[med-svn] [pbbam] branch upstream updated (ce58675 -> 11fe97d)
Afif Elghraoui
afif at moszumanska.debian.org
Sun Oct 30 21:39:23 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository pbbam.
from ce58675 Imported Upstream version 0.5.0
new 11fe97d Imported Upstream version 0.7.0
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.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 +
include/pbbam/{Strand.h => BamRecordTag.h} | 59 +-
include/pbbam/BamRecordView.h | 168 +
include/pbbam/BamWriter.h | 3 +-
include/pbbam/BarcodeQuery.h | 2 +-
include/pbbam/{TagCollection.h => ClipType.h} | 33 +-
include/pbbam/Compare.h | 4 +-
include/pbbam/Config.h | 14 +
.../pbbam/{TagCollection.h => FrameEncodingType.h} | 34 +-
include/pbbam/{Accuracy.h => IRecordWriter.h} | 65 +-
src/ChemistryTable.h => include/pbbam/MD5.h | 22 +-
include/pbbam/PbiFilterTypes.h | 43 +-
include/pbbam/PbiRawData.h | 24 +-
include/pbbam/{Strand.h => PulseBehavior.h} | 24 +-
include/pbbam/ReadGroupInfo.h | 13 +
include/pbbam/{TagCollection.h => RecordType.h} | 35 +-
include/pbbam/SamWriter.h | 130 +
include/pbbam/Validator.h | 192 ++
.../ValidationException.h} | 53 +-
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/{Cigar.inl => Validator.inl} | 63 +-
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 +
.../internal/Compare.inl => src/BamRecordTags.h | 65 +-
src/BamWriter.cpp | 65 +-
src/BarcodeQuery.cpp | 4 +-
src/ChemistryTable.cpp | 27 +-
src/CigarOperation.cpp | 43 +-
src/DataSetIO.cpp | 2 +-
src/DataSetXsd.cpp | 2 +-
.../internal/Compare.inl => src/EnumClassHash.h | 65 +-
.../src/test_TimeUtils.cpp => src/FileProducer.cpp | 44 +-
src/{DataSetIO.h => FileProducer.h} | 61 +-
src/Frames.cpp | 2 +-
src/{Accuracy.cpp => IRecordWriter.cpp} | 13 +-
.../virtual/VirtualRegionTypeMap.h => src/MD5.cpp | 39 +-
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/{Cigar.cpp => Version.cpp} | 57 +-
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/{PbiFile.i => ClipType.i} | 6 +-
src/swig/FrameEncodingType.i | 11 +
src/swig/IRecordWriter.i | 9 +
src/swig/PacBioBam.i | 14 +-
src/swig/PulseBehavior.i | 11 +
src/swig/{GroupQuery.i => RecordType.i} | 6 +-
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
...aset.xml => qnameFiltered.subreads.dataset.xml} | 31 +-
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 +-
...st_StringUtils.cpp => test_Pulse2BaseCache.cpp} | 48 +-
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, 13049 insertions(+), 15308 deletions(-)
rename docs/examples/code/{ZmwWhitelistVirtualReader.txt => WhitelistedZmwReadStitcher.txt} (63%)
copy include/pbbam/{Strand.h => BamRecordTag.h} (68%)
create mode 100644 include/pbbam/BamRecordView.h
copy include/pbbam/{TagCollection.h => ClipType.h} (72%)
copy include/pbbam/{TagCollection.h => FrameEncodingType.h} (70%)
copy include/pbbam/{Accuracy.h => IRecordWriter.h} (63%)
copy src/ChemistryTable.h => include/pbbam/MD5.h (87%)
copy include/pbbam/{Strand.h => PulseBehavior.h} (80%)
copy include/pbbam/{TagCollection.h => RecordType.h} (73%)
create mode 100644 include/pbbam/SamWriter.h
create mode 100644 include/pbbam/Validator.h
copy include/pbbam/{TagCollection.h => exception/ValidationException.h} (58%)
copy include/pbbam/internal/{BamRecord.inl => BamRecordView.inl} (65%)
copy include/pbbam/internal/{Cigar.inl => Validator.inl} (66%)
copy include/pbbam/virtual/{VirtualPolymeraseBamRecord.h => VirtualZmwBamRecord.h} (76%)
copy include/pbbam/virtual/{ZmwWhitelistVirtualReader.h => WhitelistedZmwReadStitcher.h} (67%)
copy include/pbbam/virtual/{VirtualPolymeraseReader.h => ZmwReadStitcher.h} (54%)
create mode 100644 src/BamRecordTags.cpp
copy include/pbbam/internal/Compare.inl => src/BamRecordTags.h (61%)
copy include/pbbam/internal/Compare.inl => src/EnumClassHash.h (61%)
copy tests/src/test_TimeUtils.cpp => src/FileProducer.cpp (68%)
copy src/{DataSetIO.h => FileProducer.h} (57%)
copy src/{Accuracy.cpp => IRecordWriter.cpp} (87%)
copy include/pbbam/virtual/VirtualRegionTypeMap.h => src/MD5.cpp (76%)
create mode 100644 src/Pulse2BaseCache.h
create mode 100644 src/SamWriter.cpp
create mode 100644 src/ValidationErrors.cpp
create mode 100644 src/ValidationErrors.h
create mode 100644 src/ValidationException.cpp
create mode 100644 src/Validator.cpp
copy src/{Cigar.cpp => Version.cpp} (63%)
create mode 100644 src/Version.h
delete mode 100644 src/VirtualPolymeraseReader.cpp
rename src/{VirtualPolymeraseBamRecord.cpp => VirtualZmwBamRecord.cpp} (88%)
rename src/{VirtualPolymeraseCompositeReader.cpp => VirtualZmwCompositeReader.cpp} (83%)
copy include/pbbam/virtual/VirtualPolymeraseCompositeReader.h => src/VirtualZmwCompositeReader.h (72%)
create mode 100644 src/VirtualZmwReader.cpp
copy include/pbbam/virtual/VirtualPolymeraseReader.h => src/VirtualZmwReader.h (62%)
create mode 100644 src/WhitelistedZmwReadStitcher.cpp
create mode 100644 src/ZmwReadStitcher.cpp
delete mode 100644 src/ZmwWhitelistVirtualReader.cpp
create mode 100644 src/swig/BamRecordTag.i
copy src/swig/{PbiFile.i => ClipType.i} (52%)
create mode 100644 src/swig/FrameEncodingType.i
create mode 100644 src/swig/IRecordWriter.i
create mode 100644 src/swig/PulseBehavior.i
copy src/swig/{GroupQuery.i => RecordType.i} (50%)
create mode 100644 src/swig/SamWriter.i
copy src/swig/{VirtualPolymeraseBamRecord.i => VirtualZmwBamRecord.i} (50%)
create mode 100644 src/swig/WhitelistedZmwReadStitcher.i
create mode 100644 src/swig/ZmwReadStitcher.i
create mode 100644 tests/data/aligned.bam.bai
create mode 100644 tests/data/aligned.bam.pbi
create mode 100644 tests/data/aligned.sam
create mode 100644 tests/data/aligned2.bam
create mode 100644 tests/data/aligned2.bam.bai
create mode 100644 tests/data/aligned2.bam.pbi
delete mode 100644 tests/data/chunking/chunking_emptyfilters.subreadset.xml
delete mode 100644 tests/data/chunking/chunking_missingfilters.subreadset.xml
delete mode 100644 tests/data/dataset/bam_mapping.bam.bai
delete mode 100644 tests/data/dataset/bam_mapping_1.bam.bai
delete mode 100644 tests/data/dataset/bam_mapping_2.bam.bai
delete mode 100644 tests/data/dataset/contig.dataset.xml
delete mode 100644 tests/data/dataset/fofn.fofn
delete mode 100644 tests/data/dataset/hdfsubread_dataset.xml
delete mode 100644 tests/data/dataset/lambda_contigs.fasta
delete mode 100644 tests/data/dataset/m150430_142051_Mon_p1_b25.sts.xml
delete mode 100644 tests/data/dataset/merge.fofn
delete mode 100644 tests/data/dataset/pbalchemy10kbp.pbalign.sorted.pbver1.bam
delete mode 100644 tests/data/dataset/pbalchemy10kbp.pbalign.sorted.pbver1.bam.bai
delete mode 100644 tests/data/ex2.bam
delete mode 100644 tests/data/ex2.bam.bai
delete mode 100644 tests/data/ex2.sam
delete mode 100644 tests/data/ex2_copy.bam
delete mode 100644 tests/data/ex2_copy.bam.bai
create mode 100644 tests/data/group/group.fofn.in
create mode 100644 tests/data/group/test1.bam
create mode 100644 tests/data/group/test2.bam
create mode 100644 tests/data/group/test2.bam.pbi
create mode 100644 tests/data/group/test3.bam
create mode 100644 tests/data/merge.fofn
create mode 100644 tests/data/polymerase/internal.hqregions.bam.pbi
create mode 100644 tests/data/polymerase/internal.lqregions.bam.pbi
create mode 100644 tests/data/polymerase/internal.polymerase.bam.pbi
copy tests/data/polymerase/{consolidate.subread.dataset.xml => qnameFiltered.subreads.dataset.xml} (56%)
create mode 100644 tests/data/polymerase/qname_whitelist.txt
rename tests/data/polymerase/{whitelist => }/scrapless.scraps.bam (100%)
rename tests/data/polymerase/{whitelist => }/scrapless.scraps.bam.pbi (100%)
rename tests/data/polymerase/{whitelist => }/scrapless.subreads.bam (100%)
create mode 100644 tests/data/polymerase/scrapless.subreads.bam.pbi
delete mode 100644 tests/data/polymerase/whitelist/internal.polymerase.bam
delete mode 100644 tests/data/polymerase/whitelist/internal.polymerase.bam.pbi
delete mode 100644 tests/data/polymerase/whitelist/internal.scraps.bam
delete mode 100644 tests/data/polymerase/whitelist/internal.scraps.bam.pbi
delete mode 100644 tests/data/polymerase/whitelist/internal.subreads.bam
delete mode 100644 tests/data/polymerase/whitelist/internal.subreads.bam.pbi
delete mode 100644 tests/data/polymerase/whitelist/scrapless.subreads.bam.pbi
delete mode 100644 tests/data/temp.bam
delete mode 100644 tests/data/temp.sam
delete mode 100644 tests/data/truncated.bam
create mode 100755 tests/scripts/generate_data.py
copy tests/src/{test_StringUtils.cpp => test_Pulse2BaseCache.cpp} (63%)
create mode 100644 tests/src/test_SamWriter.cpp
create mode 100644 tests/src/test_Validator.cpp
create mode 100644 tests/src/test_Version.cpp
delete mode 100644 tests/src/test_VirtualPolymeraseCompositeReader.cpp
create mode 100644 tests/src/test_WhitelistedZmwReadStitcher.cpp
rename tests/src/{test_PolymeraseStitching.cpp => test_ZmwReadStitcher.cpp} (65%)
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