[med-svn] [stacks] branch upstream updated (1574dea -> 83ef6c3)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository stacks.

      from  1574dea   Imported Upstream version 1.37
       new  83ef6c3   Imported Upstream version 1.38

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:
 ChangeLog                        |    24 +
 Makefile.am                      |    10 +-
 Makefile.in                      |   195 +-
 aclocal.m4                       |    65 +-
 config/compile                   |     2 +-
 config/depcomp                   |     2 +-
 config/install-sh                |   366 +-
 config/missing                   |     2 +-
 config/test-driver               |    15 +-
 configure                        |    33 +-
 configure.ac                     |     2 +-
 php/CatalogClass.php             |     8 +-
 php/catalog.php                  |     5 +-
 php/export_batch.php             |     6 +
 scripts/denovo_map.pl            |  1017 ++--
 scripts/ref_map.pl               |   972 ++--
 sql/stacks.sql                   |     1 +
 src/DNANSeq.cc                   |     2 +-
 src/DNANSeq.h                    |     4 +-
 src/GappedAln.h                  |   594 ++
 src/PopMap.h                     |   254 +-
 src/PopSum.h                     |  1113 ++--
 src/SamI.h                       |    31 +-
 src/aln_utils.cc                 |   216 +
 src/{log_utils.h => aln_utils.h} |    34 +-
 src/catalog_utils.cc             |   378 +-
 src/constants.h                  |     4 +-
 src/cstacks.cc                   |   642 ++-
 src/cstacks.h                    |     7 +-
 src/kmers.cc                     |   273 +-
 src/kmers.h                      |    25 +-
 src/locus.cc                     |    62 +-
 src/locus.h                      |    42 +-
 src/mstack.cc                    |    88 +-
 src/mstack.h                     |    18 +-
 src/populations.cc               | 11098 ++++++++++++++++++-------------------
 src/process_radtags.cc           |     4 +-
 src/pstacks.cc                   |    30 +-
 src/sql_utilities.h              |   660 ++-
 src/sstacks.cc                   |   496 +-
 src/sstacks.h                    |    32 +-
 src/stacks.cc                    |    28 +-
 src/stacks.h                     |   163 +-
 src/ustacks.cc                   |  2810 ++++++----
 src/ustacks.h                    |    43 +-
 src/utils.cc                     |     8 +
 src/utils.h                      |     2 +
 47 files changed, 12526 insertions(+), 9360 deletions(-)
 create mode 100644 src/GappedAln.h
 create mode 100644 src/aln_utils.cc
 copy src/{log_utils.h => aln_utils.h} (54%)

-- 
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