[med-svn] [stacks] branch master updated (b9f711c -> 7ef7ebd)

[Andreas Tille]

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tille pushed a change to branch master
in repository stacks.

      from  b9f711c   Merge tag 'upstream/1.35'
       new  d4e5152   Moved from SVN to Git
       new  70763ba   cme fix dpkg-control
       new  1574dea   Imported Upstream version 1.37
       new  0d39ceb   Merge tag 'upstream/1.37'
       new  daba5a1   New upstream version
       new  7ef7ebd   Typo and upload to unstable

The 6 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 +-
 debian/README.Debian              |   2 +-
 debian/changelog                  |   8 +
 debian/control                    |  11 +-
 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 +
 57 files changed, 1664 insertions(+), 903 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

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