From: Andreas Tille Date: Sun, 4 Aug 2019 19:16:32 +0000 (+0100) Subject: Import pbbam_0.23.0+dfsg-1.debian.tar.xz X-Git-Tag: archive/raspbian/0.23.0+dfsg-1+rpi1^2~4^2 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=bee6ac1d9467e1d3a37e6468b23f588b39fc353a;p=pbbam.git Import pbbam_0.23.0+dfsg-1.debian.tar.xz [dgit import tarball pbbam 0.23.0+dfsg-1 pbbam_0.23.0+dfsg-1.debian.tar.xz] --- bee6ac1d9467e1d3a37e6468b23f588b39fc353a diff --git a/README.source b/README.source new file mode 100644 index 0000000..c29c516 --- /dev/null +++ b/README.source @@ -0,0 +1,10 @@ +pbbam for Debian +---------------- + +* The swig bindings require a version of swig higher than 3.0.2 (currently in unstable). + Without this, python and R bindings cannot be built. + + + + -- Afif Elghraoui , Sun, 6 Sep 2015 13:57:45 -0700 + diff --git a/TODO b/TODO new file mode 100644 index 0000000..c86d636 --- /dev/null +++ b/TODO @@ -0,0 +1,5 @@ +* Manpages for pbbamtools programs + +* package python and R bindings + +* package API documentation diff --git a/changelog b/changelog new file mode 100644 index 0000000..af799f9 --- /dev/null +++ b/changelog @@ -0,0 +1,159 @@ +pbbam (0.23.0+dfsg-1) unstable; urgency=medium + + * Afif removed himself from Uploaders + * Add myself to Uploaders + * New upstream version + * debhelper-compat 12 + * Standards-Version: 4.4.0 + * Set upstream metadata fields: Contact, Name. + * Rename library to libpbbam0.23.0 due to upstream choice of ABI version + * Remove code copy of python-cram from upstream source + * Build-Depends: python3-cram + * d/control: Use instead of comment + + -- Andreas Tille Sun, 04 Aug 2019 21:16:32 +0200 + +pbbam (0.19.0+dfsg-4) unstable; urgency=medium + + * Team upload. + + [ Steve Langasek ] + * Fix autopkgtest on different architectures + + [ Andreas Tille ] + * Cleanup d/rules + * No "Provides: libpbbam" due to ABI incompatibility + + -- Andreas Tille Wed, 06 Feb 2019 09:16:06 +0100 + +pbbam (0.19.0+dfsg-3.1) unstable; urgency=medium + + * Non-maintainer upload. + * Apply autopkgtest regression fix from Steve Langasek. + (Closes: #908269) + * libpbbam0.19.0: Remove the incorrect Provides: libpbbam. + + -- Adrian Bunk Wed, 06 Feb 2019 08:53:24 +0200 + +pbbam (0.19.0+dfsg-3) unstable; urgency=medium + + * Team upload. + + [ Steve Langasek ] + * Fix build dir name for tests + Closes: #909071 + + -- Andreas Tille Mon, 04 Feb 2019 11:50:20 +0100 + +pbbam (0.19.0+dfsg-2) unstable; urgency=medium + + * Team upload. + + [ Steve Langasek ] + * Provide generated files to autopkgtest + Closes: #921122 + + [ Andreas Tille ] + * debhelper 12 + * Standards-Version: 4.3.0 + * Secure URI in copyright format + * Remove trailing whitespace in debian/copyright + + -- Andreas Tille Sun, 03 Feb 2019 08:00:29 +0100 + +pbbam (0.19.0+dfsg-1) unstable; urgency=medium + + * Team upload. + * New upstream version + * Fix samtools call in tests + * d/control: Bump (fake) SOVERSION (=release version) + + -- Andreas Tille Wed, 10 Oct 2018 12:45:02 +0200 + +pbbam (0.18.0+dfsg-2) unstable; urgency=medium + + * Team upload. + * Missing Breaks+Replaces: libpbbam (<< 0.18) + Closes: #910206 + * No needs-recommends restrictions, just Test-Depends: samtools + + -- Andreas Tille Wed, 03 Oct 2018 22:24:56 +0200 + +pbbam (0.18.0+dfsg-1) unstable; urgency=medium + + [ Andreas Tille ] + * Team upload. + * New upstream version + * Upstream is now tagging releases -> adapt watch file + * Upstream switched from cmake to meson + * debhelper 11 + * Point Vcs fields to salsa.debian.org + * Standards-Version: 4.2.1 + * Use d-shlibs + * Remove unneeded trigger + * Respect DEB_BUILD_OPTIONS in override_dh_auto_test + * hardening=+all + * Add Breaks/Provides/Replaces libpbbam + + [ Fabian Kloetzl ] + * fix dependency check for meson + + -- Andreas Tille Thu, 06 Sep 2018 14:29:53 +0200 + +pbbam (0.7.4+ds-1) unstable; urgency=medium + + * New upstream release snapshot + - Exclude dependency convenience copy + - Update patches + - Update running of tests at build-time + - Update .install files + - Update autopkgtest commands + * Use debhelper compat 10 + * libpbbam-dev: depend on libssl-dev + + -- Afif Elghraoui Sat, 21 Jan 2017 23:48:21 -0800 + +pbbam (0.7.0-1) unstable; urgency=medium + + * Imported Upstream version 0.7.0 + * Update patches + + -- Afif Elghraoui Sun, 30 Oct 2016 14:31:49 -0700 + +pbbam (0.5.0-3) unstable; urgency=low + + * Fix cmake arguments to properly position LDFLAGS for -Wl,--as-needed. + Thanks to Steve Langasek (Closes: #841671) + + -- Afif Elghraoui Sun, 23 Oct 2016 14:07:27 -0700 + +pbbam (0.5.0-2) unstable; urgency=low + + * libpbbam-dev: add dependency on libhts-dev + + -- Afif Elghraoui Sun, 17 Jul 2016 23:29:34 -0700 + +pbbam (0.5.0-1) unstable; urgency=medium + + * New upstream revision (git 79ab246 from 2016-02-23) + * Declare additional copyrights to avoid repacking tarball + * Update patches + * Update Standards-Version to 3.9.8 + * Use encrypted protocols for VCS URLs + * Clean up d/control and d/rules + * Use dh-exec for library installation rather than sed-within-d/rules + * Set up build-time tests for command-line tools + * Add binary package for command-line tools + * Install library to main library path + * Configure autopkgtests + * Use documentation page as Homepage + * Remove build-dependency on doxygen + * Add TODO list + + -- Afif Elghraoui Tue, 05 Jul 2016 03:25:49 -0700 + +pbbam (0.1.0~20150813+git4e9e417+dfsg-1) unstable; urgency=low + + * Initial release (Closes: #798220) + + -- Afif Elghraoui Fri, 18 Sep 2015 02:40:24 -0700 diff --git a/control b/control new file mode 100644 index 0000000..624e69b --- /dev/null +++ b/control @@ -0,0 +1,83 @@ +Source: pbbam +Maintainer: Debian Med Packaging Team +Uploaders: Andreas Tille +Section: science +Priority: optional +Build-Depends: debhelper-compat (= 12), + dh-exec, + d-shlibs, + meson, + pkg-config, +# swig3.0, + libboost-dev, + zlib1g-dev, + libssl-dev, + libhts-dev, + libgtest-dev , + python3-cram , + samtools +Standards-Version: 4.4.0 +Vcs-Browser: https://salsa.debian.org/med-team/pbbam +Vcs-Git: https://salsa.debian.org/med-team/pbbam.git +Homepage: http://pbbam.readthedocs.org/en/latest/index.html + +Package: pbbamtools +Architecture: any +Depends: ${shlibs:Depends}, + ${misc:Depends}, + libpbbam0.23.0 (= ${binary:Version}) +Recommends: samtools +Description: processing Pacific Biosciences binary alignment/map files + The BAM format is a binary, compressed, record-oriented container format + for raw or aligned sequence reads. The associated SAM format is a text + representation of the same data. The specifications for BAM/SAM are maintained + by the SAM/BAM Format Specification Working Group. + . + PacBio-produced BAM files are fully compatible with the BAM specification, + but makes use of the extensibility mechanisms of the BAM specification to + encode PacBio-specific information. + . + This package provides command-line utilities for working with PacBio BAM + files. + +Package: libpbbam0.23.0 +Architecture: any +Multi-Arch: same +Section: libs +Depends: ${shlibs:Depends}, + ${misc:Depends} +Pre-Depends: ${misc:Pre-Depends} +Breaks: libpbbam (<< ${source:Version}) +Replaces: libpbbam +Description: Pacific Biosciences binary alignment/map (BAM) library + The BAM format is a binary, compressed, record-oriented container format + for raw or aligned sequence reads. The associated SAM format is a text + representation of the same data. The specifications for BAM/SAM are maintained + by the SAM/BAM Format Specification Working Group. + . + PacBio-produced BAM files are fully compatible with the BAM specification, + but makes use of the extensibility mechanisms of the BAM specification to + encode PacBio-specific information. The pbbam library provides tools to + work with these files + +Package: libpbbam-dev +Architecture: any +Section: libdevel +Depends: libpbbam0.23.0 (= ${binary:Version}), + libhts-dev, + libssl-dev, + ${misc:Depends} +Breaks: libpbbam (<< 0.18) +Replaces: libpbbam (<< 0.18) +Description: Pacific Biosciences binary alignment/map (BAM) library (headers) + The BAM format is a binary, compressed, record-oriented container format + for raw or aligned sequence reads. The associated SAM format is a text + representation of the same data. The specifications for BAM/SAM are maintained + by the SAM/BAM Format Specification Working Group. + . + PacBio-produced BAM files are fully compatible with the BAM specification, + but makes use of the extensibility mechanisms of the BAM specification to + encode PacBio-specific information. The pbbam library provides tools to + work with these files + . + This package contains the library header files. diff --git a/copyright b/copyright new file mode 100644 index 0000000..9525197 --- /dev/null +++ b/copyright @@ -0,0 +1,124 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: pbbam +Upstream-Contact: Pacific Biosciences +Source: https://github.com/PacificBiosciences/pbbam +Files-Excluded: third-party + */clang-format* + */tests/scripts/cram* + +Files: * +Copyright: 2014-2016 Pacific Biosciences of California, Inc. +License: PacBio-BSD-3-Clause + +Files: src/pugixml/* +Copyright: 2006-2014 Arseny Kapoulkine + 2003 Kristen Wegner +License: MIT + +Files: tools/common/OptionParser.* +Copyright: 2010 Johannes Weißl +License: BSD-3-Clause or BSD-2-Clause + +Files: debian/* +Copyright: 2015-2016 Afif Elghraoui +License: PacBio-BSD-3-Clause + +License: PacBio-BSD-3-Clause + Redistribution and use in source and binary forms, with or without + modification, are permitted (subject to the limitations in the + disclaimer below) provided that the following conditions are met: + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + 2. Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials provided + with the distribution. + 3. Neither the name of Pacific Biosciences nor the names of its + contributors may be used to endorse or promote products derived + from this software without specific prior written permission. + . + NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE + GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC + BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED + WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF + USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND + ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + +License: BSD-3-Clause + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + 3. Neither the name of the University nor the names of its contributors + may be used to endorse or promote products derived from this software + without specific prior written permission. + . + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE HOLDERS OR + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, + EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, + PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR + PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF + LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING + NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +License: BSD-2-Clause + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + 2. Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials provided + with the distribution. + . + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS + FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE + COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, + BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER + CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT + LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY + WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE + POSSIBILITY OF SUCH DAMAGE. + +License: MIT + Permission is hereby granted, free of charge, to any person + obtaining a copy of this software and associated documentation + files (the "Software"), to deal in the Software without + restriction, including without limitation the rights to use, + copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the + Software is furnished to do so, subject to the following + conditions: + . + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + . + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + OTHER DEALINGS IN THE SOFTWARE. diff --git a/patches/debug_tests.patch b/patches/debug_tests.patch new file mode 100644 index 0000000..37495c8 --- /dev/null +++ b/patches/debug_tests.patch @@ -0,0 +1,97 @@ +Description: Only debug code to track down bug #909071 i386 (no solution yet) +Bug-Debian: https://bugs.debian.org/909071 +Author: Andreas Tille +Last-Update: Tue, 18 Sep 2018 08:40:19 +0200 + +--- a/tests/src/cram/pbmerge_pacbio_ordering.t.in ++++ b/tests/src/cram/pbmerge_pacbio_ordering.t.in +@@ -13,6 +13,8 @@ Setup: + + Sanity Check: + ++ $ ls -l $HQREGION_BAM ++ $ echo "DEBUG: $BAM2SAM --header-only $HQREGION_BAM" + $ $BAM2SAM --header-only $HQREGION_BAM + @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) + @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie (esc) +@@ -20,9 +22,11 @@ Sanity Check: + @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) + @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) + ++ $ echo "DEBUG: $BAM2SAM --no-header $HQREGION_BAM | cut -f 1" + $ $BAM2SAM --no-header $HQREGION_BAM | cut -f 1 + ArminsFakeMovie/100000/2659_7034 + ++ $ $echo "DEBUG: BAM2SAM --header-only $SCRAPS_BAM" + $ $BAM2SAM --header-only $SCRAPS_BAM + @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) + @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie (esc) +@@ -30,6 +34,7 @@ Sanity Check: + @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) + @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) + ++ $ echo "DEBUG: $BAM2SAM --no-header $SCRAPS_BAM | cut -f 1" + $ $BAM2SAM --no-header $SCRAPS_BAM | cut -f 1 + ArminsFakeMovie/100000/0_2659 + ArminsFakeMovie/100000/3025_3047 +--- a/tests/src/cram/pbmerge_aligned_ordering.t.in ++++ b/tests/src/cram/pbmerge_aligned_ordering.t.in +@@ -51,7 +51,10 @@ Sanity Check: + + Normal Merge: + ++ $ echo "DEBUG: $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM" + $ $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM ++ $ if [ ! -f $MERGED_BAM ] ; then echo "FIX 1: File $MERGED_BAM does not exists - no idea why. Try again creating it after 5s."; $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM ; fi ++ $ if [ ! -f $MERGED_BAM ] ; then echo "FIX 1: File $MERGED_BAM does not exists - even after trying again."; exit ; else echo echo "File $MERGED_BAM was created now" ; fi + + $ $BAM2SAM --header-only $MERGED_BAM + @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc) +@@ -60,6 +63,7 @@ Normal Merge: + @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc) + @PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc) + ++ $ echo "DEBUG: $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20" + $ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20 + m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc) + m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc) +@@ -86,8 +90,15 @@ Normal Merge: + + Shuffle Input: + ++ $ echo DEBUG: PATH = $PATH ++ $ which pbmerge ++ $ echo "DEBUG: $PBMERGE $INPUT_2 $INPUT_2 > $MERGED_BAM" + $ $PBMERGE $INPUT_2 $INPUT_2 > $MERGED_BAM ++ $ if [ ! -f $MERGED_BAM ] ; then echo "FIX 2: File $MERGED_BAM does not exists - no idea why. Try again creating it after 5s."; $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM ; fi ++ $ if [ ! -f $MERGED_BAM ] ; then echo "FIX 2: File $MERGED_BAM does not exists - even after trying again."; exit ; else echo echo "File $MERGED_BAM was created now" ; fi + ++ $ echo "DEBUG: $BAM2SAM --header-only $MERGED_BAM" ++ $ echo "DEBUG: That is the problematic command" + $ $BAM2SAM --header-only $MERGED_BAM + @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc) + @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc) +@@ -95,6 +106,7 @@ Shuffle Input: + @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc) + @PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc) + ++ $ echo "DEBUG: $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20" + $ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20 + m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc) + m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc) +@@ -130,6 +142,7 @@ Explicit Output Filename (also enables P + @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc) + @PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc) + ++ $ echo "DEBUG: $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20" + $ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20 + m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc) + m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc) +@@ -169,6 +182,7 @@ Explicit Output Filename (with disabled + @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc) + @PG\tID:pbmerge-@PacBioBAM_VERSION@\tPN:pbmerge\tVN:@PacBioBAM_VERSION@ (esc) + ++ $ echo "DEBUG: $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20" + $ $BAM2SAM --no-header $MERGED_BAM | cut -f 1,3,4 | head -n 20 + m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc) + m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc) diff --git a/patches/fix_gtest_depcheck.patch b/patches/fix_gtest_depcheck.patch new file mode 100644 index 0000000..490d279 --- /dev/null +++ b/patches/fix_gtest_depcheck.patch @@ -0,0 +1,15 @@ +Author: Andreas Tille, Fabian Klötzl +Last-Update: 2018-09-05 14:50:07 +0000 +Description: Use Debian packaged gtest + +--- a/tests/meson.build ++++ b/tests/meson.build +@@ -6,7 +6,7 @@ if not pbbam_cram_script.found() + pbbam_cram_script = find_program('scripts/cram.py', required : true) + endif + +-pbbam_gtest_dep = dependency('gtest_main', fallback : ['gtest', 'gtest_main_dep']) ++pbbam_gtest_dep = dependency('gtest', main: true) + + pbbam_PbbamTestData_h_config = configuration_data() + pbbam_PbbamTestData_h_config.set('PacBioBAM_BinDir', join_paths([meson.current_build_dir(), '../tools'])) diff --git a/patches/python3.patch b/patches/python3.patch new file mode 100644 index 0000000..ed1acd2 --- /dev/null +++ b/patches/python3.patch @@ -0,0 +1,38 @@ +Author: Andreas Tille +Last-Update: Sun, 04 Aug 2019 09:15:35 +0200 +Description: Use Python3 in build time test suite + +--- a/meson.build ++++ b/meson.build +@@ -80,7 +80,7 @@ subdir('src') + + if not meson.is_subproject() + if get_option('build-tools') or get_option('tests') +- pbbam_python = find_program('python') ++ pbbam_python = find_program('python3') + + if get_option('tests') + pbbam_clang_formatter = find_program('tools/check-formatting') +--- a/tests/scripts/generate_data.py ++++ b/tests/scripts/generate_data.py +@@ -1,7 +1,4 @@ +-#!/usr/bin/env python +- +-from __future__ import print_function +-from __future__ import unicode_literals ++#!/usr/bin/python3 + + import os, shutil, sys + from io import StringIO +@@ -177,9 +174,9 @@ class TestDataGenerator: + # else silent success + if self.outputFiles or self.outputSymlinks: + print('Generating test data in %s ' % self.generatedDataDir) +- for file, func in self.outputFiles.items(): ++ for file, func in list(self.outputFiles.items()): + func(file) +- for link, func in self.outputSymlinks.items(): ++ for link, func in list(self.outputSymlinks.items()): + func(link) + + # script entry point diff --git a/patches/series b/patches/series new file mode 100644 index 0000000..c953dbe --- /dev/null +++ b/patches/series @@ -0,0 +1,4 @@ +fix_gtest_depcheck.patch +# debug_tests.patch +use_debian_packaged_python3-cram.patch +python3.patch diff --git a/patches/use_debian_packaged_python3-cram.patch b/patches/use_debian_packaged_python3-cram.patch new file mode 100644 index 0000000..8a94cfc --- /dev/null +++ b/patches/use_debian_packaged_python3-cram.patch @@ -0,0 +1,14 @@ +Author: Andreas Tille +Last-Update: Sun, 04 Aug 2019 09:15:35 +0200 +Description: Use python3-cram instead of cram code copy + +--- a/tests/meson.build ++++ b/tests/meson.build +@@ -1,6 +1,6 @@ + subdir('src') + +-pbbam_cram_script = find_program('cram', required : false) ++pbbam_cram_script = find_program('cram3', required : false) + if not pbbam_cram_script.found() + warning('Using bundled cram script') + pbbam_cram_script = find_program('scripts/cram.py', required : true) diff --git a/pbbamtools.install b/pbbamtools.install new file mode 100644 index 0000000..7380180 --- /dev/null +++ b/pbbamtools.install @@ -0,0 +1 @@ +*/bin /usr diff --git a/rules b/rules new file mode 100755 index 0000000..61b3ef7 --- /dev/null +++ b/rules @@ -0,0 +1,61 @@ +#!/usr/bin/make -f + +#DH_VERBOSE = 1 +export LC_ALL=C.UTF-8 +include /usr/share/dpkg/default.mk + +export DEB_BUILD_MAINT_OPTIONS=hardening=+all + +DEB_VERSION_UPSTREAM := $(subst +ds,,$(DEB_VERSION_UPSTREAM)) +generated_data_dir = $(CURDIR)/gendata + +%: + dh $@ --buildsystem=meson + +override_dh_auto_test: $(subst .t.in,.deb.t,$(wildcard tests/src/cram/pb*.t.in)) +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) + dh_auto_configure -O--buildsystem=meson + mkdir -p $(generated_data_dir) + python3 tests/scripts/generate_data.py $(CURDIR)/tests/data $(generated_data_dir) + # Fix broken PATH + synthetic_movie_all_path=`find $$PWD -name synthetic_movie_all.subreadset.xml` ; \ + sed -i -e "s?.GENERATEDDATADIR/synthetic_movie_all.subreadset.xml?$${synthetic_movie_all_path}?" tests/src/cram/pbbamify* + BINDIR=`dirname $$(find $$PWD -name pbmerge -type f -executable)`; \ + LIBDIR=`find $$PWD -name lib -type d`; \ + PATH="$$BINDIR:$(PATH)" LD_LIBRARY_PATH="$$LIBDIR:$(LD_LIBRARY_PATH)" \ + cram3 -v --preserve-env $^ +endif + +override_dh_installchangelogs: + dh_installchangelogs CHANGELOG.md + +override_dh_auto_clean: + dh_auto_clean + find -name "*.deb.t" -delete + $(RM) -r $(generated_data_dir) + +%.deb.t: %.t.in + sed \ + -e 's/$$BAM2SAM/samtools view/g' \ + -e 's/\-\-header\-only/-H/g' \ + -e 's/\-\-no\-header//g' \ + -e 's|@PacBioBAM_BinDir@/||g' \ + -e 's|$$TOOLS_BIN/||g' \ + -e 's|@PacBioBAM_TestsDir@|$(CURDIR)/tests|g' \ + -e 's|@PacBioBAM_VERSION@|$(DEB_VERSION_UPSTREAM)|g' \ + -e 's|@GeneratedTestDataDir@|$(generated_data_dir)|g' \ + -e '/@PG/s|+dfsg||g' \ + -e 's/$$SAMTOOLS/samtools/g' \ + $< > $@ + +override_dh_install: + dh_install + d-shlibmove --commit \ + --multiarch \ + --devunversioned \ + --exclude-la \ + --exclude-a \ + --override s/libhts2-dev/libhts-dev/ \ + --movedev debian/tmp/usr/include/* usr/include \ + --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \ + debian/tmp/usr/lib/*/*.so diff --git a/source/format b/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/tests/control b/tests/control new file mode 100644 index 0000000..9b21e04 --- /dev/null +++ b/tests/control @@ -0,0 +1,5 @@ +Test-Command: debian/rules override_dh_auto_test +Depends: + @builddeps@, + pbbamtools, +Restrictions: rw-build-tree, allow-stderr diff --git a/upstream/metadata b/upstream/metadata new file mode 100644 index 0000000..b27e125 --- /dev/null +++ b/upstream/metadata @@ -0,0 +1,2 @@ +Name: pbbam +Contact: Pacific Biosciences diff --git a/watch b/watch new file mode 100644 index 0000000..1b64644 --- /dev/null +++ b/watch @@ -0,0 +1,4 @@ +version=4 + +opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ + https://github.com/PacificBiosciences/pbbam/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@