[med-svn] [stacks] branch master updated (7ef7ebd -> f61a805)

[Andreas Tille]

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tille pushed a change to branch master
in repository stacks.

      from  7ef7ebd   Typo and upload to unstable
       new  83ef6c3   Imported Upstream version 1.38
       new  bb0755c   Merge tag 'upstream/1.38'
       new  5e7e762   New upstream version
       new  c78f272   Enable PHP migration
       new  f61a805   Better hardening and upload to unstable

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
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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 +-
 debian/changelog                 |     9 +
 debian/control                   |     2 +-
 debian/rules                     |     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 +
 50 files changed, 12538 insertions(+), 9361 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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