[med-svn] [gmap] branch master updated (fb73380 -> 9b29a37)

[Alex Mestiashvili]

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

malex-guest pushed a change to branch master
in repository gmap.

      from  fb73380   d/patches/drop_tests_i386.patch: do not run tests on i386 because they fail.  As it is not clear if the program is usefull on i386 architecure,  let's leave it like that for now. d/README.Debian: note that embeded tests are skipped for i386 d/changelog: upload to unstable
       new  61cf1e5   Imported Upstream version 2014-11-25
       new  5a12dcc   Merge tag 'upstream/2014-11-25'
       new  24e5957   d/copyright: add missing information for config/* directory
       new  88e5821   Imported Upstream version 2014-12-23
       new  9619a96   Merge tag 'upstream/2014-12-23'
       new  de66f2c   d/chhangelog imported new upstrea release 2014-12-23
       new  09015de   d/*.1: updated man pages
       new  9b29a37   d/rules: apply patch provided by Graham Inggs, see #779564

The 8 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                   |  332 ++++++
 Makefile.in                 |    5 +-
 README                      |   25 +-
 TODO                        |    3 -
 VERSION                     |    2 +-
 acinclude.m4                |    3 +
 config/ax_ext.m4            |   15 +-
 config/ax_mpi.m4            |  176 +++
 configure                   |  641 +++++++++-
 configure.ac                |   65 +-
 debian/changelog            |   16 +
 debian/copyright            |   63 +-
 debian/gmap.1               |   56 +-
 debian/gmap_build.1         |   22 +-
 debian/gsnap.1              |   83 +-
 debian/rules                |    7 +-
 src/ChangeLog               |    0
 src/Makefile.in             |    5 +-
 src/access.c                |   42 +-
 src/bitpack64-read.c        |   30 +-
 src/bitpack64-read.h        |    4 +
 src/bitpack64-readtwo.c     |    6 +-
 src/bitpack64-write.c       |   14 +-
 src/bytecoding.c            |   69 +-
 src/chimera.c               |   59 +-
 src/chimera.h               |    6 +-
 src/compress-write.c        |   13 +-
 src/compress.h              |    5 +-
 src/config.h.in             |    9 +-
 src/doublelist.c            |   34 +-
 src/doublelist.h            |    6 +-
 src/dynprog.h               |    5 +-
 src/except.h                |    6 +-
 src/genome-write.c          |  131 ++-
 src/genome.c                |   32 +-
 src/genome128_hr.c          |   12 +-
 src/genome_sites.c          |  170 +--
 src/genomicpos.h            |    6 +-
 src/get-genome.c            |   28 +-
 src/gmap.c                  |  182 ++-
 src/gmapindex.c             |   58 +-
 src/gsnap.c                 |  271 +++--
 src/iit-read-univ.c         |  107 +-
 src/iit-read.c              |  200 ++--
 src/iit-read.h              |    7 +-
 src/iit-write-univ.c        |   14 +-
 src/iit_get.c               |    6 +-
 src/iit_store.c             |   27 +-
 src/indel.c                 |   10 +-
 src/indexdb-write.c         |  146 ++-
 src/indexdb-write.h         |    5 +-
 src/indexdb.c               |   30 +-
 src/indexdb.h               |    6 +-
 src/indexdb_hr.c            |   28 +-
 src/indexdbdef.h            |    5 +-
 src/mem.c                   |   62 +-
 src/oligoindex_hr.c         |   21 +-
 src/oligoindex_hr.h         |    9 +-
 src/outbuffer.c             |   88 +-
 src/pair.c                  |  857 ++++++++++----
 src/pair.h                  |   30 +-
 src/popcount.c              |    6 +-
 src/popcount.h              |    5 +-
 src/sam_sort.c              |  304 ++++-
 src/samflags.h              |   27 +-
 src/samheader.c             |   92 +-
 src/samheader.h             |    6 +-
 src/samprint.c              | 2572 +++++++++++++++++++++++++++++-----------
 src/samprint.h              |   15 +-
 src/samread.c               |  356 +++++-
 src/samread.h               |   13 +-
 src/sarray-read.c           | 1137 +++++++++++++-----
 src/sequence.h              |    7 +-
 src/snpindex.c              |   22 +-
 src/splice.c                |  767 +++++++-----
 src/stage1.c                |   23 +-
 src/stage1hr.c              | 2733 ++++++++++++++++++++++++++++---------------
 src/stage1hr.h              |   15 +-
 src/stage2.c                |   39 +-
 src/stage3.c                |  586 ++++------
 src/stage3.h                |   15 +-
 src/stage3hr.c              | 2163 +++++++++++++++++++---------------
 src/stage3hr.h              |   33 +-
 src/substring.c             |  313 +++--
 src/substring.h             |   17 +-
 src/table.c                 |   20 +-
 src/tableuint8.c            |   21 +-
 src/uniqscan.c              |   20 +-
 src/univinterval.c          |   13 +-
 tests/Makefile.in           |    3 +
 util/Makefile.in            |    3 +
 util/gff3_genes.pl.in       |    5 +-
 util/gff3_introns.pl.in     |    5 +-
 util/gff3_splicesites.pl.in |    5 +-
 util/gmap_build.pl.in       |    4 +-
 95 files changed, 10677 insertions(+), 5063 deletions(-)
 delete mode 100644 TODO
 create mode 100755 config/ax_mpi.m4
 delete mode 100644 src/ChangeLog

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