[med-svn] [bamtools] branch upstream updated (e5562b9 -> 00cf2a2)

[Kevin Murray]

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daube-guest pushed a change to branch upstream
in repository bamtools.

      from  e5562b9   Imported Upstream version 2.3.0+dfsg
       new  00cf2a2   Imported Upstream version 2.4.0+dfsg

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:
 CMakeLists.txt                              |  2 +-
 docs/Doxyfile                               |  2 +-
 src/api/BamAlignment.h                      |  8 ++++----
 src/api/BamAux.h                            |  6 ++++++
 src/api/BamReader.cpp                       |  6 +++---
 src/api/BamWriter.h                         |  2 +-
 src/api/CMakeLists.txt                      |  2 +-
 src/api/SamHeader.cpp                       |  2 ++
 src/api/SamHeader.h                         |  3 +++
 src/api/SamProgram.cpp                      |  1 +
 src/api/SamProgram.h                        |  2 ++
 src/api/SamReadGroup.cpp                    |  2 ++
 src/api/SamReadGroup.h                      |  3 +++
 src/api/SamSequence.cpp                     |  2 ++
 src/api/SamSequence.h                       |  3 +++
 src/api/internal/io/HostAddress_p.cpp       |  2 +-
 src/api/internal/io/HttpHeader_p.cpp        |  3 +--
 src/api/internal/io/TcpSocketEngine_p.h     |  2 +-
 src/api/internal/sam/SamFormatParser_p.cpp  | 24 ++++++++++++++++++++++
 src/api/internal/sam/SamFormatParser_p.h    |  2 +-
 src/api/internal/sam/SamFormatPrinter_p.cpp | 31 +++++++++++++++++++++++++++++
 src/api/internal/sam/SamFormatPrinter_p.h   |  2 +-
 src/api/internal/sam/SamHeaderValidator_p.h |  6 +++---
 src/toolkit/CMakeLists.txt                  |  2 +-
 src/toolkit/bamtools.cpp                    |  2 +-
 src/toolkit/bamtools_filter.h               |  2 +-
 src/toolkit/bamtools_resolve.cpp            |  2 --
 src/toolkit/bamtools_sort.h                 |  2 +-
 src/toolkit/bamtools_split.h                |  2 +-
 src/utils/bamtools_fasta.cpp                |  2 +-
 30 files changed, 104 insertions(+), 28 deletions(-)

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