[med-svn] [stacks] 04/06: Merge tag 'upstream/1.37'

[Andreas Tille]

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tille pushed a commit to branch master
in repository stacks.

commit 0d39ceb9e4ae2a394641461ca0bea7797b2e7cfa
Merge: 70763ba 1574dea
Author: Andreas Tille <tille at debian.org>
Date:   Thu Mar 10 23:30:37 2016 +0100

    Merge tag 'upstream/1.37'
    
    Upstream version 1.37

 ChangeLog                         |  18 ++
 Makefile.am                       |   2 +-
 Makefile.in                       |   2 +-
 README                            |  34 ++--
 configure                         |  20 +--
 configure.ac                      |   2 +-
 php/CatalogClass.php              | 150 +++++++++-------
 php/annotate_marker.php           |  45 +++--
 php/catalog.php                   | 230 ++++++++++++++----------
 php/catalog_genotypes.php         |  31 ++--
 php/correct_genotype.php          |  51 +++---
 php/correct_genotypes.php         |  71 +++++---
 php/db_functions.php              |  44 ++---
 php/export_batch.php              |   6 +-
 php/fst_view.php                  | 104 ++++++-----
 php/hapstat_view.php              |  48 ++---
 php/header.php                    |   3 +-
 php/index.php                     |  13 +-
 php/last_modified.php             |   2 +-
 php/phist_view.php                |  50 +++---
 php/pop_view.php                  | 193 +++++++++++---------
 php/population_view.js            |   3 +
 php/samples.php                   |  70 +++++---
 php/sequence_blast.php            |  28 +--
 php/stack_view.php                |  49 +++--
 php/stacks.css                    |   5 +
 php/stacks_functions.php          |   1 +
 php/sumstat_view.php              | 134 +++++++-------
 php/tag.php                       | 368 ++++++++++++++++++++++++++++++++++++++
 php/tags.php                      | 132 +++++++++-----
 php/view_sequence.php             |  15 +-
 scripts/convert_stacks.pl         |   0
 scripts/denovo_map.pl             |  65 ++++---
 scripts/exec_velvet.pl            |   0
 scripts/export_sql.pl             |   0
 scripts/extract_interpop_chars.pl |   0
 scripts/index_radtags.pl          |   0
 scripts/load_radtags.pl           |   0
 scripts/load_sequences.pl         |   0
 scripts/ref_map.pl                |  62 ++++---
 scripts/sort_read_pairs.pl        |   0
 scripts/stacks_export_notify.pl   |   0
 src/BamI.h                        |  35 ++--
 src/FastaI.h                      |   6 +-
 src/catalog_utils.cc              |   2 +-
 src/clone_filter.cc               | 317 ++++++++++++++++----------------
 src/file_io.cc                    |  23 +++
 src/file_io.h                     |  43 ++---
 src/gzFasta.h                     |   8 +-
 src/pstacks.cc                    |   1 +
 src/renz.h                        |  22 ++-
 src/sstacks.cc                    |  35 +++-
 src/sstacks.h                     |   2 +-
 src/ustacks.cc                    |   1 +
 54 files changed, 1648 insertions(+), 898 deletions(-)

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