From gany.fml@gmail.com Fri Feb 05 23:43:26 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aRp65-000A5P-AM>; Fri, 05 Feb 2016 23:43:25 +0100 Received: from mail-io0-f174.google.com ([209.85.223.174]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:AES128-GCM-SHA256:128) (envelope-from ) id <1aRp64-002GLC-Sp>; Fri, 05 Feb 2016 23:43:25 +0100 Received: by mail-io0-f174.google.com with SMTP id f81so143906354iof.0 for ; Fri, 05 Feb 2016 14:43:23 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:from:date:message-id:subject:to:content-type; bh=ginMc25DRhvDKFmrb6lxUfWV77Fu2sSMxRgAez6L3z8=; b=ijcu0V7aYxwBTdXbovzLYAEMDNy9+l6gBNwa6mjuXAuHK9l1WTG/4O9X621MKfQE/u ipYsUBFpPrbwv+qw96qx0jFUqpcUwaAGDTiwf21dMc+hYb088PJJLFsa1CVanKOUvmAR ATS32HbYi6t/menLEDJKjNqYrwa7Z2n34kV/IZjRGveQaPluUSlhgG2GjdmPBsGJTaI6 OVhVYH+rhUVlNUUkktujOjdIbJeGLpbIFJKaNr3Y0XhzzDMReGGXcSuqm8Rjp//Y20zc M74uS9xFsak0UjCuE9UdR4F0Hf4w3I9jkAB7EOsL2Q1T1HEPRWq6jlkUS65Kd9xdvJ+6 uZ9w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:mime-version:from:date:message-id:subject:to :content-type; bh=ginMc25DRhvDKFmrb6lxUfWV77Fu2sSMxRgAez6L3z8=; b=Jzqwz7CuGfB5mjqoOFwVk3TIWH21ZtAqKho7yqzAFKfkDd7uXFvr9nJtbX7/d3rKLI Atu2qoB3w+5DbCxA7RDeSi69K3/gJohxGt2kp59Gd+98jLbdOep8jqYzlAW7Dw8A8qD7 f4oKy0haV3TewMIRWZBHrrGHXJmtwF5GrUBhGMPto+vCgwGWI8Danmho2QuRI6t4nrnO DT7yOb+x+ZqZl2MhEHC0UlYlPQSsXv58rVR42EeCDurQmYeXDuoOqe9H0m1WFdYVBb3C 3EXP523PQex7V/DvRE98vvTxohC71t30gC7JUNzYN8ArSApFS2J8Eq/TQ20SNcPB5hxV 1Isw== X-Gm-Message-State: AG10YOSnrWOXR8M98okjzO0VPyV8yI3GjhiRVbRk6T9OZP8EJ2DJXIEg1YVGWJhr0/duanYGW/fbNiM3uTlCiw== X-Received: by 10.107.11.231 with SMTP id 100mr16456286iol.165.1454712202550; Fri, 05 Feb 2016 14:43:22 -0800 (PST) MIME-Version: 1.0 Received: by 10.64.168.34 with HTTP; Fri, 5 Feb 2016 14:43:03 -0800 (PST) From: Yue Gan Date: Fri, 5 Feb 2016 16:43:03 -0600 Message-ID: To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=001a113f7b6a15636d052b0d9478 X-Originating-IP: 209.85.223.174 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1454712205-00052D45-6DF57078/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.329868, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.8 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU, FREEMAIL_FROM, HTML_MESSAGE, RCVD_IN_DNSWL_LOW, RCVD_IN_MSPIKE_H2, SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Precompiled header 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: Fri, 05 Feb 2016 22:43:26 -0000 --001a113f7b6a15636d052b0d9478 Content-Type: text/plain; charset=UTF-8 Hi all, I am trying to generate precompiled header using g++/clang for seqan to reduce the compile time of my program. But it throws a lot of errors. For example for seq_io.h: In file included from seq_io.h:44: In file included from /Users/gany/Development/include/seqan/basic.h:80: In file included from /Users/gany/Development/include/seqan/basic/basic_math.h:44: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:638:9: error: no member named 'signbit' in the global namespace; did you mean 'sigwait'? using ::signbit; ~~^ /usr/include/signal.h:101:5: note: 'sigwait' declared here int sigwait(const sigset_t * __restrict, int * __restrict) __DARWIN_ALIAS_C(sigwait); ^ In file included from seq_io.h:44: In file included from /Users/gany/Development/include/seqan/basic.h:80: In file included from /Users/gany/Development/include/seqan/basic/basic_math.h:44: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:639:9: error: no member named 'fpclassify' in the global namespace using ::fpclassify; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:640:9: error: no member named 'isfinite' in the global namespace using ::isfinite; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:641:9: error: no member named 'isinf' in the global namespace using ::isinf; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:642:9: error: no member named 'isnan' in the global namespace using ::isnan; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:643:9: error: no member named 'isnormal' in the global namespace using ::isnormal; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:644:7: error: no member named 'isgreater' in the global namespace; did you mean '::std::greater'? using ::isgreater; ^~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/functional:709:30: note: '::std::greater' declared here struct _LIBCPP_TYPE_VIS_ONLY greater : binary_function<_Tp, _Tp, bool> ^ In file included from seq_io.h:44: In file included from /Users/gany/Development/include/seqan/basic.h:80: In file included from /Users/gany/Development/include/seqan/basic/basic_math.h:44: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:645:7: error: no member named 'isgreaterequal' in the global namespace; did you mean '::std::greater_equal'? using ::isgreaterequal; ^~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/functional:738:30: note: '::std::greater_equal' declared here struct _LIBCPP_TYPE_VIS_ONLY greater_equal : binary_function<_Tp, _Tp, bool> ^ In file included from seq_io.h:44: In file included from /Users/gany/Development/include/seqan/basic.h:80: In file included from /Users/gany/Development/include/seqan/basic/basic_math.h:44: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:646:9: error: no member named 'isless' in the global namespace using ::isless; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:647:9: error: no member named 'islessequal' in the global namespace using ::islessequal; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:648:9: error: no member named 'islessgreater' in the global namespace using ::islessgreater; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:649:9: error: no member named 'isunordered' in the global namespace using ::isunordered; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:650:9: error: no member named 'isunordered' in the global namespace using ::isunordered; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:652:9: error: no member named 'float_t' in the global namespace using ::float_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:653:9: error: no member named 'double_t' in the global namespace using ::double_t; ~~^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:660:39: error: use of undeclared identifier 'fabsf' abs(float __lcpp_x) _NOEXCEPT {return fabsf(__lcpp_x);} ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:664:40: error: use of undeclared identifier 'fabs' abs(double __lcpp_x) _NOEXCEPT {return fabs(__lcpp_x);} ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:668:45: error: use of undeclared identifier 'fabsl' abs(long double __lcpp_x) _NOEXCEPT {return fabsl(__lcpp_x);} ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:675:9: error: no member named 'acos' in the global namespace using ::acos; ~~^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. Could anyone help me with this? Many thanks! BTW, the command I use to generate precompiled header is: g++ -std=c++11 -x c++-header seq_io.h -o seq_io.h.pch Thanks! Yue Gan --001a113f7b6a15636d052b0d9478 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi all,

I am trying to generate precomp= iled header using g++/clang for seqan=C2=A0to reduce the compile time of my= program. But it throws a lot of errors.=C2=A0

For= example for=C2=A0seq_io.h:

In file included = from seq_io.h:44:
In file included from /Users/gany/Development/i= nclude/seqan/basic.h:80:
In file included from /Users/gany/Develo= pment/include/seqan/basic/basic_math.h:44:
/Applications/Xcode.ap= p/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include= /c++/v1/cmath:638:9: error: no member named 'signbit' in the global= namespace; did you mean 'sigwait'?
using ::signbit;
=C2=A0 =C2=A0 =C2=A0 ~~^
/usr/include/signal.h:101:5: note:= 'sigwait' declared here
int =C2=A0 =C2=A0 sigwait(const = sigset_t * __restrict, int * __restrict) __DARWIN_ALIAS_C(sigwait);
=C2=A0 =C2=A0 =C2=A0 =C2=A0 ^
In file included from seq_io.h:4= 4:
In file included from /Users/gany/Development/include/seqan/ba= sic.h:80:
In file included from /Users/gany/Development/include/s= eqan/basic/basic_math.h:44:
/Applications/Xcode.app/Contents/Deve= loper/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:6= 39:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
=C2=A0 =C2=A0 =C2=A0 ~~^
/= Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolcha= in/usr/bin/../include/c++/v1/cmath:640:9: error: no member named 'isfin= ite' in the global namespace
using ::isfinite;
=C2= =A0 =C2=A0 =C2=A0 ~~^
/Applications/Xcode.app/Contents/Developer/= Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:641:9: = error: no member named 'isinf' in the global namespace
us= ing ::isinf;
=C2=A0 =C2=A0 =C2=A0 ~~^
/Applications/Xco= de.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../in= clude/c++/v1/cmath:642:9: error: no member named 'isnan' in the glo= bal namespace
using ::isnan;
=C2=A0 =C2=A0 =C2=A0 ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault= .xctoolchain/usr/bin/../include/c++/v1/cmath:643:9: error: no member named = 'isnormal' in the global namespace
using ::isnormal;
=C2=A0 =C2=A0 =C2=A0 ~~^
/Applications/Xcode.app/Contents/D= eveloper/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmat= h:644:7: error: no member named 'isgreater' in the global namespace= ; did you mean '::std::greater'?
using ::isgreater;
=
=C2=A0 =C2=A0 =C2=A0 ^~
/Applications/Xcode.app/Contents/Dev= eloper/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/functi= onal:709:30: note: '::std::greater' declared here
struct = _LIBCPP_TYPE_VIS_ONLY greater : binary_function<_Tp, _Tp, bool>
=
=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^
In file included from seq_io.= h:44:
In file included from /Users/gany/Development/include/seqan= /basic.h:80:
In file included from /Users/gany/Development/includ= e/seqan/basic/basic_math.h:44:
/Applications/Xcode.app/Contents/D= eveloper/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmat= h:645:7: error: no member named 'isgreaterequal' in the global name= space; did you mean '::std::greater_equal'?
using ::isgre= aterequal;
=C2=A0 =C2=A0 =C2=A0 ^~
/Applications/Xcode.= app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../inclu= de/c++/v1/functional:738:30: note: '::std::greater_equal' declared = here
struct _LIBCPP_TYPE_VIS_ONLY greater_equal : binary_function= <_Tp, _Tp, bool>
=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^
I= n file included from seq_io.h:44:
In file included from /Users/ga= ny/Development/include/seqan/basic.h:80:
In file included from /U= sers/gany/Development/include/seqan/basic/basic_math.h:44:
/Appli= cations/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/us= r/bin/../include/c++/v1/cmath:646:9: error: no member named 'isless'= ; in the global namespace
using ::isless;
=C2=A0 =C2=A0= =C2=A0 ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains= /XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:647:9: error: no = member named 'islessequal' in the global namespace
using = ::islessequal;
=C2=A0 =C2=A0 =C2=A0 ~~^
/Applications/X= code.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../= include/c++/v1/cmath:648:9: error: no member named 'islessgreater' = in the global namespace
using ::islessgreater;
=C2=A0 = =C2=A0 =C2=A0 ~~^
/Applications/Xcode.app/Contents/Developer/Tool= chains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:649:9: erro= r: no member named 'isunordered' in the global namespace
= using ::isunordered;
=C2=A0 =C2=A0 =C2=A0 ~~^
/Applicat= ions/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/b= in/../include/c++/v1/cmath:650:9: error: no member named 'isunordered&#= 39; in the global namespace
using ::isunordered;
=C2=A0= =C2=A0 =C2=A0 ~~^
/Applications/Xcode.app/Contents/Developer/Too= lchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:652:9: err= or: no member named 'float_t' in the global namespace
usi= ng ::float_t;
=C2=A0 =C2=A0 =C2=A0 ~~^
/Applications/Xc= ode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../i= nclude/c++/v1/cmath:653:9: error: no member named 'double_t' in the= global namespace
using ::double_t;
=C2=A0 =C2=A0 =C2= =A0 ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/Xco= deDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:660:39: error: use of= undeclared identifier 'fabsf'
abs(float __lcpp_x) _NOEXC= EPT {return fabsf(__lcpp_x);}
=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 ^
/Applications/Xcode.app/Contents/Devel= oper/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:66= 4:40: error: use of undeclared identifier 'fabs'
abs(doub= le __lcpp_x) _NOEXCEPT {return fabs(__lcpp_x);}
=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^
/Applications/X= code.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../= include/c++/v1/cmath:668:45: error: use of undeclared identifier 'fabsl= '
abs(long double __lcpp_x) _NOEXCEPT {return fabsl(__lcpp_x)= ;}
=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 ^
/Applications/Xcode.app/Contents/Developer/To= olchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:675:9: er= ror: no member named 'acos' in the global namespace
using= ::acos;
=C2=A0 =C2=A0 =C2=A0 ~~^
fatal error: too many= errors emitted, stopping now [-ferror-limit=3D]
20 errors genera= ted.

Could anyone help me with this? Many th= anks!

BTW, the command I use to generate precompil= ed header is:

g++ -std=3Dc++11 -x c++-header seq_i= o.h -o seq_io.h.pch

Thanks!

Yue Gan
--001a113f7b6a15636d052b0d9478-- From SchulzeJa@rki.de Mon Feb 08 15:30:24 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aSmpb-003vQL-9F>; Mon, 08 Feb 2016 15:30:23 +0100 Received: from m4-bn.bund.de ([77.87.228.76]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1:DHE-RSA-AES256-SHA:256) (envelope-from ) id <1aSmpb-0029vt-2u>; Mon, 08 Feb 2016 15:30:23 +0100 Received: from m4.mfw.bn.ivbb.bund.de (localhost.mfw.bn.ivbb.bund.de [127.0.0.1]) by m4-bn.bund.de (8.14.5/8.14.5) with ESMTP id u18EULSO019716 for ; Mon, 8 Feb 2016 15:30:21 +0100 (CET) Received: (from localhost) by m4.mfw.bn.ivbb.bund.de (MSCAN) id 5/m4.mfw.bn.ivbb.bund.de/smtp-gw/mscan; Mon Feb 8 15:30:21 2016 X-P350-Id: 35c533a24f80dd88 From: "Schulze, Jakob" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: appendTagValue() for BamTagsDict Thread-Index: AdFie0ZdiV5DUJ9yQB+T9haG++zejg== Date: Mon, 8 Feb 2016 14:30:11 +0000 Message-ID: <3a7200f2969a48a787ddffcc40c6490d@EXCH01.rki.local> Accept-Language: de-DE, en-US Content-Language: de-DE X-MS-Has-Attach: yes X-MS-TNEF-Correlator: x-ms-exchange-transport-fromentityheader: Hosted x-tm-as-product-ver: SMEX-11.0.0.1191-8.000.1202-22120.000 x-tm-as-result: No--32.590300-8.000000-31 x-tm-as-user-approved-sender: No x-tm-as-user-blocked-sender: No Content-Type: multipart/mixed; boundary="_002_3a7200f2969a48a787ddffcc40c6490dEXCH01rkilocal_" MIME-Version: 1.0 X-Originating-IP: 77.87.228.76 X-Original-X-Originating-IP: [10.15.144.213] X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1454941823-00052D45-1589B365/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.002575, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-5.0 required=5.0 tests=RCVD_IN_DNSWL_HI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,UNPARSEABLE_RELAY X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] appendTagValue() for BamTagsDict 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: Mon, 08 Feb 2016 14:30:24 -0000 --_002_3a7200f2969a48a787ddffcc40c6490dEXCH01rkilocal_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi everyone, I am currently trying to write out Bam files using seqan's BamFileOut. I st= umbled across some strange behavior of appendTagValue() When using the function three times in a row, length(tags) returns 2, which= seems one to less to me. I enclosed a code example using the example from http://docs.seqan.de/seqan/2.0.0/demos/bam_io/bam_tags_dict.cpp I marked my changes. Did I miss something? Furthermore, I wondered whether there is a function, which converts a BamTa= gsDict into a String, which I can directly use as an Entry in a Sam file. Best Regards, Jakob PS: Output of the code snippet on my machine is: 3 AA -> "value1" AB -> "value2" AC -> 30 2 --_002_3a7200f2969a48a787ddffcc40c6490dEXCH01rkilocal_ Content-Type: text/plain; name="main.cpp" Content-Description: main.cpp Content-Disposition: attachment; filename="main.cpp"; size=1308; creation-date="Mon, 08 Feb 2016 14:29:29 GMT"; modification-date="Mon, 08 Feb 2016 14:26:47 GMT" Content-Transfer-Encoding: base64 I2luY2x1ZGUgPGlvc3RyZWFtPgojaW5jbHVkZSA8c2VxYW4vc3RyZWFtLmg+CiNpbmNsdWRlIDxz ZXFhbi9iYW1faW8uaD4KCnVzaW5nIG5hbWVzcGFjZSBzZXFhbjsKCmludCBtYWluKCkKewogICAg Q2hhclN0cmluZyBiYW1TdHIsIHNhbVN0ciA9ICJBQTpaOnZhbHVlMVx0QUI6Wjp2YWx1ZTJcdEFD Omk6MzAiOwogICAgYXNzaWduVGFnc1NhbVRvQmFtKGJhbVN0ciwgc2FtU3RyKTsKICAgIEJhbVRh Z3NEaWN0IHRhZ3MoYmFtU3RyKTsKICAgIEJhbVRhZ3NEaWN0IG5ld1RhZ3M7IC8vIE5FVzogYWRk ZWQgYnkgSmFrb2IgU2NodWx6ZQogICAgc3RkOjpjb3V0IDw8IGxlbmd0aCh0YWdzKSA8PCBzdGQ6 OmVuZGw7ICAvLyAjPT4gIjMiCiAgICBmb3IgKHVuc2lnbmVkIGlkID0gMDsgaWQgPCBsZW5ndGgo dGFncyk7ICsraWQpCiAgICB7CiAgICAgICAgc3RkOjpjb3V0IDw8IGdldFRhZ0tleSh0YWdzLCBp ZCkgPDwgIiAtPiAiOwoKICAgICAgICBpZiAoZ2V0VGFnVHlwZSh0YWdzLCBpZCkgPT0gJ2knKSAg Ly8gaXMgMzIgYml0IGludGVnZXIKICAgICAgICB7CiAgICAgICAgICAgIF9faW50MzIgeCA9IDA7 CiAgICAgICAgICAgIGJvb2wgcmVzID0gZXh0cmFjdFRhZ1ZhbHVlKHgsIHRhZ3MsIGlkKTsKICAg ICAgICAgICAgU0VRQU5fQVNTRVJUX01TRyhyZXMsICJOb3QgYSB2YWxpZCBpbnRlZ2VyIGF0IHBv cyAldSEiLCBpZCk7CiAgICAgICAgICAgIHN0ZDo6Y291dCA8PCB4OwoJCQlhcHBlbmRUYWdWYWx1 ZShuZXdUYWdzLCBnZXRUYWdLZXkodGFncywgaWQpLCB4KTsgLy8gTkVXOiBhZGRlZCBieSBKYWtv YiBTY2h1bHplCiAgICAgICAgfQogICAgICAgIGlmIChnZXRUYWdUeXBlKHRhZ3MsIGlkKSA9PSAn WicpICAvLyBpcyBzdHJpbmcKICAgICAgICB7CiAgICAgICAgICAgIENoYXJTdHJpbmcgc3RyOwog ICAgICAgICAgICBib29sIHJlcyA9IGV4dHJhY3RUYWdWYWx1ZShzdHIsIHRhZ3MsIGlkKTsKICAg ICAgICAgICAgU0VRQU5fQVNTRVJUX01TRyhyZXMsICJOb3QgYSB2YWxpZCBzdHJpbmcgYXQgcG9z ICV1ISIsIGlkKTsKICAgICAgICAgICAgc3RkOjpjb3V0IDw8ICciJyA8PCBzdHIgPDwgJyInOwoJ CQlhcHBlbmRUYWdWYWx1ZShuZXdUYWdzLCBnZXRUYWdLZXkodGFncywgaWQpLCBzdHIpOyAvLyBO RVc6IGFkZGVkIGJ5IEpha29iIFNjaHVsemUKICAgICAgICB9CgogICAgICAgIHN0ZDo6Y291dCA8 PCBzdGQ6OmVuZGw7CiAgICB9CgoJc3RkOjpjb3V0IDw8IGxlbmd0aChuZXdUYWdzKSA8PCBzdGQ6 OmVuZGw7IC8vIE5FVzogYWRkZWQgYnkgSmFrb2IgU2NodWx6ZQogICAgcmV0dXJuIDA7Cn0K --_002_3a7200f2969a48a787ddffcc40c6490dEXCH01rkilocal_-- From SchulzeJa@rki.de Mon Feb 15 16:34:26 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aVLAP-002QaR-FS>; Mon, 15 Feb 2016 16:34:25 +0100 Received: from m1-bln.bund.de ([77.87.224.105]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1:DHE-RSA-AES256-SHA:256) (envelope-from ) id <1aVLAP-0006rv-9Y>; Mon, 15 Feb 2016 16:34:25 +0100 Received: from m1.mfw.bln.ivbb.bund.de (localhost.mfw.bln.ivbb.bund.de [127.0.0.1]) by m1-bln.bund.de (8.14.5/8.14.5) with ESMTP id u1FFYNXa025530 for ; Mon, 15 Feb 2016 16:34:23 +0100 (CET) Received: (from localhost) by m1.mfw.bln.ivbb.bund.de (MSCAN) id 5/m1.mfw.bln.ivbb.bund.de/smtp-gw/mscan; Mon Feb 15 16:34:23 2016 X-P350-Id: 360f7ff11db3b92c From: "Schulze, Jakob" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: Error with samtools library Thread-Index: AdFoBAsRo7gh35ovQOqBvzaeRtWQKw== Date: Mon, 15 Feb 2016 15:34:21 +0000 Message-ID: <3ffd13d0d9434efaadfecc4e68c0d8d8@EXCH01.rki.local> Accept-Language: de-DE, en-US Content-Language: de-DE X-MS-Has-Attach: yes X-MS-TNEF-Correlator: x-ms-exchange-transport-fromentityheader: Hosted x-tm-as-product-ver: SMEX-11.0.0.1191-8.000.1202-22134.000 x-tm-as-result: No--40.749400-0.000000-31 x-tm-as-user-approved-sender: Yes x-tm-as-user-blocked-sender: No Content-Type: multipart/mixed; boundary="_003_3ffd13d0d9434efaadfecc4e68c0d8d8EXCH01rkilocal_" MIME-Version: 1.0 X-Originating-IP: 77.87.224.105 X-Original-X-Originating-IP: [10.15.144.213] X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1455550465-00052D45-DEAAC0A6/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.002262, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-5.0 required=5.0 tests=RCVD_IN_DNSWL_HI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,UNPARSEABLE_RELAY X-Spam-Checker-Version: SpamAssassin 3.4.1 on Vanuatu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Error with samtools library 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: Mon, 15 Feb 2016 15:34:26 -0000 --_003_3ffd13d0d9434efaadfecc4e68c0d8d8EXCH01rkilocal_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hi everyone, I came across some code which uses the samtools library. Together with seqa= n there is an error which seems to come from samtools but I do not know why= . Since I am not the author of the samtools include I cannot say much about= the corresponding lines in the CMakeLists.txt But since commenting out seqan from the main.cpp solves the error, I imagin= ed this has something to do with seqan. I provided a minimal example with a main.cpp and a CMakeLists, which hopefu= lly (on my pc it does) reproduces the error. Please note, that I did use ab= solute paths for CMAKE_MODULE_PATH and SEQAN_INCLUDE_PATH. You would need t= o change these accordingly. Best Regards, Jakob PS: Any progress on my last question concerning BamTagsDict? PPS: terminal output with error message (inside build directory) =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D $ cmake .. -- The C compiler identification is GNU 4.9.2 -- The CXX compiler identification is GNU 4.9.2 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for include file execinfo.h -- Looking for include file execinfo.h - found -- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so - = found -- Determined version is 2.0.2 bam_reheader.c: In function =91bam_reheader=92: bam_reheader.c:36:19: warning: variable =91old=92 set but not used [-Wunuse= d-but-set-variable] bam_header_t *old; ^ kprobaln.c: In function =91kpa_glocal=92: kprobaln.c:78:21: warning: variable =91is_diff=92 set but not used [-Wunuse= d-but-set-variable] int bw, bw2, i, k, is_diff =3D 0, is_backward =3D 1, Pr; ^ misc/md5.c: In function =91MD5Final=92: misc/md5.c:151:5: warning: dereferencing type-punned pointer will break str= ict-aliasing rules [-Wstrict-aliasing] ((uint32_t *) ctx->in)[14] =3D ctx->bits[0]; ^ misc/md5.c:152:5: warning: dereferencing type-punned pointer will break str= ict-aliasing rules [-Wstrict-aliasing] ((uint32_t *) ctx->in)[15] =3D ctx->bits[1]; ^ misc/md5.c: In function =91MD5Final=92: misc/md5.c:151:5: warning: dereferencing type-punned pointer will break str= ict-aliasing rules [-Wstrict-aliasing] ((uint32_t *) ctx->in)[14] =3D ctx->bits[0]; ^ misc/md5.c:152:5: warning: dereferencing type-punned pointer will break str= ict-aliasing rules [-Wstrict-aliasing] ((uint32_t *) ctx->in)[15] =3D ctx->bits[1]; ^ -- Configuring done -- Generating done -- Build files have been written to: /home/schulzeja/masterthesis/workDir/s= eqanTestForReport2/build $ make Scanning dependencies of target main [100%] Building CXX object CMakeFiles/main.dir/main.cpp.o In file included from /home/schulzeja/masterthesis/workDir/seqanTestForRepo= rt2/build/samtools-1.2/bam.h:48:0, from /home/schulzeja/masterthesis/workDir/seqanTestForRepo= rt2/build/samtools-1.2/sam.h:29, from /home/schulzeja/masterthesis/workDir/seqanTestForRepo= rt2/main.cpp:1: /home/schulzeja/masterthesis/workDir/seqanTestForReport2/build/samtools-1.2= /htslib-1.2.1/htslib/bgzf.h:38:29: error: expected unqualified-id before nu= meric constant #define BGZF_MAX_BLOCK_SIZE 0x10000 ^ /home/schulzeja/masterthesis/tools/seqan-src/include/seqan/stream/iostream_= bgzf.h:25:16: note: in expansion of macro =91BGZF_MAX_BLOCK_SIZE=92 const unsigned BGZF_MAX_BLOCK_SIZE =3D 64 * 1024; ^ /home/schulzeja/masterthesis/workDir/seqanTestForReport2/build/samtools-1.2= /htslib-1.2.1/htslib/bgzf.h:37:29: error: expected unqualified-id before nu= meric constant #define BGZF_BLOCK_SIZE 0xff00 // make sure compressBound(BGZF_BLOCK_S= IZE) < BGZF_MAX_BLOCK_SIZE ^ /home/schulzeja/masterthesis/tools/seqan-src/include/seqan/stream/iostream_= bgzf.h:32:16: note: in expansion of macro =91BGZF_BLOCK_SIZE=92 const unsigned BGZF_BLOCK_SIZE =3D BGZF_MAX_BLOCK_SIZE - BGZF_BLOCK_HEADER= _LENGTH - BGZF_BLOCK_FOOTER_LENGTH - ZLIB_BLOCK_OVERHEAD; ^ /home/schulzeja/masterthesis/workDir/seqanTestForReport2/main.cpp:5:14: war= ning: unused parameter =91argc=92 [-Wunused-parameter] int main(int argc, char* argv[]) { ^ /home/schulzeja/masterthesis/workDir/seqanTestForReport2/main.cpp:5:31: war= ning: unused parameter =91argv=92 [-Wunused-parameter] int main(int argc, char* argv[]) { ^ CMakeFiles/main.dir/build.make:54: recipe for target 'CMakeFiles/main.dir/m= ain.cpp.o' failed make[2]: *** [CMakeFiles/main.dir/main.cpp.o] Error 1 CMakeFiles/Makefile2:60: recipe for target 'CMakeFiles/main.dir/all' failed make[1]: *** [CMakeFiles/main.dir/all] Error 2 Makefile:75: recipe for target 'all' failed make: *** [all] Error 2 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --_003_3ffd13d0d9434efaadfecc4e68c0d8d8EXCH01rkilocal_ Content-Type: text/plain; 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Wed, 17 Feb 2016 14:07:25 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aW1pF-001mXJ-CI>; Wed, 17 Feb 2016 14:07:25 +0100 Received: from celegans.imp.fu-berlin.de ([160.45.111.134]) by inpost2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtpsa (TLSv1:DHE-RSA-AES256-SHA:256) (envelope-from ) id <1aW1pF-0022yd-4e>; Wed, 17 Feb 2016 14:07:25 +0100 From: Hannes Hauswedell To: SeqAn Development Date: Wed, 17 Feb 2016 14:07:23 +0100 Message-ID: <2416959.2Uba51nZT2@celegans.imp.fu-berlin.de> Organization: MPI MolGen / FU-Berlin In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" X-Originating-IP: 160.45.111.134 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1455714445-00052D45-AEED964F/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000064, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED, RP_MATCHES_RCVD, T_FILL_THIS_FORM_SHORT X-Spam-Checker-Version: SpamAssassin 3.4.1 on Palau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Precompiled header 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: Wed, 17 Feb 2016 13:07:26 -0000 Hi Yue, sorry for the late reply. I have not yet tried precompiling the header = and I=20 am not sure how it would work at all with strongly templatized code =E2= =86=92 how=20 would the compiler know which instantiations you actually use later on?= Although other sources claim its possible: https://bytes.com/topic/net/answers/438738-should-templates-included-pc= h-files Do other people have experience with this? Something else you can do to speed up the build with SeqAn when using g= cc is=20 passing -flto=3DN where N is the number of your cores, possibly +1. Thi= s=20 parallelizes most parts of the build even for a single translation unit= . Best regards, --=20 Hannes Hauswedell PhD student Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Be= rlin address Institut f=C3=BCr Informatik Takustra=C3=9Fe 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] From hannes.hauswedell@fu-berlin.de Wed Feb 17 14:22:13 2016 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aW23Y-000Ni2-Fm>; Wed, 17 Feb 2016 14:22:12 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aW23Y-001tol-B4>; Wed, 17 Feb 2016 14:22:12 +0100 Received: from celegans.imp.fu-berlin.de ([160.45.111.134]) by inpost2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtpsa (TLSv1:DHE-RSA-AES256-SHA:256) (envelope-from ) id <1aW23Y-0024ci-0n>; Wed, 17 Feb 2016 14:22:12 +0100 From: Hannes Hauswedell To: SeqAn Development Date: Wed, 17 Feb 2016 14:22:10 +0100 Message-ID: <2273845.3ty3Y8LPAs@celegans.imp.fu-berlin.de> Organization: MPI MolGen / FU-Berlin In-Reply-To: <3ffd13d0d9434efaadfecc4e68c0d8d8@EXCH01.rki.local> References: <3ffd13d0d9434efaadfecc4e68c0d8d8@EXCH01.rki.local> MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" X-Originating-IP: 160.45.111.134 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1455715332-00052D45-A49A5E79/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED, RP_MATCHES_RCVD, T_FILL_THIS_FORM_SHORT X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tokelau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Error with samtools library 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: Wed, 17 Feb 2016 13:22:13 -0000 Dear Jakob, Am Montag, 15. Februar 2016, 15:34:21 schrieb Schulze, Jakob: > Hi everyone, > I came across some code which uses the samtools library. Together wit= h seqan > there is an error which seems to come from samtools but I do not know= why. > Since I am not the author of the samtools include I cannot say much a= bout > the corresponding lines in the CMakeLists.txt But since commenting ou= t > seqan from the main.cpp solves the error, I imagined this has somethi= ng to > do with seqan. > [...] > /home/schulzeja/masterthesis/workDir/seqanTestForReport2/build/samtoo= ls-1.2 > /htslib-1.2.1/htslib/bgzf.h:38:29: error: expected unqualified-id bef= ore > numeric constant #define BGZF_MAX_BLOCK_SIZE 0x10000 > ^ > /home/schulzeja/masterthesis/tools/seqan-src/include/seqan/stream/ios= tream_b > gzf.h:25:16: note: in expansion of macro =E2=80=98BGZF_MAX_BLOCK_SIZE= =E2=80=99 const > unsigned BGZF_MAX_BLOCK_SIZE =3D 64 * 1024; that is unfortunate. It seems like both libraries use BGZF_MAX_BLOCK_SI= ZE. We=20 will discuss whether we can change this internally, but that won't help= you=20 right now. If you use the new SeqAn release you could *not look* for the compressi= on=20 libraries, i.e. do not call find_package(zlib). This should deactivate = our=20 bgzf code and then it should compile. Best regards, --=20 Hannes Hauswedell PhD student Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Be= rlin address Institut f=C3=BCr Informatik Takustra=C3=9Fe 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] From hannes.hauswedell@fu-berlin.de Wed Feb 17 14:24:15 2016 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aW25W-000Nrq-SJ>; Wed, 17 Feb 2016 14:24:14 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aW25W-001uXq-Nh>; Wed, 17 Feb 2016 14:24:14 +0100 Received: from celegans.imp.fu-berlin.de ([160.45.111.134]) by inpost2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtpsa (TLSv1:DHE-RSA-AES256-SHA:256) (envelope-from ) id <1aW25W-0024qf-Gi>; Wed, 17 Feb 2016 14:24:14 +0100 From: Hannes Hauswedell To: SeqAn Development Date: Wed, 17 Feb 2016 14:24:13 +0100 Message-ID: <10254356.XEbofcKfBt@celegans.imp.fu-berlin.de> Organization: MPI MolGen / FU-Berlin In-Reply-To: <3a7200f2969a48a787ddffcc40c6490d@EXCH01.rki.local> References: <3a7200f2969a48a787ddffcc40c6490d@EXCH01.rki.local> MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" X-Originating-IP: 160.45.111.134 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1455715454-00052D45-5C08893F/2/18947760964 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000003, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-49.0 required=5.0 tests=ALL_TRUSTED, FU_XPURGATE_SUSP, RP_MATCHES_RCVD,T_FILL_THIS_FORM_SHORT X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] appendTagValue() for BamTagsDict 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: Wed, 17 Feb 2016 13:24:15 -0000 Am Montag, 8. Februar 2016, 14:30:11 schrieb Schulze, Jakob: > Hi everyone, > I am currently trying to write out Bam files using seqan's BamFileOut= . I > stumbled across some strange behavior of appendTagValue() When using = the > function three times in a row, length(tags) returns 2, which seems on= e to > less to me. I enclosed a code example using the example from > http://docs.seqan.de/seqan/2.0.0/demos/bam_io/bam_tags_dict.cpp >=20 > I marked my changes. Did I miss something? >=20 > Furthermore, I wondered whether there is a function, which converts a= > BamTagsDict into a String, which I can directly use as an Entry in a = Sam > file. >=20 >=20 > Best Regards, > Jakob >=20 >=20 > PS: Output of the code snippet on my machine is: > 3 > AA -> "value1" > AB -> "value2" > AC -> 30 > 2 This seems like a bug. Can you check whether this behaviour is still th= e same=20 on SeqAn-2.1 and if yes open a ticket on github? Thank you very much! Best regards, --=20 Hannes Hauswedell PhD student Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Be= rlin address Institut f=C3=BCr Informatik Takustra=C3=9Fe 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] From hannes.hauswedell@fu-berlin.de Wed Feb 17 14:28:20 2016 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aW29T-000O9a-JO>; Wed, 17 Feb 2016 14:28:19 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aW29T-001wFv-El>; Wed, 17 Feb 2016 14:28:19 +0100 Received: from celegans.imp.fu-berlin.de ([160.45.111.134]) by inpost2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtpsa (TLSv1:DHE-RSA-AES256-SHA:256) (envelope-from ) id <1aW29T-0025Hs-6S>; Wed, 17 Feb 2016 14:28:19 +0100 From: Hannes Hauswedell To: 'SeqAn Development' Date: Wed, 17 Feb 2016 14:28:17 +0100 Message-ID: <7584691.5FyMajJ6eu@celegans.imp.fu-berlin.de> Organization: MPI MolGen / FU-Berlin MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" X-Originating-IP: 160.45.111.134 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1455715699-00052D45-623BF8A6/2/18948028653 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000027, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-49.0 required=5.0 tests=ALL_TRUSTED, FU_XPURGATE_SUSP, RP_MATCHES_RCVD X-Spam-Checker-Version: SpamAssassin 3.4.1 on Vanuatu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] SeqAn 2.1 released 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: Wed, 17 Feb 2016 13:28:20 -0000 Dear SeqAn-users. We are very pleased to announce the immediate availability of SeqAn-2.1= .0! The=20 new version contains a new module for BLAST e-value statistics and I/O,= as=20 well as support for Journaled String Trees. C++11 features have been=20= introduced in many places and countless smaller issues have been fixed.= The=20 entire codebase has undergone cleanup and especially the build system w= as=20 improved in many ways. Problems with newer compilers and C++-Standards = have=20 been resolved and support for FreeBSD has been added. SeqAn application= s are=20 now shipped as static binaries and the library packages correctly insta= ll a=20 cmake-module and a pkgconfig file. Very few API changes were necessary, among them the removal of the rand= om=20 module (which can be replaced with the standard library's). Support for= some=20 compilers had to be dropped, too, most notably we now only support Visu= al=20 Studio 2015 on Windows so you may be required to upgrade. For more deta= ils,=20 see the CHANGELOG [1]. We have also released a new minor level release = 2.0.2=20 which contains only bug-fixes and is fully compatible to previous 2.0.x= =20 versions. Please visit GitHub [2] for more information or head directly to the Do= wnloads=20 [3]. We would also like to remind you of the upcoming SeqAn User Group Meeti= ng [4]=20 -- a great chance to learn about new SeqAn features and discuss with th= e=20 developers. Soon we will also present a new homepage, stay tuned! Best regards, --=20 Hannes Hauswedell PhD student Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Be= rlin [1] https://github.com/seqan/seqan/blob/master/CHANGELOG.rst [2] https://github.com/seqan/seqan/ [3] http://packages.seqan.de [4] http://www.reinert-lab.de/?p=3D304 From SchulzeJa@rki.de Thu Feb 18 14:21:31 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aWOWR-003j5E-EG>; Thu, 18 Feb 2016 14:21:31 +0100 Received: from m2-bn.bund.de ([77.87.228.74]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1:DHE-RSA-AES256-SHA:256) (envelope-from ) id <1aWOWR-001Vi4-85>; Thu, 18 Feb 2016 14:21:31 +0100 Received: from m2.mfw.bn.ivbb.bund.de (localhost.mfw.bn.ivbb.bund.de [127.0.0.1]) by m2-bn.bund.de (8.14.5/8.14.5) with ESMTP id u1IDLTdO027797 for ; Thu, 18 Feb 2016 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Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aWuB0-001O7y-8R>; Sat, 20 Feb 2016 00:09:30 +0100 Received: from mail-ob0-f179.google.com ([209.85.214.179]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:AES128-GCM-SHA256:128) (envelope-from ) id <1aWuAz-0009iD-VR>; Sat, 20 Feb 2016 00:09:30 +0100 Received: by mail-ob0-f179.google.com with SMTP id gc3so120539945obb.3 for ; Fri, 19 Feb 2016 15:09:28 -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=LDPPBsyjRoW0kbEIRCrjUMu/yIw5ABDaMQcNa4NBKt4=; b=ajdZLJYtIEVZ4kLq4ZabVRYdDEboJMXrax7ZQ9JvpjYazAgJ4Nv4jG90ec5zA5YOU2 Nlr7tB6nrA9D/1iFHH8Ufu8+YIjS+AawxLLh4j0qPesSqV1lZJwtbdfFDcO4rPKYLdO/ 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2016 15:09:27 -0800 (PST) Received: by 10.76.9.195 with HTTP; Fri, 19 Feb 2016 15:09:27 -0800 (PST) Date: Fri, 19 Feb 2016 18:09:27 -0500 Message-ID: From: Leonid Rozenberg To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=089e0153686e255f38052c27931e X-Originating-IP: 209.85.214.179 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1455923370-00052D45-354D9317/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.147507, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.8 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU, FREEMAIL_FROM, HTML_MESSAGE, RCVD_IN_DNSWL_LOW, RCVD_IN_MSPIKE_H3, RCVD_IN_MSPIKE_WL,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tokelau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Downloading a specific Razers3 version 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: Fri, 19 Feb 2016 23:09:30 -0000 --089e0153686e255f38052c27931e Content-Type: text/plain; charset=UTF-8 Is there a way that I can build a specific Razers3 version from source? I couldn't find the necessary tag's in the github repo, are there maybe specific commits that correspond? Thank you Leonid --089e0153686e255f38052c27931e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Is there a way that I can build a specific Razer= s3 version from source?
I couldn't find the necessary tag'= s in the github repo, are there maybe specific commits that correspond?
=
Thank you

Leonid
--089e0153686e255f38052c27931e-- From lramirez@mpi-inf.mpg.de Mon Feb 22 11:23:27 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aXneJ-001RLS-5y>; Mon, 22 Feb 2016 11:23:27 +0100 Received: from hera.mpi-klsb.mpg.de ([139.19.1.49]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES128-SHA:128) (envelope-from ) id <1aXneJ-003wri-04>; Mon, 22 Feb 2016 11:23:27 +0100 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=mpi-inf.mpg.de; s=mail200803; h=Content-Transfer-Encoding:Content-Type:MIME-Version:To:From:Subject:Date:Message-ID; bh=Sy5i0j6bkudkkC/v//lguQpX2hcOQ+kV13001KddDJA=; b=b+ErHIglO26rnC27flbB4kJ6euwwUZyZ09+pKn1tY4miN0hTB9y/x26VtWcb5YhQq0AZ2sAQmuy4BPsAjX7MjD4PEvBSHwZwvnEs0hOaxY2jfoxk6S31BOLtmu+8EMUQXFxwnAsLE2+/bYg/eZBfJikf6GoD50oEB8+rhdF3fSY=; Received: from zak.mpi-klsb.mpg.de ([139.19.1.29]:46359) by hera.mpi-klsb.mpg.de (envelope-from ) with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128) (Exim 4.80) id 1aXneF-0005mD-LU for seqan-dev@lists.fu-berlin.de; Mon, 22 Feb 2016 11:23:25 +0100 Received: from local by zak.mpi-klsb.mpg.de (envelope-from ) with local (Exim 4.80) id 1aXneF-0003Qy-90 for seqan-dev@lists.fu-berlin.de; Mon, 22 Feb 2016 11:23:23 +0100 Received: from 87.163.132.19 (SquirrelMail authenticated user lramirez) by mail.mpi-inf.mpg.de with HTTP; Mon, 22 Feb 2016 11:23:23 +0100 Message-ID: <3275efa85bb114a748d59692074cd89f.squirrel@mail.mpi-inf.mpg.de> Date: Mon, 22 Feb 2016 11:23:23 +0100 From: "Luis Enrique Ramirez Chavez" To: seqan-dev@lists.fu-berlin.de User-Agent: SquirrelMail/1.4.23 [SVN] MIME-Version: 1.0 Content-Type: text/plain;charset=utf-8 Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) Importance: Normal X-MPI-Local-Sender: true X-Originating-IP: 139.19.1.49 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1456136607-00052D45-C6E122D9/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.498227, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-2.4 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,RCVD_IN_DNSWL_MED,RP_MATCHES_RCVD,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Tuvalu.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] problem in LoadReads 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: Mon, 22 Feb 2016 10:23:27 -0000 Hi Seqan Devs, I am currently working a project that used Seqan 1.4 and now I am updating to Seqan 2.1. I think that maybe I have found a bug in Seqan. The problem is that LoadReads from FragmentStore is not returning the same as in the previous version for the same call, I did a little research comparing both versions. The code of loadReads have change from one version to the other, in both versions it's defined in seqan/store/store_io.h at line 1159 for old version and at line 1273 for the new version but the behave is different and I think here is the problem. in old version there is this part: MultiSeqFile multiSeqFileL, multiSeqFileR; if (!open(multiSeqFileL.concat, toCString(fileNameL), OPEN_RDONLY)) return false; if (!open(multiSeqFileR.concat, toCString(fileNameR), OPEN_RDONLY)) return false; The flow is working correctly and the ifs don't reach the return false but in the new version the code is like this SeqFileIn seqFileL, seqFileR; if (!open(seqFileL, toCString(fileNameL)) || !open(seqFileR, toCString(fileNameR))) return false; here the execution always always return false. I inspected and its because a different open function its called and here is where I think is the bug. In seqan 1.4 the open function called is from string_map defined in /include/seqan/file/string_mmap.h however in 2.x the open function that is being called is from /include/seqan/stream/formatted_file.h. The open from string_mmap.h exists in 2.x and I think is the function that wanted to be called. LoadReads calls open with SeqFileIn in the new version while in previous with MultiSeqFile but MultiSeqFile is not available in new version Can you please check if that is a bug Thanks in Advance, Luis Enrique From hannes.hauswedell@fu-berlin.de Mon Feb 22 12:24:07 2016 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aXob1-001ZrK-0p>; Mon, 22 Feb 2016 12:24:07 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aXob0-003cIp-SK>; Mon, 22 Feb 2016 12:24:06 +0100 Received: from celegans.imp.fu-berlin.de ([160.45.111.134]) by inpost2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtpsa (TLSv1:DHE-RSA-AES256-SHA:256) (envelope-from ) id <1aXob0-002MaP-LI>; Mon, 22 Feb 2016 12:24:06 +0100 From: Hannes Hauswedell To: SeqAn Development Date: Mon, 22 Feb 2016 12:24:05 +0100 Message-ID: <1960016.BlySc0OUpc@celegans.imp.fu-berlin.de> Organization: MPI MolGen / FU-Berlin In-Reply-To: <3275efa85bb114a748d59692074cd89f.squirrel@mail.mpi-inf.mpg.de> References: <3275efa85bb114a748d59692074cd89f.squirrel@mail.mpi-inf.mpg.de> MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" X-Originating-IP: 160.45.111.134 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1456140247-00052D45-FE61B20B/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000001, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED, RP_MATCHES_RCVD, T_FILL_THIS_FORM_SHORT X-Spam-Checker-Version: SpamAssassin 3.4.1 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] problem in LoadReads 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: Mon, 22 Feb 2016 11:24:07 -0000 Am Montag, 22. Februar 2016, 11:23:23 schrieb Luis Enrique Ramirez Chav= ez: > Hi Seqan Devs, >=20 > I am currently working a project that used Seqan 1.4 and now I am upd= ating > to Seqan 2.1. I think that maybe I have found a bug in Seqan. The pro= blem > is that LoadReads from FragmentStore is not returning the same as in = the > previous version for the same call, I did a little research comparin= g > both versions. Thanks for your bug report and research! > The code of loadReads have change from one version to the other, in = both > versions it's defined in seqan/store/store_io.h at line 1159 for old > version and at line 1273 for the new version but the behave is differ= ent > and I think here is the problem. >=20 > in old version there is this part: >=20 > MultiSeqFile multiSeqFileL, multiSeqFileR; > if (!open(multiSeqFileL.concat, toCString(fileNameL), OPEN_RDONLY)) > return false; > if (!open(multiSeqFileR.concat, toCString(fileNameR), OPEN_RDONLY)) > return false; This looks like the file is from a previous save() so it is in SeqAn bi= nary=20 format. > The flow is working correctly and the ifs don't reach the return fals= e but > in the new version the code is like this >=20 > SeqFileIn seqFileL, seqFileR; > if (!open(seqFileL, toCString(fileNameL)) || !open(seqFileR, > toCString(fileNameR))) > return false; This looks like it is trying to load it as a regular sequence file so t= his=20 seems something different from above. You might be right, that this is = the=20 place! > here the execution always always return false. I inspected and its be= cause > a different open function its called and here is where I think is th= e > bug. >=20 > In seqan 1.4 the open function called is from string_map defined in > /include/seqan/file/string_mmap.h however in 2.x the open function th= at is > being called is from /include/seqan/stream/formatted_file.h. The open= from > string_mmap.h exists in 2.x and I think is the function that wanted t= o be > called. LoadReads calls open with SeqFileIn in the new version while = in > previous with MultiSeqFile but MultiSeqFile is not available in new > version >=20 > Can you please check if that is a bug I have created an issue in the bugtracker that you can follow: https://github.com/seqan/seqan/issues/1484 Best regards, Hannes --=20 Hannes Hauswedell PhD student Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Be= rlin address Institut f=C3=BCr Informatik Takustra=C3=9Fe 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] From hannes.hauswedell@fu-berlin.de Mon Feb 22 12:31:06 2016 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aXohk-001aUF-Ub>; Mon, 22 Feb 2016 12:31:05 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aXohk-003f6Y-Po>; Mon, 22 Feb 2016 12:31:04 +0100 Received: from celegans.imp.fu-berlin.de ([160.45.111.134]) by inpost2.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtpsa (TLSv1:DHE-RSA-AES256-SHA:256) (envelope-from ) id <1aXohk-002NIv-Im>; Mon, 22 Feb 2016 12:31:04 +0100 From: Hannes Hauswedell To: SeqAn Development Date: Mon, 22 Feb 2016 12:31:03 +0100 Message-ID: <1939196.d89q0e07sn@celegans.imp.fu-berlin.de> Organization: MPI MolGen / FU-Berlin In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" X-Originating-IP: 160.45.111.134 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1456140664-00052D45-6449924D/2/18991548320 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000104, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-49.0 required=5.0 tests=ALL_TRUSTED, FU_XPURGATE_SUSP, RP_MATCHES_RCVD,T_FILL_THIS_FORM_SHORT X-Spam-Checker-Version: SpamAssassin 3.4.1 on Palau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Downloading a specific Razers3 version 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: Mon, 22 Feb 2016 11:31:06 -0000 Am Freitag, 19. Februar 2016, 18:09:27 schrieb Leonid Rozenberg: > Is there a way that I can build a specific Razers3 version from sourc= e? > I couldn't find the necessary tag's in the github repo, are there may= be > specific commits that correspond? Why do you need old versions of RazerS? There are no tags for apps in general (with the exception of Yara). Mos= t apps=20 are also in "maintainance mode" which mean that we make sure they work = with=20 new versions of SeqAn -- and also profit from fixed bugs in SeqAn -- bu= t they=20 do not receive new features. Hence the increased version number only re= fers to=20 library updates. You can see how this changed (and at which commits) he= re: https://github.com/seqan/seqan/commits/master/apps/razers3/CMakeLists.t= xt In general we now also recommend our Yara read mapper over RazerS.... Best regards, Hannes --=20 Hannes Hauswedell PhD student Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Be= rlin address Institut f=C3=BCr Informatik Takustra=C3=9Fe 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] From leonidr@gmail.com Mon Feb 22 23:16:33 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aXymO-002FeR-J7>; Mon, 22 Feb 2016 23:16:32 +0100 Received: from mail-ob0-f175.google.com ([209.85.214.175]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:AES128-GCM-SHA256:128) (envelope-from ) id <1aXymO-002GMK-9g>; Mon, 22 Feb 2016 23:16:32 +0100 Received: by mail-ob0-f175.google.com with SMTP id jq7so179110809obb.0 for ; Mon, 22 Feb 2016 14:16:31 -0800 (PST) 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=sRvdVyxhP7iXwyciq3ybvrsBkvsjTZM5mehVlmosVZs=; b=V0pRTQiPVR1Ez3hWQZQRQJPCvqQlNRk7AHruBv1o69kgSnfWwCLyj8LWyWQs1sd2z+ rDV//7Z/KKkKklHHWvYTtzW/Gt4HjOFPMA4ObBfUUNf/q44jkE5+ci6LNgUhXvSCbJsZ o79oJD3WWaghyzNzUX2ErsioVpBcIt4hX4riL7DLnQ5/q5QA+a4/tKA0l2hZmOSeT0Fr /CLGy7a12oEkHV9XHpLF/ioaKR+jt5qVfcZPOvtgKKHfvxFWNwVf989cWooe0yTQgQSk gsdekntT/Sr7qkeJvLzykYXXjxgOZBLIEYtXQc8Sg6q1vLv0QB66nkaqdI4sq9HgpJR5 QFkQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:mime-version:in-reply-to:references:date :message-id:subject:from:to:content-type; bh=sRvdVyxhP7iXwyciq3ybvrsBkvsjTZM5mehVlmosVZs=; b=A61Z+jJRbdl9JXfYZlMu/orD00idsWpQa9CyTt6tE6miDSEaSYLBzvJqcxIs09V6s2 7A5XslKAzrNdSUUC8IZsi2sfvvaEsHL4prFGBXde0vs6bD8NG9XAU06u7SPUwbjp1pjs rsVnvf4BnUcboGmhzidzSVW1N5ivAp1j85lJqGuFb6bCvZgCEIiZ3eXqHfxpyvZsKiuj EL6f8vl7Xi7UjjwednglJFJp3/DQ9C/3Be2XAno7IC1YsnV+jZfx4HVkWq4rHhY0alNL hziU0Bhfd+VH00ydySM/L67tCUKm9Sd+1nTeCEL8HIKs/fEMLjAQjJMF5KGB9c2o8JXY h+Wg== X-Gm-Message-State: AG10YOS52EFr+3HVbc9F/bUKFS1PpLduibixldKKL9k/nWKXumCLBddDbRjRV99jiO+FaJ7VzF9lVx+42LiuIg== MIME-Version: 1.0 X-Received: by 10.60.47.195 with SMTP id f3mr25726722oen.1.1456179389418; Mon, 22 Feb 2016 14:16:29 -0800 (PST) Received: by 10.76.9.195 with HTTP; Mon, 22 Feb 2016 14:16:29 -0800 (PST) In-Reply-To: <1939196.d89q0e07sn@celegans.imp.fu-berlin.de> References: <1939196.d89q0e07sn@celegans.imp.fu-berlin.de> Date: Mon, 22 Feb 2016 17:16:29 -0500 Message-ID: From: Leonid Rozenberg To: SeqAn Development Content-Type: multipart/alternative; boundary=001a11c3029e3c5616052c632f43 X-Originating-IP: 209.85.214.175 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1456179392-00052D45-0A44B02A/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000142, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.8 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU, FREEMAIL_FROM, HTML_MESSAGE, RCVD_IN_DNSWL_LOW, RCVD_IN_MSPIKE_H2, SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Niue.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Downloading a specific Razers3 version 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: Mon, 22 Feb 2016 22:16:33 -0000 --001a11c3029e3c5616052c632f43 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hello Hannes, I'm trying to use https://github.com/FRED-2/OptiType [1] and was hoping to fix one of the dependencies. I guess I can use the CMakeList changes to back out a precise commit, but I think I'll roll the dice and work with the latest version. Thanks for your work, Leonid 1: https://github.com/FRED-2/OptiType On Mon, Feb 22, 2016 at 6:31 AM, Hannes Hauswedell < hannes.hauswedell@fu-berlin.de> wrote: > Am Freitag, 19. Februar 2016, 18:09:27 schrieb Leonid Rozenberg: > > Is there a way that I can build a specific Razers3 version from source? > > I couldn't find the necessary tag's in the github repo, are there maybe > > specific commits that correspond? > > Why do you need old versions of RazerS? > > There are no tags for apps in general (with the exception of Yara). Most > apps > are also in "maintainance mode" which mean that we make sure they work wi= th > new versions of SeqAn -- and also profit from fixed bugs in SeqAn -- but > they > do not receive new features. Hence the increased version number only > refers to > library updates. You can see how this changed (and at which commits) here= : > https://github.com/seqan/seqan/commits/master/apps/razers3/CMakeLists.txt > > In general we now also recommend our Yara read mapper over RazerS.... > > Best regards, > Hannes > -- > Hannes Hauswedell > > PhD student > Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Berl= in > > address Institut f=C3=BCr Informatik > Takustra=C3=9Fe 9 > Room 019 > 14195 Berlin > telephone +49 (0)30 838-75241 > fax +49 (0)30 838-75218 > e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > --001a11c3029e3c5616052c632f43 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello Hannes,

I'm trying to use= https://github.com/FRED-2/O= ptiType [1] and was hoping to fix one of the dependencies.
I guess I can use the CMakeList changes to back out a precise commit, but= I think I'll roll the dice and
work with the latest vers= ion.

Thanks for your work,

Leonid

On Mon, Feb 22, 2016 at 6:31 AM, Hannes Hauswedell <hannes.hauswedell@fu-berlin.de> wrote:
Am Freitag, 19. Februar 2016, 18:09:27 s= chrieb Leonid Rozenberg:
> Is there a way that I can build a specific Razers3 version from source= ?
> I couldn't find the necessary tag's in the github repo, are th= ere maybe
> specific commits that correspond?

Why do you need old versions of RazerS?

There are no tags for apps in general (with the exception of Yara). Most ap= ps
are also in "maintainance mode" which mean that we make sure they= work with
new versions of SeqAn -- and also profit from fixed bugs in SeqAn -- but th= ey
do not receive new features. Hence the increased version number only refers= to
library updates. You can see how this changed (and at which commits) here:<= br> https://github.com/seqan/se= qan/commits/master/apps/razers3/CMakeLists.txt

In general we now also recommend our Yara read mapper over RazerS....

Best regards,
Hannes
--
Hannes Hauswedell

PhD student
Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Berlin=

address=C2=A0 =C2=A0 =C2=A0Institut f=C3=BCr Informatik
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Takustra=C3=9Fe 9
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Room 019
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 14195 Berlin
telephone=C2=A0 =C2=A0+49 (0)30 838-75241
fax=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0+49 (0)30 838-75218
e-mail=C2=A0 =C2=A0 =C2=A0 hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]

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seqan-dev mailing list
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--001a11c3029e3c5616052c632f43-- From enrico.siragusa@gmail.com Mon Feb 22 23:55:00 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aXzNb-002HvE-Dq>; Mon, 22 Feb 2016 23:54:59 +0100 Received: from mail-qg0-f44.google.com ([209.85.192.44]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:AES128-GCM-SHA256:128) (envelope-from ) id <1aXzNb-002Lul-1y>; Mon, 22 Feb 2016 23:54:59 +0100 Received: by mail-qg0-f44.google.com with SMTP id b35so123568854qge.0 for ; Mon, 22 Feb 2016 14:54:57 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=from:content-type:message-id:mime-version:subject:date:references :to:in-reply-to; bh=yzdPBHypk90D4qVWaFogkduGJmSRnFFKk0kGMK+ZD4c=; b=z3ptJJJtVJOw8fnTPffqs3DarPUyVe7LCG1t/hv/I81QXoY1leSSiapWW5UFIpvSLR qUMxTfQ86nvNeAFEx+EXkYzeBjMQv3IW3JwqwtTW6qHtIWI1E0elNfp7Ix8hrk7MnUuk pNf26rxzcm9L7yRvkJI/ivlEIRqNUdxylsF/IBwxiFVrkZJDnvPQNrfcONoSrOGBLbTs Qi83ovUBspu5Q5IT/2+KAMsXi7AHQ/mQ0IZ2KQ6VB8f6cOi2/BIAUe9Q8qVemnJEa9Mz SM6SjBJiWfvpKqollgXqaLhysI7PFA7Fnig79NsT+j1+O+XgcKMep8ALBePMYagI3Acn +3lw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:from:content-type:message-id:mime-version :subject:date:references:to:in-reply-to; bh=yzdPBHypk90D4qVWaFogkduGJmSRnFFKk0kGMK+ZD4c=; b=SdcJyZsgoVQuuzaJRsiBN963jPNpsA19sOsB2ROsM696IplxCQj3wGyWiIWaz/FKvP JR4xi6FWqD5k01FdMG4EfzNRas/pHise1bFAyV0pCmY7WfAuGtr7lsvBGrIgoD6t5cIx DagrHadlK8ybVsINd984b6g0QiaRoQxYNVGY/Yp8VgkHkaiGoxblF4bE7lWqIgLjPL4s dnTiUwIRk0UWM6EmiuNeRn0e33gWhhm2KeIBI+gz24Vz51nw2Oc1KgshZuZXpAYPI2Lb cZpOQyuYJItxb9JNJENP6H0cx9WXKZSKm8V9UcjVNzL8ECi9XsO8ycOnYXoSBFAeUXU9 CNuQ== X-Gm-Message-State: AG10YOTMnuL0I7JJCAIopuR3JwZAM1H6wf1jeKy0pQ1mconvdqmQ4TAjeETHJXcmIp3puA== X-Received: by 10.140.93.87 with SMTP id c81mr38507084qge.46.1456181696999; Mon, 22 Feb 2016 14:54:56 -0800 (PST) Received: from enricos-air.fios-router.home (pool-108-6-31-250.nycmny.fios.verizon.net. [108.6.31.250]) by smtp.gmail.com with ESMTPSA id v187sm10996978qhb.20.2016.02.22.14.54.55 for (version=TLSv1/SSLv3 cipher=OTHER); Mon, 22 Feb 2016 14:54:55 -0800 (PST) From: Enrico Siragusa Content-Type: multipart/alternative; boundary="Apple-Mail=_D9B2522D-32BC-44DF-9B1F-ABE94A0B22CB" Message-Id: Mime-Version: 1.0 (Mac OS X Mail 9.2 \(3112\)) Date: Mon, 22 Feb 2016 17:54:54 -0500 References: <1939196.d89q0e07sn@celegans.imp.fu-berlin.de> To: SeqAn Development In-Reply-To: X-Mailer: Apple Mail (2.3112) X-Originating-IP: 209.85.192.44 X-ZEDAT-Hint: A X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1456181699-00052D45-56708DD1/2/18997885598 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000002, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.2 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,FREEMAIL_FROM,FU_XPURGATE_SUSP,HTML_MESSAGE,RCVD_IN_DNSWL_LOW, RCVD_IN_MSPIKE_H2,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Downloading a specific Razers3 version 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: Mon, 22 Feb 2016 22:55:00 -0000 --Apple-Mail=_D9B2522D-32BC-44DF-9B1F-ABE94A0B22CB Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi Leonid, Yara is going to be much faster than RazerS. As far as I know, Yara = works well with OptiType, but you might want to ask the author of = OptiType for a confirmation. Enrico > On Feb 22, 2016, at 5:16 PM, Leonid Rozenberg = wrote: >=20 > Hello Hannes, >=20 > I'm trying to use https://github.com/FRED-2/OptiType = [1] and was hoping to fix one of = the dependencies. > I guess I can use the CMakeList changes to back out a precise commit, = but I think I'll roll the dice and > work with the latest version. >=20 > Thanks for your work, >=20 > Leonid >=20 > 1: https://github.com/FRED-2/OptiType = >=20 > On Mon, Feb 22, 2016 at 6:31 AM, Hannes Hauswedell = > = wrote: > Am Freitag, 19. Februar 2016, 18:09:27 schrieb Leonid Rozenberg: > > Is there a way that I can build a specific Razers3 version from = source? > > I couldn't find the necessary tag's in the github repo, are there = maybe > > specific commits that correspond? >=20 > Why do you need old versions of RazerS? >=20 > There are no tags for apps in general (with the exception of Yara). = Most apps > are also in "maintainance mode" which mean that we make sure they work = with > new versions of SeqAn -- and also profit from fixed bugs in SeqAn -- = but they > do not receive new features. Hence the increased version number only = refers to > library updates. You can see how this changed (and at which commits) = here: > = https://github.com/seqan/seqan/commits/master/apps/razers3/CMakeLists.txt = >=20 > In general we now also recommend our Yara read mapper over RazerS.... >=20 > Best regards, > Hannes > -- > Hannes Hauswedell >=20 > PhD student > Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t = Berlin >=20 > address Institut f=C3=BCr Informatik > Takustra=C3=9Fe 9 > Room 019 > 14195 Berlin > telephone +49 (0)30 838-75241 > fax +49 (0)30 838-75218 > e-mail hannes.hauswedell@[molgen.mpg.de = |fu-berlin.de ] >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev = >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --Apple-Mail=_D9B2522D-32BC-44DF-9B1F-ABE94A0B22CB Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi Leonid,

Yara is going to be much faster than RazerS. As far as I = know, Yara works well with OptiType, but you might want to ask the = author of OptiType for a confirmation.

Enrico

On Feb 22, 2016, at 5:16 PM, Leonid Rozenberg <leonidr@gmail.com> = wrote:

Hello Hannes,

I'm trying = to use https://github.com/FRED-2/OptiType [1] and was hoping to = fix one of the dependencies.
I guess = I can use the CMakeList changes to back out a precise commit, but I = think I'll roll the dice and
work = with the latest version.

Thanks for your = work,

Leonid

1: https://github.com/FRED-2/OptiType

On Mon, Feb 22, 2016 at 6:31 AM, Hannes Hauswedell = <hannes.hauswedell@fu-berlin.de> wrote:
Am = Freitag, 19. Februar 2016, 18:09:27 schrieb Leonid Rozenberg:
> Is there a way that I can build a specific Razers3 version from = source?
> I couldn't find the necessary tag's in the github repo, are there = maybe
> specific commits that correspond?

Why do you need old versions of RazerS?

There are no tags for apps in general (with the exception of Yara). Most = apps
are also in "maintainance mode" which mean that we make sure they work = with
new versions of SeqAn -- and also profit from fixed bugs in SeqAn -- but = they
do not receive new features. Hence the increased version number only = refers to
library updates. You can see how this changed (and at which commits) = here:
https://github.com/seqan/seqan/commits/master/apps/razers3/CMak= eLists.txt

In general we now also recommend our Yara read mapper over RazerS....

Best regards,
Hannes
--
Hannes Hauswedell

PhD student
Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t = Berlin

address     Institut f=C3=BCr Informatik
            Takustra=C3=9Fe 9
=             Room 019
            14195 Berlin
telephone   +49 (0)30 838-75241
fax         +49 (0)30 838-75218
e-mail      hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]

_______________________________________________
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

= --Apple-Mail=_D9B2522D-32BC-44DF-9B1F-ABE94A0B22CB-- From hw5@sanger.ac.uk Wed Feb 24 11:17:29 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aYWVb-000KSv-MX>; Wed, 24 Feb 2016 11:17:27 +0100 Received: from smtp.sanger.ac.uk ([193.62.202.243]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aYWVb-003vGo-Fa>; Wed, 24 Feb 2016 11:17:27 +0100 Received: from deskpro101282.internal.sanger.ac.uk ([172.19.25.51]) by intmail3a.internal.sanger.ac.uk with esmtpsa (TLSv1.2:DHE-RSA-AES128-SHA:128) (Exim 4.80.1) (envelope-from ) id 1aYWVZ-000Epd-HK for seqan-dev@lists.fu-berlin.de; Wed, 24 Feb 2016 10:17:25 +0000 To: seqan-dev@lists.fu-berlin.de From: Hendrik Weisser Message-ID: <56CD8335.7060005@sanger.ac.uk> Date: Wed, 24 Feb 2016 10:17:25 +0000 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:38.0) Gecko/20100101 Thunderbird/38.5.1 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit X-Message-Source: deskpro101282.internal.sanger.ac.uk X-Originating-IP: 193.62.202.243 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1456309047-00052D45-FBAFFC65/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.456972, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-2.3 required=5.0 tests=RCVD_IN_DNSWL_MED, RP_MATCHES_RCVD,SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Kiribati.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Creating a Dependent StringSet 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: Wed, 24 Feb 2016 10:17:29 -0000 Hi! I'm working on some code in OpenMS that matches peptides to a protein sequence database using SeqAn algorithms. There are two cases: 1. An exact string search of the whole peptide/protein sets, followed by an approximate search of only unmatched peptides against only proteins with sequence ambiguities. 2. An approximate string search of the whole peptide/protein sets. I'm starting out with StringSets that store the peptides and proteins, which are used in the exact search. For the approximate search, I then use Dependent StringSets that I fill with either a subset of the peptides/proteins (case 1) or with the whole sets (case 2). My problem is that in case 2, initializing the Dependent StringSet for the proteins is agonizingly slow. For a big protein database with >300,000 entries it takes more than a day! It is much, much slower than generating the Owner StringSet in the first place. This is the code I use: > seqan::StringSet prot_DB; // full protein DB > [...] > seqan::StringSet > prot_DB_SA; // for approx. search > Size length_prot_DB = length(prot_DB); > reserve(prot_DB_SA, length_prot_DB); > for (Size i = 0; i < length_prot_DB; ++i) > { > assignValueById(prot_DB_SA, prot_DB, i); > } Is this just not a good way of doing it? Based on the documentation of "assignValueById" for StringSets (http://docs.seqan.de/seqan/master/class_StringSet.html#StringSet%23assignValueById - note that the function is erroneously called "getValueById") I would have expected that "assignValueById(prot_DB_SA, prot_DB)" would append the whole StringSet, but that doesn't compile. This is all based on SeqAn 1.4, which OpenMS still uses. Has this problem been solved already in the newer releases? Cheers Hendrik -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From xenigmax@gmail.com Thu Feb 25 17:22:30 2016 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:DHE-RSA-AES256-GCM-SHA384:256) (envelope-from ) id <1aYygN-003iB5-8I>; Thu, 25 Feb 2016 17:22:27 +0100 Received: from mail-wm0-f45.google.com ([74.125.82.45]) by relay1.zedat.fu-berlin.de (Exim 4.85) for seqan-dev@lists.fu-berlin.de with esmtps (TLSv1.2:AES128-GCM-SHA256:128) (envelope-from ) id <1aYygN-001Mzd-2D>; Thu, 25 Feb 2016 17:22:27 +0100 Received: by mail-wm0-f45.google.com with SMTP id g62so36433445wme.1 for ; Thu, 25 Feb 2016 08:22:26 -0800 (PST) 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; bh=dgm4Yk04y4sGfgcERL0NBfL6s/khD9Ng8JwmhLRhMNg=; b=JsfPs1XPD7OZeNj1A5Toj342CsXbEw/LKrnfKmNKyMqBjKopPMy/COH3i4zeIEXUcA YBfk2Uw6ivDPxykfvOixcfVbJO1SvKeiF2UknQscGJY3fd3Y/eEIW/foLxuABD4KoZJ1 gUGsH5ZD0FEX8gx3/+NHZP6xMTj4xYPjI4xOUwz5LGZTdkC2hN95pqbcVOzPZoK9jcWb n/zGUhd3XQroR6OyfRefPGRZFjF5qaRbbxLYUnhPNmD3sW4VURuYt6wURIOwMmpRlDR/ XuhZ5uyJH4JVIAf0NV2ReBZmxY+jgkLy0lv/gM3ATZJlIwra1LJTtqTEEu+HT5zkfM1H 4Skg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:mime-version:in-reply-to:references:date :message-id:subject:from:to; bh=dgm4Yk04y4sGfgcERL0NBfL6s/khD9Ng8JwmhLRhMNg=; b=VoBjoMPUsM9CqeMCcRDOYzQ5jlrpMpcTuE6mL0Xb6FYxnAaxzQiLdENPRs5BzPuknS 0IdO8qGVVps1hA/87pfBLbnnutM7StNp7JqetQUbFVoeBnqc4LbddNZ9jMMIlhamplSq 7ohDhZVLgABAk62h+ZpN8Wkfs9WvIZS2B9lOOaYCNVV7ZNKmBC2jxaarLY4+M9HlAEB1 Ii/eU+Hm/oK6M5vcZCclnM8rUNZChcqLFSxEEL2WyS8JuijXEu0VmWzm7w3UxnggLv5E 4SyUVmLZPDwedbDl/qObaDGiIABxFP/CA6dQ08Ig1cypTiTrQjznkQn6q3uP4x5hiDPr 5ffA== X-Gm-Message-State: AG10YORJHRPB0w3YJQaUktY4mhTVkU/NVDb0Kli8mjGEgpEF4cNNSmLfRn+A1/WWKV43Q7TwbTz4K0e9RW/p+A== MIME-Version: 1.0 X-Received: by 10.28.222.214 with SMTP id v205mr4335931wmg.92.1456417345631; Thu, 25 Feb 2016 08:22:25 -0800 (PST) Received: by 10.195.13.106 with HTTP; Thu, 25 Feb 2016 08:22:25 -0800 (PST) In-Reply-To: <2416959.2Uba51nZT2@celegans.imp.fu-berlin.de> References: <2416959.2Uba51nZT2@celegans.imp.fu-berlin.de> Date: Thu, 25 Feb 2016 17:22:25 +0100 Message-ID: From: Jongkyu Kim To: SeqAn Development Content-Type: multipart/alternative; boundary=001a114b115e87fc10052c9a96df X-Originating-IP: 74.125.82.45 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1456417347-00052D45-16EBF08E/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.003083, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.1 required=5.0 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU, FREEMAIL_FROM, HTML_MESSAGE, RCVD_IN_MSPIKE_H3, RCVD_IN_MSPIKE_WL, SPF_PASS X-Spam-Checker-Version: SpamAssassin 3.4.1 on Palau.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Precompiled header 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: Thu, 25 Feb 2016 16:22:30 -0000 --001a114b115e87fc10052c9a96df Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Yue Gan! I can make precompiled header without any problem. (g++ 4.9.2, Debian) Would you give me more information about your environment? (eg. gcc / OS versions) Best, Jongkyu On Wed, Feb 17, 2016 at 2:07 PM, Hannes Hauswedell < hannes.hauswedell@fu-berlin.de> wrote: > Hi Yue, > > sorry for the late reply. I have not yet tried precompiling the header an= d > I > am not sure how it would work at all with strongly templatized code =E2= =86=92 how > would the compiler know which instantiations you actually use later on? > Although other sources claim its possible: > > https://bytes.com/topic/net/answers/438738-should-templates-included-pch-= files > > Do other people have experience with this? > > Something else you can do to speed up the build with SeqAn when using gcc > is > passing -flto=3DN where N is the number of your cores, possibly +1. This > parallelizes most parts of the build even for a single translation unit. > > Best regards, > -- > Hannes Hauswedell > > PhD student > Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Berl= in > > address Institut f=C3=BCr Informatik > Takustra=C3=9Fe 9 > Room 019 > 14195 Berlin > telephone +49 (0)30 838-75241 > fax +49 (0)30 838-75218 > e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de] > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > --001a114b115e87fc10052c9a96df Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Yue Gan!

I can make precompiled head= er without any problem. (g++ 4.9.2, Debian)
Would you give me mor= e information about your environment? (eg. gcc=C2=A0/ OS versions)

Best,
Jongkyu




On Wed, Feb 17, 2016 at 2:07 PM, Hannes Hauswedell &= lt;hann= es.hauswedell@fu-berlin.de> wrote:
Hi Yue,

sorry for the late reply. I have not yet tried precompiling the header and = I
am not sure how it would work at all with strongly templatized code =E2=86= =92 how
would the compiler know which instantiations you actually use later on?
Although other sources claim its possible:
https://bytes.com/topi= c/net/answers/438738-should-templates-included-pch-files

Do other people have experience with this?

Something else you can do to speed up the build with SeqAn when using gcc i= s
passing -flto=3DN where N is the number of your cores, possibly +1. This parallelizes most parts of the build even for a single translation unit.
Best regards,
--
Hannes Hauswedell

PhD student
Max Planck Institute for Molecular Genetics / Freie Universit=C3=A4t Berlin=

address=C2=A0 =C2=A0 =C2=A0Institut f=C3=BCr Informatik
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Takustra=C3=9Fe 9
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Room 019
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 14195 Berlin
telephone=C2=A0 =C2=A0+49 (0)30 838-75241
fax=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0+49 (0)30 838-75218
e-mail=C2=A0 =C2=A0 =C2=A0 hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]

_______________________________________________
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