From rene.maerker@fu-berlin.de Fri Dec 05 17:39:06 2014 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XwvuK-001Cmv-Q0>; Fri, 05 Dec 2014 17:39:04 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XwvuK-003aRL-Oc>; Fri, 05 Dec 2014 17:39:04 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1XwvuK-0035wM-CJ>; Fri, 05 Dec 2014 17:39:04 +0100 Received: from EX03B.campus.fu-berlin.de ([130.133.170.135]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0210.002; Fri, 5 Dec 2014 17:39:03 +0100 From: =?utf-8?B?UmFobiwgUmVuw6k=?= To: SeqAn Development Thread-Topic: [Seqan-dev] Trouble Using Custom SeedSpec 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Dec 2014 21:29:42 +0100 Received: by mail-yh0-f48.google.com with SMTP id i57so7427634yha.7 for ; Tue, 30 Dec 2014 12:29:39 -0800 (PST) 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=gMaclkQLvrAYVFV+h58LX+vfRLNCXaXV7OnOGtlR6j4=; b=jV8hf0o+eeD6aadojWc7MNoHyu4gYYxh8gbUxmVaMXPvdAc1wqsgPIylbsBfkPqmZM Vbv+a5kCzzUlKfIZCsI2pj83ld1yab7ElPtnqXMbeLIcdn5+ptrjYJ9u/u9Kxl0H61s/ bP4E9H1CED+8vIJ5lbMzeXVZJknTGiP09VofbygQYZMhsEoqGbyeWcKmSNpAwqGaM4fB rWvPWlRirK9S7qk10TiAGQsFKnYaAm/xK98DeG3eu7mcb7aZzTXhA7X8HpaRwERRj8fQ D+0+B93nLSO6JEYjkJNs+NjQpVbJveQ5SfXCQuFCLDtSOZQyYrPpqcSzLZ3PDkrcEdKc 3ddQ== MIME-Version: 1.0 X-Received: by 10.170.57.211 with SMTP id 202mr47455198ykz.116.1419971379399; Tue, 30 Dec 2014 12:29:39 -0800 (PST) Received: by 10.170.86.86 with HTTP; Tue, 30 Dec 2014 12:29:39 -0800 (PST) Date: Tue, 30 Dec 2014 12:29:39 -0800 Message-ID: From: Brett Bowman To: SeqAn Development Content-Type: multipart/alternative; boundary=001a1139489ea9142f050b74d9fa X-Originating-IP: 209.85.213.48 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1419971382-0000127A-F2DF2DAA/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.483462, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.4 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H2,T_DKIM_INVALID,URIBL_RHS_DOB X-Spam-Checker-Version: SpamAssassin 3.4.0 on Tokelau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Two Alignment Questions X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 30 Dec 2014 20:29:43 -0000 --001a1139489ea9142f050b74d9fa Content-Type: text/plain; charset=UTF-8 1) Is there an easy way to get the accuracy of an Alignment object, or is that something I need to calculate myself? 2) bandedChainAlignment fails messily when given a Vector of Seeds instead of a String, where as other functions work fine (e.g. chainSeedsGlobally). Why does it work for the one and not the other? Excerpt from error message below. """ /usr/include/seqan/seeds/banded_chain_alignment_impl.h:1195:57: error: call to 'end' is ambiguous SEQAN_ASSERT(itEnd != static_cast(end(seedSet))); ^~~ /usr/include/seqan/basic/debug_test_system.h:2146:44: note: expanded from macro 'SEQAN_ASSERT' (_arg1), # _arg1)) { \ ^ /usr/include/seqan/seeds/banded_chain_alignment_profile.h:254:16: note: in instantiation of function template specialization ... /usr/include/seqan/seeds/banded_chain_alignment.h:207:12: note: in instantiation of function template specialization 'seqan::bandedChainAlignment, seqan::Alloc >, seqan::Tag, std::vector, seqan::DefaultSeedConfig>, std::allocator, seqan::DefaultSeedConfig> > >, long, seqan::Tag, seqan::Tag, false, false, false, false, seqan::Tag >' requested here return bandedChainAlignment(align, seedSet, scoreScheme, scoreScheme, alignConfig, bandExtension); ^ /home/bbowman/git/SRSLI/src/C++/SparseAlignment2.cpp:72:25: note: in instantiation of function template specialization 'seqan::bandedChainAlignment, seqan::Alloc >, seqan::Tag, std::vector, seqan::DefaultSeedConfig>, std::allocator, seqan::DefaultSeedConfig> > >, long, seqan::Tag, false, false, false, false, seqan::Tag >' requested here long alnScore = bandedChainAlignment(alignment, *seedChain, scoring, globalConfig); ^ /home/bbowman/git/SRSLI/src/C++/main.cpp:95:27: note: in instantiation of function template specialization 'RefChainsToAlignments > ()>' requested here auto alignments = RefChainsToAlignments(record->Seq, ^ /usr/include/seqan/seeds/banded_chain_alignment_impl.h:583:1: note: candidate template ignored: substitution failure [with TSeedSet = std::vector, seqan::DefaultSeedConfig>, std::allocator, seqan::DefaultSeedConfig> > >] _findFirstAnchor(TSeedSet const & seedSet, int bandExtension) """ Sincerely, -Brett --001a1139489ea9142f050b74d9fa Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
1) =C2=A0Is there an easy way to get the accuracy of = an Alignment object, or is that something I need to calculate myself?
=

2) =C2=A0bandedChainAlignment fails messily when given = a Vector of Seeds instead of a String, where as other functions work fine (= e.g. chainSeedsGlobally).=C2=A0 Why does it work for the one and not the ot= her?=C2=A0 Excerpt from error message below.

"= ;""
/usr/include/seqan/seeds/banded_chain_alignmen= t_impl.h:1195:57: error: call to 'end' is ambiguous
=C2= =A0 =C2=A0 SEQAN_ASSERT(itEnd !=3D static_cast<TSeedSetIterator>(end(= seedSet)));
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ^~~
/usr/include/seqan/basic/debug_test_system.h:2146:44: note: expand= ed from macro 'SEQAN_ASSERT'
=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 (_arg1), # _arg1)) { =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 \
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^
/usr/include/seqan= /seeds/banded_chain_alignment_profile.h:254:16: note: in instantiation of f= unction template specialization

...

=
/usr/include/seqan/seeds/banded_chain_alignment.h:207:12: note: = in instantiation of function template specialization
=C2=A0 =C2= =A0 =C2=A0 'seqan::bandedChainAlignment<seqan::String<seqan::Simp= leType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >, s= eqan::Tag<seqan::ArrayGaps_>,
=C2=A0 =C2=A0 =C2=A0 std::vec= tor<seqan::Seed<seqan::Tag<seqan::Simple_>, seqan::DefaultSeedC= onfig>, std::allocator<seqan::Seed<seqan::Tag<seqan::Simple_>= ;, seqan::DefaultSeedConfig> > >, long,
=C2=A0 =C2=A0 = =C2=A0 seqan::Tag<seqan::Simple_>, seqan::Tag<seqan::Simple_>, = false, false, false, false, seqan::Tag<seqan::Default_> >' req= uested here
=C2=A0 =C2=A0 return bandedChainAlignment(align, seed= Set, scoreScheme, scoreScheme, alignConfig, bandExtension);
=C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^
/home/bbowman/git/SRSLI/s= rc/C++/SparseAlignment2.cpp:72:25: note: in instantiation of function templ= ate specialization
=C2=A0 =C2=A0 =C2=A0 'seqan::bandedChainAl= ignment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5= _>, seqan::Alloc<void> >, seqan::Tag<seqan::ArrayGaps_>,<= /div>
=C2=A0 =C2=A0 =C2=A0 std::vector<seqan::Seed<seqan::Tag<= seqan::Simple_>, seqan::DefaultSeedConfig>, std::allocator<seqan::= Seed<seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> >= >, long,
=C2=A0 =C2=A0 =C2=A0 seqan::Tag<seqan::Simple_>= ;, false, false, false, false, seqan::Tag<seqan::Default_> >' = requested here
=C2=A0 =C2=A0 =C2=A0 =C2=A0 long alnScore =3D band= edChainAlignment(alignment, *seedChain, scoring, globalConfig);
= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 ^
/home/bbowman/git/SRSLI/src/C++/main.cpp:95:27: note= : in instantiation of function template specialization 'RefChainsToAlig= nments<seqan::AlignConfig<false, true, true, false,
=C2=A0 = =C2=A0 =C2=A0 seqan::Tag<seqan::Default_> > ()>' requested = here
=C2=A0 =C2=A0 =C2=A0 =C2=A0 auto alignments =3D RefChainsToA= lignments(record->Seq,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ^
/usr/inclu= de/seqan/seeds/banded_chain_alignment_impl.h:583:1: note: candidate templat= e ignored: substitution failure [with TSeedSet =3D std::vector<seqan::Se= ed<seqan::Tag<seqan::Simple_>,
=C2=A0 =C2=A0 =C2=A0 seqa= n::DefaultSeedConfig>, std::allocator<seqan::Seed<seqan::Tag<se= qan::Simple_>, seqan::DefaultSeedConfig> > >]
_findFi= rstAnchor(TSeedSet const & seedSet, int bandExtension)
= """=C2=A0

Sincerely,
-Brett
--001a1139489ea9142f050b74d9fa--