[med-svn] [harvest-tools] branch master updated (7e42d85 -> 14d98c4)

[Andreas Tille]

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tille pushed a change to branch master
in repository harvest-tools.

      from  7e42d85   Finalise changelog
       new  a2f141c   New upstream version 1.3
       new  99b1e83   Merge tag 'upstream/1.3'
       new  4b17fba   New upstream version
       new  05bcbb3   cme fix dpkg-control
       new  fecbc6f   Adapt patches
       new  14d98c4   Upload to unstable

The 6 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:
 INSTALL.txt                         |  38 +++++--
 Makefile.in                         |   6 +-
 README.md                           |  18 ++--
 configure.ac                        |   2 +-
 debian/changelog                    |   7 ++
 debian/control                      |   2 +-
 debian/patches/remove_memwrap.patch |  16 +--
 src/harvest/AnnotationList.cpp      |  27 ++++-
 src/harvest/AnnotationList.h        |   7 +-
 src/harvest/HarvestIO.cpp           |  42 +++++++-
 src/harvest/HarvestIO.h             |   3 +-
 src/harvest/LcbList.cpp             | 121 +++++++++++++++++++++
 src/harvest/LcbList.h               |   1 +
 src/harvest/PhylogenyTree.cpp       |  43 ++++++++
 src/harvest/PhylogenyTree.h         |   1 +
 src/harvest/PhylogenyTreeNode.cpp   |   5 +-
 src/harvest/PhylogenyTreeNode.h     |   5 +-
 src/harvest/ReferenceList.cpp       |  14 +--
 src/harvest/ReferenceList.h         |  12 +--
 src/harvest/VariantList.cpp         | 210 +++++++++++++++++++++++++++++++-----
 src/harvest/VariantList.h           | 139 +++++++++++++++++++++++-
 src/harvest/harvest.cpp             | 141 ++++++++++++++++++++++--
 22 files changed, 762 insertions(+), 98 deletions(-)
 mode change 100644 => 100755 src/harvest/HarvestIO.cpp
 mode change 100644 => 100755 src/harvest/LcbList.cpp
 mode change 100644 => 100755 src/harvest/harvest.cpp

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