 2012 16:51:13 +0100 Message-ID: <1331221873.2093.13.camel@ZOO97.IUF.loc> Mime-Version: 1.0 X-Mailer: Evolution 2.28.3 Content-Transfer-Encoding: quoted-printable X-Originating-IP: 160.45.63.17 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1331221881-000018DE-41527A2C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.134689, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: [Seqan-dev] SplazerS crash X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 08 Mar 2012 15:51:22 -0000 Hi, I am trying to use SplazerS for RNA read mapping. For certain input files I get the following error: "/home/heeger/seqan/core/include/seqan/sequence/segment_infix.h:722 Assertion failed : pos < static_cast(length(me)) was: 0 >=3D 0 (Trying to acces an element behind the last one!)" This is compiled from the head version of the svn. I am running on Debian 64. The input files I used for this are here: reference: http://page.mi.fu-berlin.de/heeger/problem.fa reads: http://page.mi.fu-berlin.de/heeger/reads.fa I am running the following command line: splazers -vv -m1 -id -i95 problem.fa reads.fa I will attach the complete output at the bottom. I tired to download the release version of SplazerS, but the download does not work (probably due to changes in the homepage). Thanks in advance, felix Complete output of SplazerS: bin/splazers -vv -m1 -id -i95 problem.fa reads.fas=20 Read length =3D 18bp Max num errors =3D 1 Recognition rate =3D 99% --> Reading bin/gapped_params/results_N18_L.dat Couldn't open file bin/gapped_params/results_N18_L.dat Couldn't find preprocessed parameter files. Please configure manually (options --shape and --threshold). Using default configurations (shape =3D 11111111111 and q-gram lemma). ___PARAMETER_CHOOSING__ Read length =3D 18bp Max num errors =3D 1 Recognition rate =3D 99% --> Reading bin/gapped_params/results_N18_L.dat Couldn't open file bin/gapped_params/results_N18_L.dat Couldn't find preprocessed parameter files. Please configure manually (options --shape and --threshold). Using default configurations (shape =3D 11111111111 and q-gram lemma). ___SETTINGS____________ Genome file: problem.fa Read file: reads.fasta Compute forward matches: YES Compute reverse matches: YES Error rate: 0.05 Minimal threshold: 1 Shape: 11111111111 Suffix Minimal threshold: 1 Suffix Shape: 11111111111 Repeat threshold: 1000 Overabundance threshold: 1 Taboo length: 1 Ignoring 202 low quality reads. 26734561 bps of 356659 reads loaded. Loading reads took 6.10979 seconds Expected number of random deletion-indicating matches: 7.98111e-19 Expected number of random insertion-indicating matches: 0.000145028 Performing spliced mapping. Make index left right Patterns created Process genome seq #0[fwd]/home/heeger/seqan/core/include/seqan/sequence/segment_infix.h:722 A= ssertion failed : pos < static_cast(length(me)) was: 0 >=3D 0 (Trying= to acces an element behind the last one!) stack trace: 0 [0x5c5675] seqan::ClassTest::fail() + 0xe 1 [0x601f10] seqan::Reference, seqan::Alloc >, seqan::InfixSegment> const>::Type seqan::value, seqan::Alloc >, seqan::InfixSegment, int>(seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&, int) + 0x59 2 [0x601f49] seqan::SimpleType& seqan::Segment, seqan::Alloc >, seqan::InfixSegment>::operator[](int) const + 0x1b 3 [0x601f71] int seqan::score, int, int, seqan::Segment, seqan::Alloc >, seqan::InfixSegment>, seqan::Segment, seqan::Alloc >, seqan::InfixSegment> >(seqan::Score > const&, int, int, seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&, seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&) + 0x26 4 [0x602278] int seqan::_extendSeedOneDirection const, int, seqan::Segment, seqan::Alloc >, seqan::InfixSegment>, seqan::Segment, seqan::Alloc >, seqan::InfixSegment>, int, int>(seqan::Seed const>&, seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&, seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&, int, seqan::Score > const&, int) + 0x2d0 5 [0x602cef] void seqan::extendSeedScore const, int, seqan::Segment, seqan::Alloc >, seqan::InfixSegment>, seqan::Segment, seqan::Alloc >, seqan::InfixSegment>, int, int>(seqan::Seed const>&, int&, int, seqan::Score > const&, seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&, seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&, int, seqan::Tag) + 0x285 6 [0x603a35] void seqan::extendMatch, seqan::Alloc >, seqan::Owner > >, unsigned int, seqan::Segment, seqan::Alloc >, seqan::InfixSegment>,= seqan::ReadMatch, seqan::RazerSOptions > const>(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, unsigned int, seqan::Segment, seqan::Alloc >, seqan::InfixSegment>&, seqa= n::ReadMatch&, seqan::RazerSOptions >= const&, seqan::LongestPrefix) + 0x204 7 [0x603f67] bool seqan::matchVerify, seqan::String, seqan::Alloc >, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::InfixSegment>,= seqan::Myers >, seqan::Alloc >,= seqan::RazerSSpec, seqan::LongestPrefix>(seqan::ReadMatch&, seqan::Segment, seqan::Alloc >, seqan::InfixSegment>, unsigned int, seqan::S= tringSet, seq= an::Alloc >, seqan::Owner > >&, seqan::Stri= ng, seqan::Alloc >, seqan::InfixSegment>, seqan::Mye= rs >, seqan::Alloc >&, seqan::Ra= zerSOptions > const&, seqan::Tag >, seqan::LongestPrefix) + 0x42a 8 [0x6716d3] void seqan::mapSplicedReads, seqan::Alloc >, seqan::String, seqan::Alloc >, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::Index, seqan::Alloc >, seqan::InfixSegment>= , seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0u>= >, seqan::Tag > >, seqan::Index, seqan= ::Alloc >, seqan::InfixSegment>, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0u> >, seqan::Tag > >, s= eqan::Tag >, seqan::String, = seqan::Alloc >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc >, seqan::String >, seqan::Alloc >, seqan::RazerSSpec<= false, false> >(seqan::String, seqan::Alloc >&= , seqan::String, seqan::All= oc >&, unsigned int, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, seqan::Pattern, seqan::Alloc= >, seqan::InfixSegment>, seqan::Owner > >, seq= an::IndexQGram, = seqan::UngappedShape<0u> >, seqan::Tag > >, seqan::Swift > > >&, seqan::Pattern, seqan::Alloc >, seqan::InfixSegment>, seqan::Own= er > >, seqan::IndexQGram, seqan::UngappedShape<0u> >, seqan::T= ag > >, seqan::Swift > > >&, seqan::String, seqan::Alloc >, seqan::In= fixSegment>, seqan::Myers >, seqan::Al= loc >&, seqan::String, seqan::Alloc >, seqan::= InfixSegment>, seqan::Myers >, seqan::= Alloc >&, seqan::String >, seqan::Alloc >&, char, seqan::RazerSOptions >&) + 0x110f 9 [0x673333] int seqan::mapSplicedReads, seqan::Alloc >, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String >, seqan::Alloc >, seqan::RazerSSpec, seqan::Shape, seqan::UngappedShape<0u> >, seqan::Shape, seqan::UngappedShape<0u> >, seqan::Tag > >(seqan::String, seqan::Alloc >&, seqan::StringSet >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, std::map, std::less, std::allocator > > >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, seqan::String >, seqan::Alloc >&, seqan::RazerSOptions >&, seqan::Shape, seqan::UngappedShape<0u> > const&, seqan::Shape, seqan::UngappedShape<0u> > const&, seqan::Swift > >) + 0xd98 10 [0x68dda6] int seqan::mapSplicedReads, seqan::Alloc >, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String >, seqan::Alloc >, seqan::RazerSSpec >(seqan::String, seqan::Alloc >&, seqan::StringSet >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, std::map, std::less, std::allocator > > >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, seqan::String >, seqan::Alloc >&, seqan::RazerSOptions >&) + 0x703 11 [0x68e3ed] int seqan::mapReads, seqan::Alloc >, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String >, seqan::Alloc >, seqan::RazerSSpec >(seqan::String, seqan::Alloc >&, seqan::StringSet >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, std::map, std::less, std::allocator > > >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, seqan::String >, seqan::Alloc >&, seqan::RazerSOptions >&) + 0x98 12 [0x69a4b4] int mapReads >(seqan::StringSet >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >&, seqan::RazerSOptions >&) + 0xbae 13 [0x56f5c4] main + 0x8125 14 [0x7fc1c67591a6] __libc_start_main + 0xe6 15 [0x566f59] std::ios_base::Init::~Init() + 0x41 Aborted From Anne-Katrin.Emde@fu-berlin.de Thu Mar 08 20:45:05 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5jGq-0000TL-77>; Thu, 08 Mar 2012 20:45:04 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5jGq-00080N-3f>; Thu, 08 Mar 2012 20:45:04 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5jGp-00080O-Pg>; Thu, 08 Mar 2012 20:45:04 +0100 Received: from EX01A.campus.fu-berlin.de ([169.254.1.252]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.02.0283.003; Thu, 8 Mar 2012 20:45:03 +0100 From: "Emde, Anne-Katrin" To: SeqAn Development Thread-Topic: [Seqan-dev] SplazerS crash Thread-Index: AQHM/UNWihp3LpEPUUShJj1fEJDUsJZgw2Pl Date: Thu, 8 Mar 2012 19:45:01 +0000 Message-ID: References: <1331221873.2093.13.camel@ZOO97.IUF.loc> In-Reply-To: <1331221873.2093.13.camel@ZOO97.IUF.loc> Accept-Language: de-DE, en-US Content-Language: de-DE X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 130.133.170.202 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1331235904-000018DE-32BB5207/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.027769, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.0 required=5.0 tests=none Subject: Re: [Seqan-dev] SplazerS crash X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 08 Mar 2012 19:45:05 -0000 Hi Felix,=0A= =0A= the crash seems to have something to do with SeqAn's old seeds module. We w= ill fix this problem as quickly as possible.=0A= =0A= For now, I would recommend you to run SplazerS in Hamming distance mode (wi= thout option -id), i.e. allowing for only one split gap and no additional g= aps in read prefix and suffix alignment. Especially as it looks like you ar= e dealing with relatively short Illumina reads (75bp). This can save a lot = of runtime while not sacrificing much in terms of sensitivity on Illumina d= ata.=0A= =0A= As a side note: by specifying the parameter directory (-pd seqan-trunk/core= /apps/splazers/gapped_params/) performance will be optimized, both in terms= of sensitivity as well as runtime. Alternatively, you can copy the splazer= s binary and the gapped_params folder to the same directory, then splazers = will locate the folder automatically. Otherwise, splazers may use suboptima= l filtering parameters possibly leading to decreased mapping sensitivity. = =0A= =0A= Hope this helps for the moment, we will send another email once the problem= is fixed.=0A= =0A= Best,=0A= Anne-Katrin=0A= =0A= =0A= -----------------------------------------------=0A= Anne-Katrin Emde=0A= +49 30 83875240=0A= emde@inf.fu-berlin.de=0A= =0A= Algorithmic Bioinformatics=0A= Department of Computer Science=0A= Freie Universit=E4t Berlin=0A= ----------------------------------------------=0A= ________________________________________=0A= Von: Felix Heeger [fheeger@mi.fu-berlin.de]=0A= Gesendet: Donnerstag, 8. M=E4rz 2012 16:51=0A= An: seqan-dev@lists.fu-berlin.de=0A= Betreff: [Seqan-dev] SplazerS crash=0A= =0A= Hi,=0A= =0A= I am trying to use SplazerS for RNA read mapping.=0A= =0A= For certain input files I get the following error:=0A= "/home/heeger/seqan/core/include/seqan/sequence/segment_infix.h:722=0A= Assertion failed : pos < static_cast(length(me)) was: 0 >=3D 0=0A= (Trying to acces an element behind the last one!)"=0A= =0A= This is compiled from the head version of the svn. I am running on=0A= Debian 64.=0A= =0A= The input files I used for this are here:=0A= reference: http://page.mi.fu-berlin.de/heeger/problem.fa=0A= reads: http://page.mi.fu-berlin.de/heeger/reads.fa=0A= =0A= I am running the following command line:=0A= splazers -vv -m1 -id -i95 problem.fa reads.fa=0A= =0A= I will attach the complete output at the bottom.=0A= =0A= I tired to download the release version of SplazerS, but the download=0A= does not work (probably due to changes in the homepage).=0A= =0A= Thanks in advance,=0A= felix=0A= =0A= Complete output of SplazerS:=0A= =0A= bin/splazers -vv -m1 -id -i95 problem.fa reads.fas=0A= =0A= Read length =3D 18bp=0A= Max num errors =3D 1=0A= Recognition rate =3D 99%=0A= =0A= --> Reading bin/gapped_params/results_N18_L.dat=0A= Couldn't open file bin/gapped_params/results_N18_L.dat=0A= Couldn't find preprocessed parameter files. Please configure manually=0A= (options --shape and --threshold).=0A= Using default configurations (shape =3D 11111111111 and q-gram lemma).=0A= =0A= ___PARAMETER_CHOOSING__=0A= =0A= Read length =3D 18bp=0A= Max num errors =3D 1=0A= Recognition rate =3D 99%=0A= =0A= --> Reading bin/gapped_params/results_N18_L.dat=0A= Couldn't open file bin/gapped_params/results_N18_L.dat=0A= Couldn't find preprocessed parameter files. Please configure manually=0A= (options --shape and --threshold).=0A= Using default configurations (shape =3D 11111111111 and q-gram lemma).=0A= =0A= ___SETTINGS____________=0A= Genome file: problem.fa=0A= Read file: reads.fasta=0A= Compute forward matches: YES=0A= Compute reverse matches: YES=0A= Error rate: 0.05=0A= Minimal threshold: 1=0A= Shape: 11111111111=0A= Suffix Minimal threshold: 1=0A= Suffix Shape: 11111111111=0A= Repeat threshold: 1000=0A= Overabundance threshold: 1=0A= Taboo length: 1=0A= =0A= Ignoring 202 low quality reads.=0A= 26734561 bps of 356659 reads loaded.=0A= Loading reads took 6.10979 seconds=0A= Expected number of random deletion-indicating matches: 7.98111e-19=0A= Expected number of random insertion-indicating matches: 0.000145028=0A= Performing spliced mapping.=0A= Make index left right=0A= Patterns created=0A= =0A= Process genome seq=0A= #0[fwd]/home/heeger/seqan/core/include/seqan/sequence/segment_infix.h:722 A= ssertion failed : pos < static_cast(length(me)) was: 0 >=3D 0 (Trying= to acces an element behind the last one!)=0A= =0A= stack trace:=0A= 0 [0x5c5675] seqan::ClassTest::fail() + 0xe=0A= 1 [0x601f10]=0A= seqan::Reference, seqan::Alloc >, seqan::InfixSegment>=0A= const>::Type seqan::value, seqan::Alloc >, seqan::InfixSegment,=0A= int>(seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&, int)=0A= + 0x59=0A= 2 [0x601f49] seqan::SimpleType& seqan::Segment, seqan::Alloc >,=0A= seqan::InfixSegment>::operator[](int) const + 0x1b=0A= 3 [0x601f71] int seqan::score, int, int,=0A= seqan::Segment, seqan::Alloc >, seqan::InfixSegment>,=0A= seqan::Segment, seqan::Alloc >, seqan::InfixSegment>=0A= >(seqan::Score > const&, int, int,=0A= seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&,=0A= seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&) +=0A= 0x26=0A= 4 [0x602278] int=0A= seqan::_extendSeedOneDirection const,=0A= int, seqan::Segment, seqan::Alloc >, seqan::InfixSegment>,=0A= seqan::Segment, seqan::Alloc >, seqan::InfixSegment>, int,=0A= int>(seqan::Seed const>&,=0A= seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&,=0A= seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&, int,=0A= seqan::Score > const&, int) + 0x2d0=0A= 5 [0x602cef] void=0A= seqan::extendSeedScore const, int,=0A= seqan::Segment, seqan::Alloc >, seqan::InfixSegment>,=0A= seqan::Segment, seqan::Alloc >, seqan::InfixSegment>, int,=0A= int>(seqan::Seed const>&, int&, int,=0A= seqan::Score > const&,=0A= seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&,=0A= seqan::Segment, seqan::Alloc >, seqan::InfixSegment> const&, int,=0A= seqan::Tag) + 0x285=0A= 6 [0x603a35] void=0A= seqan::extendMatch, seqan::Alloc >, seqan::Owner > >, unsigned int, seqan::Segment, seqan::Alloc >, seqan::InfixSegment>,= seqan::ReadMatch, seqan::RazerSOptions > const>(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, unsigned int, seqan::Segment, seqan::Alloc >, seqan::InfixSegment>&, seqa= n::ReadMatch&, seqan::RazerSOptions >= const&, seqan::LongestPrefix) + 0x204=0A= 7 [0x603f67] bool seqan::matchVerify,=0A= seqan::String,=0A= seqan::Alloc >,=0A= seqan::StringSet, seqan::Alloc >,=0A= seqan::Owner > >,=0A= seqan::String, seqan::Alloc >, seqan::InfixSegment>,= seqan::Myers >, seqan::Alloc >,= seqan::RazerSSpec, seqan::LongestPrefix>(seqan::ReadMatch&, seqan::Segment, seqan::Alloc >, seqan::InfixSegment>, unsigned int, seqan::S= tringSet, seq= an::Alloc >, seqan::Owner > >&, seqan::Stri= ng, seqan::Alloc >, seqan::InfixSegment>, seqan::Mye= rs >, seqan::Alloc >&, seqan::Ra= zerSOptions > const&, seqan::Tag >, seqan::LongestPrefix) + 0x42a=0A= 8 [0x6716d3] void=0A= seqan::mapSplicedReads,=0A= seqan::Alloc >, seqan::String, seqan::Alloc >,=0A= seqan::StringSet, seqan::Alloc >,=0A= seqan::Owner > >,=0A= seqan::Index, seqan::Alloc >, seqan::InfixSegment>= , seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0u>= >, seqan::Tag > >, seqan::Index, seqan= ::Alloc >, seqan::InfixSegment>, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0u> >, seqan::Tag > >, s= eqan::Tag >, seqan::String, = seqan::Alloc >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc >, seqan::String >, seqan::Alloc >, seqan::RazerSSpec<= false, false> >(seqan::String, seqan::Alloc >&= , seqan::String, seqan::All= oc >&, unsigned int, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, seqan::Pattern, seqan::Alloc= >, seqan::InfixSegment>, seqan::Owner > >, seq= an::IndexQGram, = seqan::UngappedShape<0u> >, seqan::Tag > >, seqan::Swift > > >&, seqan::Pattern, seqan::Alloc >, seqan::InfixSegment>, seqan::Own= er > >, seqan::IndexQGram, seqan::UngappedShape<0u> >, seqan::T= ag > >, seqan::Swift > > >&, seqan::String, seqan::Alloc >, seqan::In= fixSegment>, seqan::Myers >, seqan::Al= loc >&, seqan::String, seqan::Alloc >, seqan::= InfixSegment>, seqan::Myers >, seqan::= Alloc >&, seqan::String >, seqan::Alloc >&, char, seqan::RazerSOptions >&) + 0x110f=0A= 9 [0x673333] int=0A= seqan::mapSplicedReads,=0A= seqan::Alloc >,=0A= seqan::StringSet, seqan::Alloc >,=0A= seqan::Owner > >,=0A= seqan::String >,=0A= seqan::Alloc >, seqan::RazerSSpec,=0A= seqan::Shape,=0A= seqan::UngappedShape<0u> >, seqan::Shape, seqan::UngappedShape<0u> >,=0A= seqan::Tag >=0A= >(seqan::String, seqan::Alloc >&,=0A= seqan::StringSet >,=0A= seqan::Owner > >&,=0A= seqan::StringSet >,=0A= seqan::Owner > >&, std::map, std::less,=0A= std::allocator > > >&,=0A= seqan::StringSet, seqan::Alloc >,=0A= seqan::Owner > >&,=0A= seqan::String >, void>, seqan::Alloc >&,=0A= seqan::String >,=0A= seqan::Alloc >&, seqan::RazerSOptions >&, seqan::Shape,=0A= seqan::UngappedShape<0u> > const&,=0A= seqan::Shape,=0A= seqan::UngappedShape<0u> > const&,=0A= seqan::Swift > >) + 0xd98=0A= 10 [0x68dda6] int=0A= seqan::mapSplicedReads,=0A= seqan::Alloc >,=0A= seqan::StringSet, seqan::Alloc >,=0A= seqan::Owner > >,=0A= seqan::String >,=0A= seqan::Alloc >, seqan::RazerSSpec=0A= >(seqan::String, seqan::Alloc >&,=0A= seqan::StringSet >,=0A= seqan::Owner > >&,=0A= seqan::StringSet >,=0A= seqan::Owner > >&, std::map, std::less,=0A= std::allocator > > >&,=0A= seqan::StringSet, seqan::Alloc >,=0A= seqan::Owner > >&,=0A= seqan::String >, void>, seqan::Alloc >&,=0A= seqan::String >,=0A= seqan::Alloc >&, seqan::RazerSOptions >&) + 0x703=0A= 11 [0x68e3ed] int=0A= seqan::mapReads, seqan::Alloc=0A= >, seqan::StringSet, seqan::Alloc >,=0A= seqan::Owner > >,=0A= seqan::String >,=0A= seqan::Alloc >, seqan::RazerSSpec=0A= >(seqan::String, seqan::Alloc >&,=0A= seqan::StringSet >,=0A= seqan::Owner > >&,=0A= seqan::StringSet >,=0A= seqan::Owner > >&, std::map, std::less,=0A= std::allocator > > >&,=0A= seqan::StringSet, seqan::Alloc >,=0A= seqan::Owner > >&,=0A= seqan::String >, void>, seqan::Alloc >&,=0A= seqan::String >,=0A= seqan::Alloc >&, seqan::RazerSOptions >&) + 0x98=0A= 12 [0x69a4b4] int mapReads=0A= >(seqan::StringSet >,=0A= seqan::Owner > >&,=0A= seqan::StringSet >,=0A= seqan::Owner > >&, seqan::String >&, seqan::RazerSOptions >&) + 0xbae=0A= 13 [0x56f5c4] main + 0x8125=0A= 14 [0x7fc1c67591a6] __libc_start_main + 0xe6=0A= 15 [0x566f59] std::ios_base::Init::~Init() + 0x41=0A= =0A= Aborted=0A= =0A= =0A= =0A= _______________________________________________=0A= seqan-dev mailing list=0A= seqan-dev@lists.fu-berlin.de=0A= https://lists.fu-berlin.de/listinfo/seqan-dev=0A= From bernd.jagla@pasteur.fr Fri Mar 09 08:18:43 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5u65-0004bG-TW>; Fri, 09 Mar 2012 08:18:42 +0100 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S5u65-0005Ff-MR>; Fri, 09 Mar 2012 08:18:41 +0100 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 128C938104F for ; Fri, 9 Mar 2012 08:18:40 +0100 (CET) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id CDB3438104C for ; Fri, 9 Mar 2012 08:18:39 +0100 (CET) Message-ID: <4F59AECF.6000508@pasteur.fr> Date: Fri, 09 Mar 2012 08:18:39 +0100 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:10.0.2) Gecko/20120216 Thunderbird/10.0.2 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary="------------040104070204080109040700" X-Originating-IP: 157.99.64.82 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1331277521-000018DE-952151BF/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.217756, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST, HTML_MESSAGE Subject: [Seqan-dev] double pass record reader X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 09 Mar 2012 07:18:43 -0000 This is a multi-part message in MIME format. --------------040104070204080109040700 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi, I have one comment: the link in the web page http://trac.seqan.de/wiki/Tutorial/FileIO2 that should link to "Double-Pass Record Reader :" is not workin... and I have one question: is it possible to write out to a file the things done in the first pass of the "double pass record reader"? I would like to write a function/program that is only working on a given partition. If I repeat this n times I think it would be beneficial to put the first pass of the reading into an external program... Thanks for the advice. Bernd --------------040104070204080109040700 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi,

I have one comment:

the link in the web page http://trac.seqan.de/wiki/Tutorial/FileIO2 that should link to "Double-Pass Record Reader:" is not workin...

and I have one question:

is it possible to write out to a file the things done in the first pass of the "double pass record reader"?

I would like to write a function/program that is only working on a given partition. If I repeat this n times I think it would be beneficial to put the first pass of the reading into an external program...

Thanks for the advice.

Bernd
 --------------040104070204080109040700-- From manuel.holtgrewe@fu-berlin.de Fri Mar 09 16:34:39 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S61q2-0004ne-LF>; Fri, 09 Mar 2012 16:34:38 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1S61q2-00087s-Iu>; Fri, 09 Mar 2012 16:34:38 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1S61q2-0002es-GR>; Fri, 09 Mar 2012 16:34:38 +0100 Message-ID: <4F5A22BB.1000603@fu-berlin.de> Date: Fri, 09 Mar 2012 16:33:15 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:10.0.2) Gecko/20120216 Thunderbird/10.0.2 MIME-Version: 1.0 To: SeqAn Development References: <4F59AECF.6000508@pasteur.fr> In-Reply-To: <4F59AECF.6000508@pasteur.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1331307278-000018DE-27A72247/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.274759, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] double pass record reader X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 09 Mar 2012 15:34:39 -0000 On 03/09/2012 08:18 AM, Bernd Jagla wrote: > Hi, > > I have one comment: > > the link in the web page http://trac.seqan.de/wiki/Tutorial/FileIO2 that > should link to "Double-Pass Record Reader > :" is > not workin... Good catch, I fixed this. > and I have one question: > > is it possible to write out to a file the things done in the first pass > of the "double pass record reader"? > > I would like to write a function/program that is only working on a given > partition. If I repeat this n times I think it would be beneficial to > put the first pass of the reading into an external program... Hm, you could try to use MultiSeqFile, following this tutorial here: http://trac.seqan.de/wiki/HowTo/EfficientImportOfMillionsOfSequences This gives you random access, albeit without storing an index into your reads file. Currently, storing such indices is not possible. However: I can see how this would be useful for processing chunks of data. Let me see whether we can cook up something reuseable in this direction. There is the FAI index format from samtools, but that's only for FASTA files. *m From Sabrina.Krakau@fu-berlin.de Tue Mar 13 12:48:21 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S7QDE-0001yF-Pa>; Tue, 13 Mar 2012 12:48:20 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S7QDE-0004yE-Mk>; Tue, 13 Mar 2012 12:48:20 +0100 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S7QDE-0004vS-Cf>; Tue, 13 Mar 2012 12:48:20 +0100 Received: from EX03A.campus.fu-berlin.de ([169.254.1.96]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.02.0283.003; Tue, 13 Mar 2012 12:48:19 +0100 From: "Krakau, Sabrina" To: SeqAn Development Thread-Topic: SeqAn Developer Retreat March 26th-28th Thread-Index: AQHNAQ8vd9w/XmodgEyqUezN7fRetQ== Date: Tue, 13 Mar 2012 11:48:19 +0000 Message-ID: <594645B8-4961-4C14-B96A-D2FB2DB4C787@fu-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_594645B849614C14B96AD2FB2DB4C787fuberlinde_" MIME-Version: 1.0 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1331639300-000018DE-6ED09837/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000005, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.0 required=5.0 tests=HTML_60_70,HTML_MESSAGE Subject: [Seqan-dev] SeqAn Developer Retreat March 26th-28th X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 13 Mar 2012 11:48:21 -0000 --_000_594645B849614C14B96AD2FB2DB4C787fuberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable SeqAn Developer Retreat March 26th-28th We would like to invite you to the SeqAn developer retreat, which is of int= erest for all active developers that use SeqAn. During this retreat we will= as a team work on the code of the library, or collaborate with external gr= oups to assist them hands-on on their SeqAn projects. We will start on the 26th 10am, and stop on the 28th in the afternoon. If you are interested in joining, please mail to Sabrina Krakau (sabrina.kr= akau@fu-berlin.de) for further infos. The detailed schedule and task list you will find on our BioStore website: http://www.seqan-biostore.de/wp/seqan-workshops/2012-developer-retreat/ The SeqAn team ------------------------------------------------------------ Sabrina Krakau Freie Universit=E4t Berlin Institut f=FCr Informatik Algorithmic Bioinformatics - Project BioStore Takustr. 9, 14195 Berlin Telefon: +49 (0)30 838 75228 sabrina.krakau@fu-berlin.de --_000_594645B849614C14B96AD2FB2DB4C787fuberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-ID: Content-Transfer-Encoding: quoted-printable

SeqAn Developer Retreat March 26th-28th


We would like to invite you to the SeqAn developer retreat, which is o= f interest for all active developers that use SeqAn. During this retreat we= will as a team work on the code of the library, or collaborate with extern= al groups to assist them hands-on on their SeqAn projects.

We will start on the 26th 10am, and stop on the 28th in the afternoon.=  
If you are interested in joining, please mail to Sabrina Krakau (sabrina.krakau@fu-berlin.de) = for further infos.

The detailed schedule and task list you will find on our BioStore website:<= br> http://www.seqan-biostore.de/wp/se= qan-workshops/2012-developer-retreat/


The SeqAn team


------------------------------------------------------------
 
Sabrina Krakau
Freie Universit=E4t Berlin
Institut f=FCr Informatik
Algorithmic Bioinformatics - Project BioStore

Takustr. 9, 14195 Berlin
Telefon: +49 (0)30 838 75228
sabrina.krakau@fu-berlin.de<= /a>

--_000_594645B849614C14B96AD2FB2DB4C787fuberlinde_-- From peter.robinson@charite.de Tue Mar 13 12:56:42 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S7QLH-0002DK-US>; Tue, 13 Mar 2012 12:56:40 +0100 Received: from mail2.charite.de ([141.42.206.200]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S7QLH-0008BM-QI>; Tue, 13 Mar 2012 12:56:39 +0100 Received: from localhost (localhost [127.0.0.1]) by mail2.charite.de (Postfix) with ESMTP id 3V6ZKf50L9z1tJr for ; Tue, 13 Mar 2012 12:56:38 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=charite.de; h= mime-version:content-type:content-type:content-language :accept-language:in-reply-to:references:message-id:subject :subject:date:date:from:from:received:received:received; s= default; t=1331639797; x=1333454198; bh=/OwFy6e6+lK+PGQ0AXxPmbIK 8FF8SAiK/Bu8JTkWjlM=; b=RUBxSNZtkSnACk6QiUNNQMoExoSjXj6BVCAiHkGt IUZnpVKPJ3uUT4u8vDIPUjyFqfDqSVw+SE/K5meW05JzRKOjDn26ll1//ehjtjGr u4fMzvKwSHQsq9TiEDjfHEnP55UvtZid5N2SIa/00EXp51aGkyaPXUBHZMw5tKVX +KM= Received: from exchange.charite.de (unknown [10.32.37.106]) (using TLSv1 with cipher AES128-SHA (128/128 bits)) (No client certificate requested) by mail2.charite.de (Postfix) with ESMTPS for ; Tue, 13 Mar 2012 12:56:37 +0100 (CET) Received: from s-mx-ht3.charite.de (10.32.32.96) by s-mx14-ht02.charite.de (10.32.37.106) with Microsoft SMTP Server (TLS) id 14.2.247.3; Tue, 13 Mar 2012 12:56:37 +0100 Received: from Exchange41.charite.de ([10.32.32.88]) by s-mx-ht3.charite.de ([::1]) with mapi; Tue, 13 Mar 2012 12:56:36 +0100 From: "Robinson, Peter" To: SeqAn Development Date: Tue, 13 Mar 2012 12:55:54 +0100 Thread-Topic: SeqAn Developer Retreat March 26th-28th Thread-Index: AQHNAQ8vd9w/XmodgEyqUezN7fRetZZoHl6V Message-ID: References: <594645B8-4961-4C14-B96A-D2FB2DB4C787@fu-berlin.de> In-Reply-To: <594645B8-4961-4C14-B96A-D2FB2DB4C787@fu-berlin.de> Accept-Language: de-DE Content-Language: de-DE X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: multipart/alternative; boundary="_000_B8432BC2D6CC56478D81956053FE7D1D0173696DF534EXCHANGE41c_" MIME-Version: 1.0 X-Originating-IP: 141.42.206.200 X-ZEDAT-Hint: A X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1331639799-000018DE-D9E0227B/0-8068933487/0-2 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.1 required=5.0 tests=FU_XPURGATE_SUSP,HTML_40_50, HTML_MESSAGE,SPF_HELO_PASS,SPF_PASS Subject: Re: [Seqan-dev] SeqAn Developer Retreat March 26th-28th X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 13 Mar 2012 11:56:42 -0000 --_000_B8432BC2D6CC56478D81956053FE7D1D0173696DF534EXCHANGE41c_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Liebe Frau Krakau, ich w=FCrde gern am 27/28 kommen, am 26. bin ich noch im Ausland. Einige Le= ute von meiner AG kommen auch. VG Peter Nick Robinson PD Dr. med. Peter N. Robinson, MSc. Institut f=FCr Medizinische Genetik und Humangenetik Charit=E9 - Universit=E4tsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany +4930 450566006 Mobile: 0160 93769872 peter.robinson@charite.de http://compbio.charite.de http://www.human-phenotype-ontology.org Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/978143= 9836651 ________________________________ Von: Krakau, Sabrina [Sabrina.Krakau@fu-berlin.de] Gesendet: Dienstag, 13. M=E4rz 2012 12:48 An: SeqAn Development Betreff: [Seqan-dev] SeqAn Developer Retreat March 26th-28th SeqAn Developer Retreat March 26th-28th We would like to invite you to the SeqAn developer retreat, which is of int= erest for all active developers that use SeqAn. During this retreat we will= as a team work on the code of the library, or collaborate with external gr= oups to assist them hands-on on their SeqAn projects. We will start on the 26th 10am, and stop on the 28th in the afternoon. If you are interested in joining, please mail to Sabrina Krakau (sabrina.kr= akau@fu-berlin.de) for further infos. The detailed schedule and task list you will find on our BioStore website: http://www.seqan-biostore.de/wp/seqan-workshops/2012-developer-retreat/ The SeqAn team ------------------------------------------------------------ Sabrina Krakau Freie Universit=E4t Berlin Institut f=FCr Informatik Algorithmic Bioinformatics - Project BioStore Takustr. 9, 14195 Berlin Telefon: +49 (0)30 838 75228 sabrina.krakau@fu-berlin.de --_000_B8432BC2D6CC56478D81956053FE7D1D0173696DF534EXCHANGE41c_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Liebe Frau Krakau,
ich w=FCrde gern am 27/28 kommen, am 26. bin ich= noch im Ausland. Einige Leute von meiner AG kommen auch.
VG Peter Nick Robinson
PD Dr. med. Peter N. Robinson, MSc.
Institut f=FCr Medizinische Genetik und Humangenetik
Charit=E9 - Universit=E4tsmedizin Berlin
Augustenburger Platz 1
13353 Berlin
Germany
+4930 450566006
Mobile: 0160 93769872
peter.robinson@charite.de
http://compbio.charite.de
http://www.human-phenotype-ontology.org
Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/978143= 9836651
=  
Von: Krakau, Sabr= ina [Sabrina.Krakau@fu-berlin.de]
Gesendet: Dienstag, 13. M=E4rz 2012 12:48
An: SeqAn Development
Betreff: [Seqan-dev] SeqAn Developer Retreat March 26th-28th


------------------------------------------------------------
 
Sabrina Krakau
Freie Universit=E4t Berlin
Institut f=FCr Informatik
Algorithmic Bioinformatics - Project BioStore

Takustr. 9, 14195 Berlin
Telefon: +49 (0)30 838 75228
sabrina.krakau@fu-berlin.de<= /a>

--_000_B8432BC2D6CC56478D81956053FE7D1D0173696DF534EXCHANGE41c_-- From han88@zedat.fu-berlin.de Wed Mar 14 11:43:13 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S7lfl-00048w-1B>; Wed, 14 Mar 2012 11:43:13 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S7lfk-0001wE-V8>; Wed, 14 Mar 2012 11:43:13 +0100 Received: from portal.zedat.fu-berlin.de ([130.133.3.2]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S7lfk-0000Yc-Rc>; Wed, 14 Mar 2012 11:43:12 +0100 Received: from 77.87.224.99 (ZEDAT-Webmail authenticated user han88) by portal.zedat.fu-berlin.de with HTTP; Wed, 14 Mar 2012 11:43:12 +0100 Message-ID: <11859.77.87.224.99.1331721792.webmail@portal.zedat.fu-berlin.de> Date: Wed, 14 Mar 2012 11:43:12 +0100 From: "Sven Giese" To: seqan-dev@lists.fu-berlin.de User-Agent: ZEDAT-Webmail MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 130.133.3.2 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1331721793-000018DE-8E891AEE/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: [Seqan-dev] Rabema input X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 14 Mar 2012 10:43:13 -0000 Hi everyone, I recently started using Rabema and I also want to compare some ReadMappers which do not support the .SAM format. Could anyone tell me which columns are mandatory for the comparison so that I could reconstruct a pseudo-Sam file? thanks in advance! best regards Sven Giese From manuel.holtgrewe@fu-berlin.de Wed Mar 14 12:34:30 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S7mTN-0006kg-HR>; Wed, 14 Mar 2012 12:34:29 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S7mTN-00050Y-EM>; Wed, 14 Mar 2012 12:34:29 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1S7mTN-0004bK-0l>; Wed, 14 Mar 2012 12:34:29 +0100 Received: from EX02A.campus.fu-berlin.de ([169.254.1.147]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.02.0283.003; Wed, 14 Mar 2012 12:34:28 +0100 From: "Holtgrewe, Manuel" To: 'SeqAn Development' Thread-Topic: [Seqan-dev] Rabema input Thread-Index: AQHNAc9H8Me4iAXgQ0CFTrPfT+J6xJZpp+JA Date: Wed, 14 Mar 2012 11:34:27 +0000 Message-ID: References: <11859.77.87.224.99.1331721792.webmail@portal.zedat.fu-berlin.de> In-Reply-To: <11859.77.87.224.99.1331721792.webmail@portal.zedat.fu-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 130.133.170.203 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1331724869-000018DE-DAE527CB/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.0 required=5.0 tests=none Subject: Re: [Seqan-dev] Rabema input X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 14 Mar 2012 11:34:30 -0000 Sven, The SAM header is optional. I fear all fields are required. Don't despair, some can be set to constant = values since we don't need paired-end mappings for Rabema. QNAME - make sure you truncate at the first space FLAG - only mapped/unmapped flag and strand flag are required RNAME - make sure you truncate at the first space POS - any output should contain this MAPQ - ignored, set to any value CIGAR - required for determining the alignment length RNEXT - fix to * PNEXT - fix to 0 TLEN - fix to 0 SEQ - required QUAL - ignored, can be set to length(SEQ) * "!" HTH *m -----Original Message----- From: Sven Giese [mailto:sven.giese@fu-berlin.de]=20 Sent: Mittwoch, 14. M=E4rz 2012 11:43 To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] Rabema input Hi everyone, I recently started using Rabema and I also want to compare some ReadMappers= which do not support the .SAM format. Could anyone tell me which columns are mandatory for the comparison so that= I could reconstruct a pseudo-Sam file? thanks in advance! best regards Sven Giese _______________________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev From bernd.jagla@pasteur.fr Fri Mar 30 15:58:54 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SDcLt-00064g-7h>; Fri, 30 Mar 2012 15:58:53 +0200 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SDcLs-00069O-Vj>; Fri, 30 Mar 2012 15:58:53 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id A5A72381053 for ; Fri, 30 Mar 2012 15:58:50 +0200 (CEST) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 6BEF638104C for ; Fri, 30 Mar 2012 15:58:50 +0200 (CEST) Message-ID: <4F75BC1A.1010500@pasteur.fr> Date: Fri, 30 Mar 2012 15:58:50 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:11.0) Gecko/20120312 Thunderbird/11.0 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 157.99.64.82 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1333115933-000018DE-82765CE4/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST Subject: [Seqan-dev] project problem X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 30 Mar 2012 13:58:54 -0000 Hi, I copied a project from one sandbox to another by just copying the directory. (I need to move to another computer) Unfortunately this directory is not being recognized as a project somehow... What do I have to do in order to get this working? Thanks, Bernd PS: executing cmake -G "Unix Makefiles" -D CMAKE_BUILD_TYPE=Debug ../.. in ......seqan/Build/Debug is not enough... From bernd.jagla@pasteur.fr Fri Mar 30 16:32:26 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SDcsK-0007EB-84>; Fri, 30 Mar 2012 16:32:24 +0200 Received: from mail-interne3.pasteur.fr ([157.99.64.82]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SDcsK-0007Ld-0A>; Fri, 30 Mar 2012 16:32:24 +0200 Received: from maroilles.sis.pasteur.fr (localhost [127.0.0.1]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id AB7DC381058 for ; Fri, 30 Mar 2012 16:32:21 +0200 (CEST) X-Virus-Scanned: amavisd-new at pasteur.fr Received: from [127.0.0.1] (zillumina.pt2.pasteur.fr [157.99.241.40]) by mail-interne3.pasteur.fr (Postfix) with ESMTP id 88E7638104C for ; Fri, 30 Mar 2012 16:32:21 +0200 (CEST) Message-ID: <4F75C3F5.100@pasteur.fr> Date: Fri, 30 Mar 2012 16:32:21 +0200 From: Bernd Jagla User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:11.0) Gecko/20120312 Thunderbird/11.0 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: <4F75BC1A.1010500@pasteur.fr> In-Reply-To: <4F75BC1A.1010500@pasteur.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 157.99.64.82 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1333117944-000018DE-80DBC3DC/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_POST Subject: Re: [Seqan-dev] project problem X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 30 Mar 2012 14:32:26 -0000 It seems that while I was trying to solve a build problem somehow the CMakeLists.txt have been removed... So I added them again from the other computer... BUT... now there seems to be a cmake problem: CMake Error at CMakeLists.txt:1 (seqan_project_just_include_all_subdirs): Unknown CMake command "seqan_project_just_include_all_subdirs". CMake Warning (dev) in CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 2.8) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring incomplete, errors occurred! That is I am using cmake version 2.8.7 on the new machine and have no idea which version I used to create the project... Thanks ... Bernd On 3/30/2012 3:58 PM, Bernd Jagla wrote: > Hi, > > I copied a project from one sandbox to another by just copying the > directory. (I need to move to another computer) > Unfortunately this directory is not being recognized as a project > somehow... > What do I have to do in order to get this working? > > Thanks, > > Bernd > > PS: > > executing > cmake -G "Unix Makefiles" -D CMAKE_BUILD_TYPE=Debug ../.. > in ......seqan/Build/Debug is not enough... > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > From manuel.holtgrewe@fu-berlin.de Fri Mar 30 17:30:14 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SDdmG-0000Z5-TT>; Fri, 30 Mar 2012 17:30:13 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SDdmG-0006OM-QM>; Fri, 30 Mar 2012 17:30:12 +0200 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SDdmG-0007io-Go>; Fri, 30 Mar 2012 17:30:12 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.02.0283.003; Fri, 30 Mar 2012 17:30:11 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] project problem Thread-Index: AQHNDn1KcFtREv4Gf0GmmICmIojNm5aCxVOAgAAxoQk= Date: Fri, 30 Mar 2012 15:30:10 +0000 Message-ID: References: <4F75BC1A.1010500@pasteur.fr>,<4F75C3F5.100@pasteur.fr> In-Reply-To: <4F75C3F5.100@pasteur.fr> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 130.133.170.202 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1333121412-000018DE-22EA22CA/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] project problem X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 30 Mar 2012 15:30:14 -0000 Just try to put =0A= =0A= cmake_minimum_required(VERSION 2.8)=0A= =0A= at the top of your file.=0A= ________________________________________=0A= From: Bernd Jagla [bernd.jagla@pasteur.fr]=0A= Sent: Friday, March 30, 2012 4:32 PM=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: Re: [Seqan-dev] project problem=0A= =0A= It seems that while I was trying to solve a build problem somehow the=0A= CMakeLists.txt have been removed...=0A= So I added them again from the other computer...=0A= =0A= BUT...=0A= =0A= now there seems to be a cmake problem:=0A= =0A= CMake Error at CMakeLists.txt:1 (seqan_project_just_include_all_subdirs):= =0A= Unknown CMake command "seqan_project_just_include_all_subdirs".=0A= =0A= =0A= CMake Warning (dev) in CMakeLists.txt:=0A= No cmake_minimum_required command is present. A line of code such as=0A= =0A= cmake_minimum_required(VERSION 2.8)=0A= =0A= should be added at the top of the file. The version specified may be=0A= lower=0A= if you wish to support older CMake versions for this project. For more= =0A= information run "cmake --help-policy CMP0000".=0A= This warning is for project developers. Use -Wno-dev to suppress it.=0A= =0A= -- Configuring incomplete, errors occurred!=0A= =0A= That is I am using cmake version 2.8.7 on the new machine and have no=0A= idea which version I used to create the project...=0A= =0A= =0A= Thanks ...=0A= =0A= Bernd=0A= =0A= On 3/30/2012 3:58 PM, Bernd Jagla wrote:=0A= > Hi,=0A= >=0A= > I copied a project from one sandbox to another by just copying the=0A= > directory. (I need to move to another computer)=0A= > Unfortunately this directory is not being recognized as a project=0A= > somehow...=0A= > What do I have to do in order to get this working?=0A= >=0A= > Thanks,=0A= >=0A= > Bernd=0A= >=0A= > PS:=0A= >=0A= > executing=0A= > cmake -G "Unix Makefiles" -D CMAKE_BUILD_TYPE=3DDebug ../..=0A= > in ......seqan/Build/Debug is not enough...=0A= >=0A= >=0A= > _______________________________________________=0A= > seqan-dev mailing list=0A= > seqan-dev@lists.fu-berlin.de=0A= > https://lists.fu-berlin.de/listinfo/seqan-dev=0A= >=0A= >=0A= =0A= =0A= _______________________________________________=0A= seqan-dev mailing list=0A= seqan-dev@lists.fu-berlin.de=0A= https://lists.fu-berlin.de/listinfo/seqan-dev=0A= From ngsgeek@gmail.com Fri Mar 30 19:44:53 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SDfsa-0004ap-DX>; Fri, 30 Mar 2012 19:44:52 +0200 Received: from mail-gx0-f182.google.com ([209.85.161.182]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SDfsa-00008C-6q>; Fri, 30 Mar 2012 19:44:52 +0200 Received: by ggnk4 with SMTP id k4so613420ggn.13 for ; Fri, 30 Mar 2012 10:44:49 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:date:message-id:subject:from:to:content-type; bh=s9YsSf4MRy52rx+8BNEpgjvyn8AsiEp6/OpG0pnI6f0=; b=OZHaUgPhuMeAB1Xmj2sY0uHcNiWCXwF+lYjoRFzMSDCbJbEEJoH0dNGaHdVoqJfCgX nEHN0Vj1oxz/HjcUKvpLN9vehUXcmJIterHLrNZ9NdlULo3RUkaUS/4VyOCRp5cTctpm xRTwFu2v7zTR2HEjkoB58JbIzeIr57X/Q0XUNhWDjaQyegxqDOObqFR7ImoMfT2MPFND DOi4FUGQHK8fjoZ4zMCXVvS8UW79+wmXe5FZgSjUNMLOndn8oiu8bWSkPL5IM/l4EQyS Q4i3V8eFHKh5evw9uR1mgDVU+A1UCreYMNa5aKd0WinhqMbxAICziRU+p1ALi5YQRkIW iEEA== MIME-Version: 1.0 Received: by 10.68.230.104 with SMTP id sx8mr3840361pbc.16.1333129489258; Fri, 30 Mar 2012 10:44:49 -0700 (PDT) Received: by 10.66.220.66 with HTTP; Fri, 30 Mar 2012 10:44:49 -0700 (PDT) Date: Fri, 30 Mar 2012 13:44:49 -0400 Message-ID: From: ngs geek To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=047d7b339e67a5992804bc7965ad X-Originating-IP: 209.85.161.182 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1333129492-000018DE-B6E20BA1/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.202878, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.5 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_40_50, HTML_MESSAGE,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] Reading FastQ files from GZ archive X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 30 Mar 2012 17:44:53 -0000 --047d7b339e67a5992804bc7965ad Content-Type: text/plain; charset=ISO-8859-1 Hi All: I'm trying to filter reads contained in a gz file based on quality score; I was able to stream the id and the sequence with GZFile stream and using a singlepass reader (I don't want to keep the reads in memory). Unfortunately, I can't access the quality string. RecordReader, SinglePass<> > reader(fastq_file); CharString id; String seq; CharString qual; while (!atEnd(reader)) { if (readRecord(id, seq, reader, Fastq()) != 0) { std::cerr << "Problem with your FASTQ file." << std::endl; return 1; } // reading qual } Any idea on this? I tried assignQualities etc. with no luck. Thanks JD --047d7b339e67a5992804bc7965ad Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All:

I'm trying to filter reads contained in a gz= file based on quality score; I was able to stream the id and the=A0
<= div>sequence with GZFile stream and using a singlepass reader (I don't = want to keep the reads in memory).
Unfortunately, I can't access the quality string.

=A0RecordReader<Stream<GZFile>, SinglePass<> &= gt; reader(fastq_file);
=A0 CharString id;
=A0 String&l= t;Dna5Q> seq;
CharS= tring qual;

while (!atEnd(reader))
=A0 {
=A0 =A0 =A0 if (readRecord(id, seq, reader, Fastq()) !=3D 0)
=A0 =A0 =A0 {
=A0 =A0 =A0 =A0 =A0 std::cerr << "P= roblem with your FASTQ file." << std::endl;
=A0 =A0 = =A0 =A0 =A0 return 1;
=A0 =A0 =A0 }

=A0 = =A0 =A0 // reading qual
=A0 }

Any idea on this? I tried assignQ= ualities etc. with no luck.

Thanks
JD

--047d7b339e67a5992804bc7965ad-- From manuel.holtgrewe@fu-berlin.de Sat Mar 31 11:22:52 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SDuWJ-0005oy-Bd>; Sat, 31 Mar 2012 11:22:51 +0200 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SDuWJ-0001sl-7t>; Sat, 31 Mar 2012 11:22:51 +0200 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SDuWJ-0003iZ-1K>; Sat, 31 Mar 2012 11:22:51 +0200 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.02.0283.003; Sat, 31 Mar 2012 11:22:49 +0200 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] Reading FastQ files from GZ archive Thread-Index: AQHNDpzY33OFSU8hF0esGtVhmzzKHJaEIiih Date: Sat, 31 Mar 2012 09:22:48 +0000 Message-ID: References: In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_FCCAB9D80C3DAB47B5601C5B0E62872B06C6CDEX02Acampusfuberl_" MIME-Version: 1.0 X-Originating-IP: 130.133.170.202 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1333185771-000018DE-5656945B/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=ALL_TRUSTED,HTML_50_60, HTML_MESSAGE Subject: Re: [Seqan-dev] Reading FastQ files from GZ archive X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 31 Mar 2012 09:22:52 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B06C6CDEX02Acampusfuberl_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi JD, good catch, you found a bug I just fixed. The problem was that assignQualit= yValues() did not resize the target string, it does now. Update your SVN ch= eckout and it should work. Also, there now is a demo for reading FASTQ from gzipped files in core/demo= s/stream_read_fastq_gz.cpp HTH Manuel ________________________________ From: ngs geek [ngsgeek@gmail.com] Sent: Friday, March 30, 2012 7:44 PM To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] Reading FastQ files from GZ archive Hi All: I'm trying to filter reads contained in a gz file based on quality score; I= was able to stream the id and the sequence with GZFile stream and using a singlepass reader (I don't want to = keep the reads in memory). Unfortunately, I can't access the quality string. RecordReader, SinglePass<> > reader(fastq_file); CharString id; String seq; CharString qual; while (!atEnd(reader)) { if (readRecord(id, seq, reader, Fastq()) !=3D 0) { std::cerr << "Problem with your FASTQ file." << std::endl; return 1; } // reading qual } Any idea on this? I tried assignQualities etc. with no luck. Thanks JD --_000_FCCAB9D80C3DAB47B5601C5B0E62872B06C6CDEX02Acampusfuberl_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi JD,

good catch, you found a bug I just fixed. The problem was that assignQ= ualityValues() did not resize the target string, it does now. Update your S= VN checkout and it should work.

Also, there now is a demo for reading FASTQ from gzipped files in = ;core/demos/stream_read_fastq_gz.cpp

HTH
Manuel

From: ngs geek [ngsgeek@gmail.com]
Sent: Friday, March 30, 2012 7:44 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Reading FastQ files from GZ archive

Hi All:

I'm trying to filter reads contained in a gz file based on quality sco= re; I was able to stream the id and the 
sequence with GZFile stream and using a singlepass reader (I don't wan= t to keep the reads in memory).
Unfortunately, I can't access the quality string.

 RecordReader<Stream<GZFile>, SinglePass<> > re= ader(fastq_file);
  CharString id;
  String<Dna5Q> seq;
CharSt= ring qual;

while = (!atEnd(reader))
  {
      if (readRecord(id, seq, reader, Fastq()) !=3D 0)<= /div>
      {
          std::cerr << "Problem wi= th your FASTQ file." << std::endl;
          return 1;
      }

      // reading qual
  }

Any idea on this? I tried assignQualities etc. with no luck.

Thanks
JD

--_000_FCCAB9D80C3DAB47B5601C5B0E62872B06C6CDEX02Acampusfuberl_-- From ngsgeek@gmail.com Sat Mar 31 21:39:16 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SE48o-0000P3-Ar>; Sat, 31 Mar 2012 21:39:14 +0200 Received: from mail-pz0-f54.google.com ([209.85.210.54]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SE48n-0000rF-Rn>; Sat, 31 Mar 2012 21:39:14 +0200 Received: by dady13 with SMTP id y13so984280dad.27 for ; Sat, 31 Mar 2012 12:39:11 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=vSCo2tLjQ3nUG4mPXFIfOPCKxgN2hq5z7GZ80XWtAH4=; b=ihc3XIlKjivSENdGUI2ToGVB8WC5c4Zms9uS8aovTBiZ5SWDUYtXV2VnV5idkGGcQq I9QU1MOkNAy8orm1l7Po824GCSMvoPkaYJ2bKQH8oqtB2/IOcLHTM/e9nxN0GbOz/pP4 eO6Hv4lgUrY2DrUVK6kYoRglYbAbSuapqgYSySjMicSTHtWaAqXKG+SpcB/CGy+jwBfJ WN1gZu37/XFsNcvH5au4VyE8FMQL1H1WdxDKB09iBbJIOzS/U0eamTjvfV8rqaTyiCpv xIOU/r4OYH7gGBpayi/+LADtLUdjLb0G2sFDDJb1VU2kFqcuDTdnAtlJoN5Z5BMPFlsn 2uUg== MIME-Version: 1.0 Received: by 10.68.229.73 with SMTP id so9mr7590072pbc.163.1333222751453; Sat, 31 Mar 2012 12:39:11 -0700 (PDT) Received: by 10.66.220.66 with HTTP; Sat, 31 Mar 2012 12:39:11 -0700 (PDT) In-Reply-To: References: Date: Sat, 31 Mar 2012 15:39:11 -0400 Message-ID: From: ngs geek To: SeqAn Development Content-Type: multipart/alternative; boundary=047d7b0721cc81c1da04bc8f1c3e X-Originating-IP: 209.85.210.54 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1333222754-000018DE-D6AFD7F5/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000112, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.5 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_40_50, HTML_MESSAGE,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: Re: [Seqan-dev] Reading FastQ files from GZ archive X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 31 Mar 2012 19:39:16 -0000 --047d7b0721cc81c1da04bc8f1c3e Content-Type: text/plain; charset=ISO-8859-1 Thanks! I'm seeing that the quality string is not the same that I read from the fastq file. Are they scaled? I read the doc here http://trac.seqan.de/wiki/WhitePapers/QualityHandling but I can't figure out if these are guess by assignQualityValues ... in any case, I can't see consistent results for my Illumina 1.3+ reads. Thanks JD On Sat, Mar 31, 2012 at 5:22 AM, Holtgrewe, Manuel < manuel.holtgrewe@fu-berlin.de> wrote: > Hi JD, > > good catch, you found a bug I just fixed. The problem was that > assignQualityValues() did not resize the target string, it does now. Update > your SVN checkout and it should work. > > Also, there now is a demo for reading FASTQ from gzipped files > in core/demos/stream_read_fastq_gz.cpp > > HTH > Manuel > > ------------------------------ > *From:* ngs geek [ngsgeek@gmail.com] > *Sent:* Friday, March 30, 2012 7:44 PM > *To:* seqan-dev@lists.fu-berlin.de > *Subject:* [Seqan-dev] Reading FastQ files from GZ archive > > Hi All: > > I'm trying to filter reads contained in a gz file based on quality > score; I was able to stream the id and the > sequence with GZFile stream and using a singlepass reader (I don't want to > keep the reads in memory). > Unfortunately, I can't access the quality string. > > RecordReader, SinglePass<> > reader(fastq_file); > CharString id; > String seq; > CharString qual; > > while (!atEnd(reader)) > { > if (readRecord(id, seq, reader, Fastq()) != 0) > { > std::cerr << "Problem with your FASTQ file." << std::endl; > return 1; > } > > // reading qual > } > > Any idea on this? I tried assignQualities etc. with no luck. > > Thanks > JD > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > --047d7b0721cc81c1da04bc8f1c3e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks! I'm seeing that the quality string is not the same that I read = from the fastq file.
but I can't figure out if these are guess by assignQualityValues .= .. in any case, I can't see
consistent results for my Illumin= a 1.3+ reads.

Thanks
JD=A0
On Sat, Mar 31, 2012 at 5:22 AM, Holtgrewe, Manu= el <m= anuel.holtgrewe@fu-berlin.de> wrote:
Hi JD,

good catch, you found a bug I just fixed. The problem was that assignQ= ualityValues() did not resize the target string, it does now. Update your S= VN checkout and it should work.

Also, there now is a demo for reading FASTQ from gzipped files in=A0co= re/demos/stream_read_fastq_gz.cpp

HTH
Manuel

Fro= m: ngs geek [ngs= geek@gmail.com]
Sent: Friday, March 30, 2012 7:44 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Reading FastQ files from GZ archive

Hi All:

I'm trying to filter reads contained in a gz file based on quality= score; I was able to stream the id and the=A0
sequence with GZFile stream and using a singlepass reader (I don't= want to keep the reads in memory).
Unfortunately, I can't access the quality string.

=A0RecordReader<Stream<GZFile>, SinglePass<> > reade= r(fastq_file);
=A0 CharString id;
=A0 String<Dna5Q> seq;
CharString qual;

while (!atEnd(reader))
=A0 {
=A0 =A0 =A0 if (readRecord(id, seq, reader, Fastq()) !=3D 0)
=A0 =A0 =A0 {
=A0 =A0 =A0 =A0 =A0 std::cerr << "Problem with your FASTQ f= ile." << std::endl;
=A0 =A0 =A0 =A0 =A0 return 1;
=A0 =A0 =A0 }

=A0 =A0 =A0 // reading qual
=A0 }

Any idea on this? I tried assignQualities etc. with no luck.

Thanks
JD


_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-berlin.de/listinfo/seqan-dev


--047d7b0721cc81c1da04bc8f1c3e-- From ngsgeek@gmail.com Sat Mar 31 22:36:00 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SE51h-0001vq-8E>; Sat, 31 Mar 2012 22:35:57 +0200 Received: from mail-pb0-f54.google.com ([209.85.160.54]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1SE51g-0004f0-PV>; Sat, 31 Mar 2012 22:35:57 +0200 Received: by pbcwz17 with SMTP id wz17so3476217pbc.13 for ; Sat, 31 Mar 2012 13:35:54 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=jGo9j6UTp9OyYqEfn6lCxIe3xwTMQ21j41H+VTFxRTs=; b=PxpJb5rGm/UroYB2QfUCsKVsonp9T0Zz+66Krwt/2+a0V8sjDSkrmDdoCs6sxZXPfm e890714koAr+Ay5FQ7k/HLnnPtERoGvz3pqL0EufbeVuAk17oDf0ei1X1rzJtbXDTL5N G5PutBDy/FA3Hdf83ax1j4otOVl8rwabETcPY373BffP909ftQPCuproSqqZhvXJS3B/ S/ZDK2X3q1QlsprZjIKV3c1pWge2pRayAUUyIxNP1Jzhh6AFb69SZJhw3sY07Qh2rUam MgTXVdjmxjyFfMhZGOFM/WcQbBEoYZ6QVQU+1tD4Wo6JiegoXDn94TQNDvkSCdElynHx AGZQ== MIME-Version: 1.0 Received: by 10.68.223.67 with SMTP id qs3mr8463530pbc.142.1333226154038; Sat, 31 Mar 2012 13:35:54 -0700 (PDT) Received: by 10.66.220.66 with HTTP; Sat, 31 Mar 2012 13:35:53 -0700 (PDT) In-Reply-To: References: Date: Sat, 31 Mar 2012 16:35:53 -0400 Message-ID: From: ngs geek To: SeqAn Development Content-Type: multipart/alternative; boundary=047d7b2e07135114a704bc8fe767 X-Originating-IP: 209.85.160.54 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1333226157-000018DE-7DA22546/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000049, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.5 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_50_60, HTML_MESSAGE,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: Re: [Seqan-dev] Reading FastQ files from GZ archive X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 31 Mar 2012 20:36:00 -0000 --047d7b2e07135114a704bc8fe767 Content-Type: text/plain; charset=ISO-8859-1 I forgot to add an example: raw quality string: bbbeeeeegfggfiiiiiiidgfagdghfdfhdcdfdfb_ca`BOWU^GBBOLGLU_H_Z_BLLLGLLFX]aNWWWY_bb_``BBBBBBBBBBBBBBBBB seqan quality string: ___________________________________________!OWU^G!!OLGLU_H_Z_!LLLGLLFX]_NWWWY______B!BBBBBBBBBBBBBBB Best JD On Sat, Mar 31, 2012 at 3:39 PM, ngs geek wrote: > Thanks! I'm seeing that the quality string is not the same that I read > from the fastq file. > Are they scaled? I read the doc here > http://trac.seqan.de/wiki/WhitePapers/QualityHandling > but I can't figure out if these are guess by assignQualityValues ... in > any case, I can't see > consistent results for my Illumina 1.3+ reads. > > Thanks > JD > > On Sat, Mar 31, 2012 at 5:22 AM, Holtgrewe, Manuel < > manuel.holtgrewe@fu-berlin.de> wrote: > >> Hi JD, >> >> good catch, you found a bug I just fixed. The problem was that >> assignQualityValues() did not resize the target string, it does now. Update >> your SVN checkout and it should work. >> >> Also, there now is a demo for reading FASTQ from gzipped files >> in core/demos/stream_read_fastq_gz.cpp >> >> HTH >> Manuel >> >> ------------------------------ >> *From:* ngs geek [ngsgeek@gmail.com] >> *Sent:* Friday, March 30, 2012 7:44 PM >> *To:* seqan-dev@lists.fu-berlin.de >> *Subject:* [Seqan-dev] Reading FastQ files from GZ archive >> >> Hi All: >> >> I'm trying to filter reads contained in a gz file based on quality >> score; I was able to stream the id and the >> sequence with GZFile stream and using a singlepass reader (I don't want >> to keep the reads in memory). >> Unfortunately, I can't access the quality string. >> >> RecordReader, SinglePass<> > reader(fastq_file); >> CharString id; >> String seq; >> CharString qual; >> >> while (!atEnd(reader)) >> { >> if (readRecord(id, seq, reader, Fastq()) != 0) >> { >> std::cerr << "Problem with your FASTQ file." << std::endl; >> return 1; >> } >> >> // reading qual >> } >> >> Any idea on this? I tried assignQualities etc. with no luck. >> >> Thanks >> JD >> >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >> >> > --047d7b2e07135114a704bc8fe767 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I forgot to add an example:

raw quality string:
bbbeeeeegfggfiiiiiiidgfagdghfdfhdcdfdfb_ca`BOWU^GBBOLGLU_H_Z_BLLLGLLFX]aN= WWWY_bb_``BBBBBBBBBBBBBBBBB

seqan quality stri= ng:
___________________________________________!OWU^G!!OLGLU_H_Z_!LLLGLLFX= ]_NWWWY______B!BBBBBBBBBBBBBBB

Best
JD

On Sat, Mar 31, 2012 at 3:39 PM, ng= s geek <ngsgeek@g= mail.com> wrote:
Thanks! I'm seeing that the quality stri= ng is not the same that I read from the fastq file.
Are they scaled? I = read the doc here http://trac.seqan.de/wiki/WhitePapers/QualityHan= dling
but I can't figure out if these are guess by assignQualityValues .= .. in any case, I can't see
consistent results for my Illumin= a 1.3+ reads.

Thanks
JD=A0

On Sat, Mar 31, 2012 at 5= :22 AM, Holtgrewe, Manuel <manuel.holtgrewe@fu-berlin.de&g= t; wrote:
Hi JD,

good catch, you found a bug I just fixed. The problem was that assignQ= ualityValues() did not resize the target string, it does now. Update your S= VN checkout and it should work.

Also, there now is a demo for reading FASTQ from gzipped files in=A0co= re/demos/stream_read_fastq_gz.cpp

HTH
Manuel

Fro= m: ngs geek [ngs= geek@gmail.com]
Sent: Friday, March 30, 2012 7:44 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Reading FastQ files from GZ archive

Hi All:

I'm trying to filter reads contained in a gz file based on quality= score; I was able to stream the id and the=A0
sequence with GZFile stream and using a singlepass reader (I don't= want to keep the reads in memory).
Unfortunately, I can't access the quality string.

=A0RecordReader<Stream<GZFile>, SinglePass<> > reade= r(fastq_file);
=A0 CharString id;
=A0 String<Dna5Q> seq;
CharString qual;

while (!atEnd(reader))
=A0 {
=A0 =A0 =A0 if (readRecord(id, seq, reader, Fastq()) !=3D 0)
=A0 =A0 =A0 {
=A0 =A0 =A0 =A0 =A0 std::cerr << "Problem with your FASTQ f= ile." << std::endl;
=A0 =A0 =A0 =A0 =A0 return 1;
=A0 =A0 =A0 }

=A0 =A0 =A0 // reading qual
=A0 }

Any idea on this? I tried assignQualities etc. with no luck.

Thanks
JD


_______________________________________________
seqan-dev mailing list
seqan-dev= @lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev



--047d7b2e07135114a704bc8fe767--