[med-svn] [stacks] branch upstream updated (83ef6c3 -> 7773661)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository stacks.

      from  83ef6c3   Imported Upstream version 1.38
       new  7773661   Imported Upstream version 1.40

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                       |  16 ++
 Makefile.am                     |   3 +-
 Makefile.in                     |   3 +-
 configure                       |  20 +-
 configure.ac                    |   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 +-
 18 files changed, 898 insertions(+), 113 deletions(-)
 create mode 100755 scripts/integrate_alignments.py

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