[med-svn] [stacks] 02/05: Merge tag 'upstream/1.38'

[Andreas Tille]

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tille pushed a commit to branch master
in repository stacks.

commit bb0755c6414359bde461ec5bdb7de0dbfcd4a595
Merge: 7ef7ebd 83ef6c3
Author: Andreas Tille <tille at debian.org>
Date:   Tue Apr 19 10:43:16 2016 +0200

    Merge tag 'upstream/1.38'
    
    Upstream version 1.38

 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/aln_utils.h        |    42 +
 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, 12550 insertions(+), 9344 deletions(-)

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