[med-svn] [pbbam] 02/04: Merge tag 'upstream/0.7.0'
Afif Elghraoui
afif at moszumanska.debian.org
Sun Oct 30 21:39:22 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository pbbam.
commit 32318917d5cb8bf7d4f517ce3d49d6539b6e8fd4
Merge: 22675a2 11fe97d
Author: Afif Elghraoui <afif at debian.org>
Date: Mon Oct 24 23:57:46 2016 -0700
Merge tag 'upstream/0.7.0'
Upstream version 0.7.0
.gitignore | 18 +-
CHANGELOG.md | 666 ++--
CMakeLists.txt | 8 +-
docs/examples/code/PbiBarcodeFilter.txt | 2 +-
docs/examples/code/PbiBarcodeForwardFilter.txt | 2 +-
docs/examples/code/PbiBarcodeReverseFilter.txt | 2 +-
...alReader.txt => WhitelistedZmwReadStitcher.txt} | 2 +-
docs/source/conf.py | 4 +-
include/pbbam/BamFile.h | 4 +
include/pbbam/BamRecord.h | 328 +-
include/pbbam/BamRecordImpl.h | 88 +
.../TestData.h.in => include/pbbam/BamRecordTag.h | 63 +-
include/pbbam/BamRecordView.h | 168 +
include/pbbam/BamWriter.h | 3 +-
include/pbbam/BarcodeQuery.h | 2 +-
.../src/TestData.h.in => include/pbbam/ClipType.h | 35 +-
include/pbbam/Compare.h | 4 +-
include/pbbam/Config.h | 14 +
.../pbbam/FrameEncodingType.h | 36 +-
.../TestData.h.in => include/pbbam/IRecordWriter.h | 60 +-
tests/src/TestData.h.in => include/pbbam/MD5.h | 23 +-
include/pbbam/PbiFilterTypes.h | 43 +-
include/pbbam/PbiRawData.h | 24 +-
.../TestData.h.in => include/pbbam/PulseBehavior.h | 30 +-
include/pbbam/ReadGroupInfo.h | 13 +
.../TestData.h.in => include/pbbam/RecordType.h | 37 +-
include/pbbam/SamWriter.h | 130 +
include/pbbam/Validator.h | 192 ++
.../ValidationException.h} | 72 +-
include/pbbam/internal/BamRecord.inl | 82 +-
.../internal/{BamRecord.inl => BamRecordView.inl} | 75 +-
include/pbbam/internal/CompositeBamReader.inl | 6 +-
include/pbbam/internal/PbiFilterTypes.inl | 39 +-
include/pbbam/internal/ReadGroupInfo.inl | 14 +
.../pbbam/internal/Validator.inl | 62 +-
include/pbbam/virtual/VirtualPolymeraseBamRecord.h | 71 +-
.../virtual/VirtualPolymeraseCompositeReader.h | 62 +-
include/pbbam/virtual/VirtualPolymeraseReader.h | 86 +-
...PolymeraseBamRecord.h => VirtualZmwBamRecord.h} | 35 +-
...irtualReader.h => WhitelistedZmwReadStitcher.h} | 71 +-
...VirtualPolymeraseReader.h => ZmwReadStitcher.h} | 85 +-
include/pbbam/virtual/ZmwWhitelistVirtualReader.h | 101 +-
src/BamFile.cpp | 39 +-
src/BamHeader.cpp | 116 +-
src/BamReader.cpp | 6 +
src/BamRecord.cpp | 2130 ++++++++-----
src/BamRecordBuilder.cpp | 14 +-
src/BamRecordImpl.cpp | 52 +-
src/BamRecordTags.cpp | 99 +
src/{ChemistryTable.cpp => BamRecordTags.h} | 66 +-
src/BamWriter.cpp | 65 +-
src/BarcodeQuery.cpp | 4 +-
src/ChemistryTable.cpp | 27 +-
src/CigarOperation.cpp | 43 +-
src/DataSetIO.cpp | 2 +-
src/DataSetXsd.cpp | 2 +-
src/{ChemistryTable.cpp => EnumClassHash.h} | 58 +-
src/{BarcodeQuery.cpp => FileProducer.cpp} | 51 +-
src/{ChemistryTable.cpp => FileProducer.h} | 67 +-
src/Frames.cpp | 2 +-
tests/src/TestData.h.in => src/IRecordWriter.cpp | 30 +-
tests/src/TestData.h.in => src/MD5.cpp | 40 +-
src/PbiBuilder.cpp | 17 +-
src/PbiFilter.cpp | 561 ++--
src/PbiFilterTypes.cpp | 285 +-
src/PbiIndex.cpp | 6 +-
src/PbiIndexIO.cpp | 122 +-
src/PbiIndexIO.h | 8 +-
src/PbiRawData.cpp | 27 +-
src/Pulse2BaseCache.h | 154 +
src/ReadGroupInfo.cpp | 11 +-
src/SamWriter.cpp | 142 +
src/SequenceUtils.h | 20 +
src/ValidationErrors.cpp | 144 +
src/ValidationErrors.h | 115 +
src/ValidationException.cpp | 122 +
src/Validator.cpp | 470 +++
src/{BarcodeQuery.cpp => Version.cpp} | 59 +-
src/Version.h | 209 ++
src/VirtualPolymeraseReader.cpp | 285 --
...meraseBamRecord.cpp => VirtualZmwBamRecord.cpp} | 52 +-
...iteReader.cpp => VirtualZmwCompositeReader.cpp} | 27 +-
.../VirtualZmwCompositeReader.h | 38 +-
src/VirtualZmwReader.cpp | 143 +
.../VirtualZmwReader.h | 82 +-
src/WhitelistedZmwReadStitcher.cpp | 186 ++
src/ZmwReadStitcher.cpp | 223 ++
src/ZmwWhitelistVirtualReader.cpp | 141 -
src/files.cmake | 42 +-
src/swig/BamRecordTag.i | 11 +
src/swig/ClipType.i | 11 +
src/swig/FrameEncodingType.i | 11 +
src/swig/IRecordWriter.i | 9 +
src/swig/PacBioBam.i | 14 +-
src/swig/PulseBehavior.i | 11 +
src/swig/RecordType.i | 11 +
src/swig/SamWriter.i | 15 +
src/swig/VirtualPolymeraseBamRecord.i | 30 +-
src/swig/VirtualPolymeraseReader.i | 14 +-
...PolymeraseBamRecord.i => VirtualZmwBamRecord.i} | 16 +-
src/swig/WhitelistedZmwReadStitcher.i | 11 +
src/swig/ZmwReadStitcher.i | 11 +
src/swig/ZmwWhitelistVirtualReader.i | 12 +
tests/CMakeLists.txt | 21 +-
tests/data/aligned.bam | Bin 593 -> 786 bytes
tests/data/aligned.bam.bai | Bin 0 -> 96 bytes
tests/data/aligned.bam.pbi | Bin 0 -> 168 bytes
tests/data/aligned.sam | 8 +
tests/data/aligned2.bam | Bin 0 -> 22511 bytes
tests/data/aligned2.bam.bai | Bin 0 -> 96 bytes
tests/data/aligned2.bam.pbi | Bin 0 -> 366 bytes
.../chunking/chunking_emptyfilters.subreadset.xml | 59 -
.../chunking_missingfilters.subreadset.xml | 58 -
tests/data/dataset/bam_mapping.bam.bai | Bin 184 -> 0 bytes
tests/data/dataset/bam_mapping_1.bam.bai | Bin 184 -> 0 bytes
tests/data/dataset/bam_mapping_2.bam.bai | Bin 184 -> 0 bytes
tests/data/dataset/contig.dataset.xml | 18 -
tests/data/dataset/fofn.fofn | 3 -
tests/data/dataset/hdfsubread_dataset.xml | 72 -
tests/data/dataset/lambda_contigs.fasta | 156 -
.../data/dataset/m150430_142051_Mon_p1_b25.sts.xml | 1 -
tests/data/dataset/merge.fofn | 2 -
.../pbalchemy10kbp.pbalign.sorted.pbver1.bam | Bin 35235 -> 0 bytes
.../pbalchemy10kbp.pbalign.sorted.pbver1.bam.bai | Bin 632 -> 0 bytes
tests/data/ex2.bam | Bin 126008 -> 0 bytes
tests/data/ex2.bam.bai | Bin 176 -> 0 bytes
tests/data/ex2.sam | 3310 --------------------
tests/data/ex2_copy.bam | Bin 125999 -> 0 bytes
tests/data/ex2_copy.bam.bai | Bin 176 -> 0 bytes
tests/data/group/group.fofn.in | 3 +
tests/data/group/test1.bam | Bin 0 -> 2186 bytes
tests/data/group/test2.bam | Bin 0 -> 13025 bytes
tests/data/group/test2.bam.pbi | Bin 0 -> 199 bytes
tests/data/group/test3.bam | Bin 0 -> 19332 bytes
tests/data/merge.fofn | 2 +
tests/data/polymerase/internal.hqregions.bam | Bin 84164 -> 84188 bytes
tests/data/polymerase/internal.hqregions.bam.pbi | Bin 0 -> 95 bytes
tests/data/polymerase/internal.lqregions.bam | Bin 53088 -> 53115 bytes
tests/data/polymerase/internal.lqregions.bam.pbi | Bin 0 -> 110 bytes
tests/data/polymerase/internal.polymerase.bam | Bin 133770 -> 400570 bytes
tests/data/polymerase/internal.polymerase.bam.pbi | Bin 0 -> 116 bytes
tests/data/polymerase/internal.scraps.bam | Bin 67986 -> 203276 bytes
tests/data/polymerase/internal.scraps.bam.pbi | Bin 275 -> 447 bytes
tests/data/polymerase/internal.subreads.bam | Bin 73170 -> 218924 bytes
tests/data/polymerase/internal.subreads.bam.pbi | Bin 185 -> 281 bytes
tests/data/polymerase/production.scraps.bam.pbi | Bin 279 -> 284 bytes
tests/data/polymerase/production.subreads.bam.pbi | Bin 186 -> 188 bytes
.../data/polymerase/production_hq.hqregion.bam.pbi | Bin 90 -> 91 bytes
tests/data/polymerase/production_hq.scraps.bam.pbi | Bin 104 -> 104 bytes
.../polymerase/qnameFiltered.subreads.dataset.xml | 37 +
tests/data/polymerase/qname_whitelist.txt | 3 +
.../{whitelist => }/scrapless.scraps.bam | Bin
.../{whitelist => }/scrapless.scraps.bam.pbi | Bin
.../{whitelist => }/scrapless.subreads.bam | Bin
tests/data/polymerase/scrapless.subreads.bam.pbi | Bin 0 -> 114 bytes
.../polymerase/whitelist/internal.polymerase.bam | Bin 400494 -> 0 bytes
.../whitelist/internal.polymerase.bam.pbi | Bin 105 -> 0 bytes
.../data/polymerase/whitelist/internal.scraps.bam | Bin 203149 -> 0 bytes
.../polymerase/whitelist/internal.scraps.bam.pbi | Bin 420 -> 0 bytes
.../polymerase/whitelist/internal.subreads.bam | Bin 218703 -> 0 bytes
.../polymerase/whitelist/internal.subreads.bam.pbi | Bin 264 -> 0 bytes
.../whitelist/scrapless.subreads.bam.pbi | Bin 113 -> 0 bytes
tests/data/relative/a/test.bam | Bin 351 -> 462 bytes
tests/data/relative/b/test1.bam | Bin 351 -> 462 bytes
tests/data/relative/b/test2.bam | Bin 351 -> 462 bytes
tests/data/segfault.bam | Bin 262 -> 425 bytes
tests/data/temp.bam | Bin 125999 -> 0 bytes
tests/data/temp.sam | 3310 --------------------
tests/data/truncated.bam | Bin 200 -> 0 bytes
tests/data/unmap1.bam | Bin 896 -> 484 bytes
tests/files.cmake | 8 +-
tests/scripts/generate_data.py | 140 +
tests/src/CSharp/TestPbbam.cs.in | 15 +
tests/src/R/tests/test_BamFile.R | 2 +-
tests/src/R/tests/test_BamHeader.R | 6 +-
tests/src/R/tests/test_EndToEnd.R | 120 +-
tests/src/R/tests/test_PolymeraseStitching.R | 16 +-
tests/src/TestData.h.in | 1 +
tests/src/cram/pbmerge_aligned_ordering.t | 8 +-
tests/src/cram/pbmerge_dataset.t | 6 +-
tests/src/cram/pbmerge_fofn.t | 78 +-
tests/src/cram/pbmerge_pacbio_ordering.t | 238 +-
tests/src/python/test/test_BamFile.py | 6 +-
tests/src/python/test/test_BamHeader.py | 8 +-
tests/src/python/test/test_EndToEnd.py | 2 +-
tests/src/python/test/test_PolymeraseStitching.py | 25 -
tests/src/test_AlignmentPrinter.cpp | 30 +-
tests/src/test_BamFile.cpp | 125 +-
tests/src/test_BamHeader.cpp | 63 +-
tests/src/test_BamRecord.cpp | 2598 ++++++---------
tests/src/test_BamRecordClipping.cpp | 1716 ++++++----
tests/src/test_BamRecordImplCore.cpp | 14 +
tests/src/test_BamRecordMapping.cpp | 852 +++--
tests/src/test_BamWriter.cpp | 236 +-
tests/src/test_Compare.cpp | 16 +-
tests/src/test_DataSetCore.cpp | 14 +
tests/src/test_DataSetIO.cpp | 33 +-
tests/src/test_DataSetQuery.cpp | 228 +-
tests/src/test_EndToEnd.cpp | 4 +-
tests/src/test_EntireFileQuery.cpp | 89 +-
tests/src/test_GenomicIntervalQuery.cpp | 63 +-
tests/src/test_PacBioIndex.cpp | 130 +-
tests/src/test_PbiFilter.cpp | 2659 ++++++++--------
tests/src/test_PbiFilterQuery.cpp | 20 +-
...eadLengthQuery.cpp => test_Pulse2BaseCache.cpp} | 63 +-
tests/src/test_QNameQuery.cpp | 2 +-
tests/src/test_ReadAccuracyQuery.cpp | 2 +-
tests/src/test_ReadGroupInfo.cpp | 158 +-
tests/src/test_SamWriter.cpp | 150 +
tests/src/test_SubreadLengthQuery.cpp | 2 +-
tests/src/test_Validator.cpp | 615 ++++
tests/src/test_Version.cpp | 335 ++
.../src/test_VirtualPolymeraseCompositeReader.cpp | 132 -
tests/src/test_WhitelistedZmwReadStitcher.cpp | 260 ++
...eraseStitching.cpp => test_ZmwReadStitcher.cpp} | 435 ++-
tools/pbmerge/CMakeLists.txt | 6 +-
216 files changed, 13173 insertions(+), 15272 deletions(-)
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