[med-svn] [stacks] branch master updated (f61a805 -> c0ff32a)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository stacks.

      from  f61a805   Better hardening and upload to unstable
       new  709db0d   Imported Upstream version 1.40
       new  8a0b5fe   New upstream version
       new  f7c6a7f   cme fix dpkg-control
       new  e44c3dd   Build-Depends: samtools to ensure that package builds only on those architectures where samtools is available
       new  c0ff32a   Add Python depencency since new tool in Python was included by upstream

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:
 ChangeLog                       |  16 ++
 Makefile.am                     |   3 +-
 Makefile.in                     |   3 +-
 configure                       |  20 +-
 configure.ac                    |   2 +-
 debian/changelog                |   9 +
 debian/control                  |   7 +-
 debian/rules                    |   2 +-
 scripts/denovo_map.pl           |  14 +-
 scripts/integrate_alignments.py | 426 ++++++++++++++++++++++++++++++++++++++++
 scripts/ref_map.pl              |   8 +-
 src/aln_utils.cc                | 258 ++++++++++++++++++++++++
 src/aln_utils.h                 |   5 +
 src/cstacks.cc                  |  59 +++---
 src/locus.cc                    |  13 ++
 src/locus.h                     |   1 +
 src/rxstacks.cc                 | 104 +++++++---
 src/rxstacks.h                  |   1 +
 src/sql_utilities.h             |  57 +++---
 src/sstacks.cc                  |   5 +-
 src/write.cc                    |  16 +-
 21 files changed, 913 insertions(+), 116 deletions(-)
 create mode 100755 scripts/integrate_alignments.py

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/stacks.git