[med-svn] [bamtools] branch master updated (ba80e50 -> 53fe449)

[Kevin Murray]

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

      from  ba80e50   Upload to unstable
       new  00cf2a2   Imported Upstream version 2.4.0+dfsg
       new  e21f2f2   Merge tag 'upstream/2.4.0+dfsg'
       new  e0a9522   Correct d/watch to add +dfsg to repacked tarball
       new  f964536   gbp pq import/export to refresh package queue
       new  53fe449   Update d/changelog for version 2.4.0

The 5 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 +-
 debian/changelog                                   |  7 ++++
 .../0001-ignore-thirdparty-and-fix-jsoncpp.patch   | 33 +++++++++-------
 .../patches/0002-support-out-of-source-build.patch | 18 ++++++---
 ...om-ExportHeader-function-use-install-inst.patch | 45 +++++++++++++---------
 ...ls-statically-with-libbamtools-utils-as-w.patch | 22 -----------
 ...bamtools-to-lib.-Installing-libraries-to-.patch | 14 +++++--
 debian/patches/0006-Doxygen-reproducibility        | 15 +++++---
 debian/patches/series                              |  1 -
 debian/watch                                       |  3 +-
 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 +-
 39 files changed, 192 insertions(+), 98 deletions(-)
 delete mode 100644 debian/patches/0004-Link-bamtools-statically-with-libbamtools-utils-as-w.patch

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