From: Andreas Tille Date: Wed, 6 Feb 2019 08:16:06 +0000 (+0000) Subject: pbbam (0.19.0+dfsg-4) unstable; urgency=medium X-Git-Tag: archive/raspbian/0.19.0+dfsg-4+rpi1^2~2 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=41cd41f13b85055ada8e4359ad80e09d0fa882d4;p=pbbam.git 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 [dgit import unpatched pbbam 0.19.0+dfsg-4] --- 41cd41f13b85055ada8e4359ad80e09d0fa882d4 diff --cc debian/README.source index 0000000,0000000..c29c516 new file mode 100644 --- /dev/null +++ b/debian/README.source @@@ -1,0 -1,0 +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 --cc debian/TODO index 0000000,0000000..c86d636 new file mode 100644 --- /dev/null +++ b/debian/TODO @@@ -1,0 -1,0 +1,5 @@@ ++* Manpages for pbbamtools programs ++ ++* package python and R bindings ++ ++* package API documentation diff --cc debian/changelog index 0000000,0000000..a8a1e30 new file mode 100644 --- /dev/null +++ b/debian/changelog @@@ -1,0 -1,0 +1,135 @@@ ++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) 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 --cc debian/compat index 0000000,0000000..48082f7 new file mode 100644 --- /dev/null +++ b/debian/compat @@@ -1,0 -1,0 +1,1 @@@ ++12 diff --cc debian/control index 0000000,0000000..8425df7 new file mode 100644 --- /dev/null +++ b/debian/control @@@ -1,0 -1,0 +1,85 @@@ ++Source: pbbam ++Maintainer: Debian Med Packaging Team ++Uploaders: Afif Elghraoui ++Section: science ++Priority: optional ++Build-Depends: debhelper (>= 12~), ++ dh-exec, ++ d-shlibs, ++ meson, ++ pkg-config, ++ python, ++# swig3.0, ++ libboost-dev (>= 1.54), ++ zlib1g-dev, ++ libssl-dev, ++ libhts-dev, ++# Test-Depends: ++ libgtest-dev, ++ python-cram, ++ samtools ++Standards-Version: 4.3.0 ++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}, ++ libpbbam0.19.0 (= ${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: libpbbam0.19.0 ++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: libpbbam0.19.0 (= ${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 --cc debian/copyright index 0000000,0000000..1945f9d new file mode 100644 --- /dev/null +++ b/debian/copyright @@@ -1,0 -1,0 +1,123 @@@ ++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* ++ ++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 --cc debian/patches/debug_tests.patch index 0000000,0000000..37495c8 new file mode 100644 --- /dev/null +++ b/debian/patches/debug_tests.patch @@@ -1,0 -1,0 +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 --cc debian/patches/fix_gtest_depcheck.patch index 0000000,0000000..490d279 new file mode 100644 --- /dev/null +++ b/debian/patches/fix_gtest_depcheck.patch @@@ -1,0 -1,0 +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 --cc debian/patches/series index 0000000,0000000..dd84c68 new file mode 100644 --- /dev/null +++ b/debian/patches/series @@@ -1,0 -1,0 +1,2 @@@ ++fix_gtest_depcheck.patch ++# debug_tests.patch diff --cc debian/pbbamtools.install index 0000000,0000000..7380180 new file mode 100644 --- /dev/null +++ b/debian/pbbamtools.install @@@ -1,0 -1,0 +1,1 @@@ ++*/bin /usr diff --cc debian/rules index 0000000,0000000..34e18a0 new file mode 100755 --- /dev/null +++ b/debian/rules @@@ -1,0 -1,0 +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) ++ python 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="$$LIBDIR:$(LD_LIBRARY_PATH)" \ ++ cram -v --preserve-env $^ ++endif ++ ++override_dh_installchangelogs: ++ dh_installchangelogs CHANGELOG.md ++ ++override_dh_auto_clean: ++ dh_auto_clean ++ find -name "*.deb.t" -delete ++ $(RM) -r $(generated_data_dir) ++ ++%.deb.t: %.t.in ++ sed \ ++ -e 's/$$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 --cc debian/source/format index 0000000,0000000..163aaf8 new file mode 100644 --- /dev/null +++ b/debian/source/format @@@ -1,0 -1,0 +1,1 @@@ ++3.0 (quilt) diff --cc debian/tests/control index 0000000,0000000..9b21e04 new file mode 100644 --- /dev/null +++ b/debian/tests/control @@@ -1,0 -1,0 +1,5 @@@ ++Test-Command: debian/rules override_dh_auto_test ++Depends: ++ @builddeps@, ++ pbbamtools, ++Restrictions: rw-build-tree, allow-stderr diff --cc debian/watch index 0000000,0000000..1b64644 new file mode 100644 --- /dev/null +++ b/debian/watch @@@ -1,0 -1,0 +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@