[med-svn] [stacks] branch master updated (b9f711c -> 7ef7ebd)
Andreas Tille
tille at debian.org
Thu Mar 10 22:44:54 UTC 2016
This is an automated email from the git hooks/post-receive script.
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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