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commit 0d39ceb9e4ae2a394641461ca0bea7797b2e7cfa Merge: 70763ba 1574dea Author: Andreas Tille <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/stacks.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
