[med-svn] [pbbam] 03/04: Merge tag 'upstream/0.7.4+ds'

[Afif Elghraoui]

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afif pushed a commit to branch master
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commit 5fb94eed78fa008b1bfd91b9c3e89cec553ab582
Merge: 007467b a9374dc
Author: Afif Elghraoui <afif at debian.org>
Date:   Sun Dec 18 21:18:05 2016 -0800

    Merge tag 'upstream/0.7.4+ds'
    
    Upstream version 0.7.4+ds

 CHANGELOG.md                                       |   39 +-
 CMakeLists.txt                                     |  165 +--
 cmake/PbbamTool.cmake                              |    6 +-
 cmake/pbbam-ccache.cmake                           |    8 +
 cmake/pbbam-compilerflags.cmake                    |   44 +
 cmake/pbbam-dependencies.cmake                     |   23 +
 cmake/pbbam-libtype.cmake                          |   21 +
 docs/source/conf.py                                |    4 +-
 docs/specs/pbbam_structure.png                     |  Bin 0 -> 23521 bytes
 docs/specs/pbbam_updated_release3_2.rst            |  618 ++++++++++
 include/pbbam/Config.h                             |   37 +
 .../ValidationException.h => FastaReader.h}        |   86 +-
 .../TestData.h.in => include/pbbam/FastaSequence.h |   70 +-
 .../InvalidSequencingChemistryException.h          |    7 +-
 include/pbbam/exception/ValidationException.h      |    6 +-
 .../pbbam/internal/FastaSequence.inl               |   33 +-
 include/pbbam/internal/ReadGroupInfo.inl           |    1 +
 src/BamHeader.cpp                                  |   41 +-
 src/BamRecord.cpp                                  |    2 +-
 src/CMakeLists.txt                                 |  112 +-
 src/ChemistryTable.cpp                             |   13 +-
 src/DataSet.cpp                                    |   42 +-
 src/FastaReader.cpp                                |  155 +++
 src/PbiFilter.cpp                                  |   85 +-
 src/PbiIndexedBamReader.cpp                        |    4 +-
 src/Pulse2BaseCache.h                              |    2 +-
 src/SequenceUtils.h                                |    2 +-
 src/files.cmake                                    |    4 +
 src/swig/CMakeLists.txt                            |    2 +-
 src/swig/WrapCSharp.cmake                          |    2 +-
 src/swig/WrapPython.cmake                          |    3 +-
 tests/CMakeLists.txt                               |  136 ++-
 tests/data/dataset/malformed.xml                   |    3 +-
 tests/data/empty.bam                               |  Bin 0 -> 350 bytes
 tests/data/empty.bam.pbi                           |  Bin 0 -> 67 bytes
 tests/data/phi29.bam.pbi                           |  Bin 0 -> 1394 bytes
 tests/files.cmake                                  |    1 +
 tests/scripts/generate_data.py                     |   24 +
 tests/src/CSharp/buildAssembly.sh.in               |    8 +-
 tests/src/TestData.h.in                            |    1 +
 tests/src/cram/{bam2sam.t => bam2sam.t.in}         |    4 +-
 .../{pbindexdump_cpp.t => pbindexdump_cpp.t.in}    |    4 +-
 .../{pbindexdump_json.t => pbindexdump_json.t.in}  |    4 +-
 ...ed_ordering.t => pbmerge_aligned_ordering.t.in} |   16 +-
 .../{pbmerge_dataset.t => pbmerge_dataset.t.in}    |   14 +-
 .../src/cram/{pbmerge_fofn.t => pbmerge_fofn.t.in} |   12 +-
 ...ixed_ordering.t => pbmerge_mixed_ordering.t.in} |    6 +-
 ...bio_ordering.t => pbmerge_pacbio_ordering.t.in} |   16 +-
 tests/src/test_BamHeader.cpp                       |   12 +-
 tests/src/test_BamRecord.cpp                       | 1231 ++++++++++++++++++++
 tests/src/test_BamWriter.cpp                       |    2 +-
 tests/src/test_DataSetCore.cpp                     |    1 +
 tests/src/test_DataSetIO.cpp                       |    4 +-
 tests/src/test_DataSetQuery.cpp                    |    2 +-
 tests/src/test_EndToEnd.cpp                        |    4 +-
 tests/src/test_Fasta.cpp                           |  105 ++
 tests/src/test_FileUtils.cpp                       |    7 +-
 tests/src/test_PacBioIndex.cpp                     |   10 +-
 tests/src/test_PbiFilterQuery.cpp                  |  187 ++-
 tests/src/test_ReadGroupInfo.cpp                   |   25 +
 tests/src/test_SamWriter.cpp                       |    4 +-
 tools/CMakeLists.txt                               |   58 +-
 tools/bam2sam/CMakeLists.txt                       |   11 +-
 tools/pbindex/CMakeLists.txt                       |    2 +-
 tools/pbindexdump/CMakeLists.txt                   |   18 +-
 tools/pbmerge/CMakeLists.txt                       |   52 +-
 66 files changed, 3148 insertions(+), 473 deletions(-)

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