[med-svn] [pbbam] branch upstream updated (11fe97d -> a9374dc)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository pbbam.

      from  11fe97d   Imported Upstream version 0.7.0
       new  a9374dc   Imported Upstream version 0.7.4+ds

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
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Summary of changes:
 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
 .../{pbbam.rst => pbbam_updated_release3_2.rst}    |  205 ++--
 include/pbbam/Config.h                             |   37 +
 include/pbbam/{Accuracy.h => FastaReader.h}        |   76 +-
 include/pbbam/{Accuracy.h => FastaSequence.h}      |   64 +-
 .../InvalidSequencingChemistryException.h          |    7 +-
 include/pbbam/exception/ValidationException.h      |    6 +-
 .../FastaSequence.inl}                             |   28 +-
 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 +-
 ...{test_SubreadLengthQuery.cpp => test_Fasta.cpp} |   82 +-
 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, 2549 insertions(+), 615 deletions(-)
 create mode 100644 cmake/pbbam-ccache.cmake
 create mode 100644 cmake/pbbam-compilerflags.cmake
 create mode 100644 cmake/pbbam-dependencies.cmake
 create mode 100644 cmake/pbbam-libtype.cmake
 create mode 100755 docs/specs/pbbam_structure.png
 copy docs/specs/{pbbam.rst => pbbam_updated_release3_2.rst} (81%)
 mode change 100644 => 100755
 copy include/pbbam/{Accuracy.h => FastaReader.h} (59%)
 copy include/pbbam/{Accuracy.h => FastaSequence.h} (65%)
 copy include/pbbam/{PulseBehavior.h => internal/FastaSequence.inl} (81%)
 create mode 100644 src/FastaReader.cpp
 create mode 100644 tests/data/empty.bam
 create mode 100644 tests/data/empty.bam.pbi
 create mode 100644 tests/data/phi29.bam.pbi
 rename tests/src/cram/{bam2sam.t => bam2sam.t.in} (99%)
 rename tests/src/cram/{pbindexdump_cpp.t => pbindexdump_cpp.t.in} (88%)
 rename tests/src/cram/{pbindexdump_json.t => pbindexdump_json.t.in} (92%)
 rename tests/src/cram/{pbmerge_aligned_ordering.t => pbmerge_aligned_ordering.t.in} (96%)
 rename tests/src/cram/{pbmerge_dataset.t => pbmerge_dataset.t.in} (91%)
 rename tests/src/cram/{pbmerge_fofn.t => pbmerge_fofn.t.in} (94%)
 rename tests/src/cram/{pbmerge_mixed_ordering.t => pbmerge_mixed_ordering.t.in} (94%)
 rename tests/src/cram/{pbmerge_pacbio_ordering.t => pbmerge_pacbio_ordering.t.in} (96%)
 copy tests/src/{test_SubreadLengthQuery.cpp => test_Fasta.cpp} (51%)

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