[med-svn] [stacks] branch upstream updated (f2fe6a3 -> 1574dea)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository stacks.

      from  f2fe6a3   Imported Upstream version 1.35
       new  1574dea   Imported Upstream version 1.37

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                         |  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(-)
 create mode 100644 php/tag.php
 mode change 100644 => 100755 scripts/convert_stacks.pl
 mode change 100644 => 100755 scripts/denovo_map.pl
 mode change 100644 => 100755 scripts/exec_velvet.pl
 mode change 100644 => 100755 scripts/export_sql.pl
 mode change 100644 => 100755 scripts/extract_interpop_chars.pl
 mode change 100644 => 100755 scripts/index_radtags.pl
 mode change 100644 => 100755 scripts/load_radtags.pl
 mode change 100644 => 100755 scripts/load_sequences.pl
 mode change 100644 => 100755 scripts/ref_map.pl
 mode change 100644 => 100755 scripts/sort_read_pairs.pl
 mode change 100644 => 100755 scripts/stacks_export_notify.pl

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/stacks.git