[med-svn] [gmap] branch master updated (fe772e8 -> c4b4665)

[Andreas Tille]

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

tille pushed a change to branch master
in repository gmap.

      from  fe772e8   push to unstable d/*.1: updated man pages
       new  c510225   Imported Upstream version 2014-10-09
       new  03c34e7   Merge tag 'upstream/2014-10-09'
       new  73b2377   New upstream version
       new  c4b4665   DEP5 fix

The 4 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             |  466 +++++
 INSTALL               |  200 ++-
 Makefile.in           |  212 ++-
 README                |   20 +-
 VERSION               |    2 +-
 aclocal.m4            |  304 ++--
 config/ax_ext.m4      |  418 +++--
 config/builtin.m4     |    9 +
 config/compile        |   21 +-
 config/config.guess   |  287 ++-
 config/config.sub     |   91 +-
 config/depcomp        |   87 +-
 config/install-sh     |    5 +-
 config/libtool.m4     |    5 +-
 config/ltmain.sh      |   16 +-
 config/ltversion.m4   |   10 +-
 config/missing        |   49 +-
 configure             | 4721 ++++++++++++++++++++++++++++++++++++-------------
 configure.ac          |  206 ++-
 debian/changelog      |    8 +
 debian/control        |   10 +-
 debian/copyright      |    6 +-
 NEWS => src/ChangeLog |    0
 src/Makefile.am       |   41 +-
 src/Makefile.in       | 3386 +++++++++++++++++++----------------
 src/boyer-moore.c     |   97 +-
 src/boyer-moore.h     |    6 +-
 src/chimera.c         |   39 +-
 src/chimera.h         |    4 +-
 src/chrnum.h          |    7 +-
 src/config.h.in       |   10 +-
 src/diag.c            |   83 +-
 src/doublelist.c      |   17 +-
 src/doublelist.h      |    4 +-
 src/dynprog.c         |   11 +-
 src/dynprog_cdna.c    |   65 +-
 src/dynprog_end.c     |   64 +-
 src/dynprog_genome.c  |  238 ++-
 src/dynprog_simd.c    |   35 +-
 src/dynprog_single.c  |   49 +-
 src/genome.c          |   70 +-
 src/genome.h          |   10 +-
 src/genome128_hr.c    |  159 +-
 src/genome_sites.c    |    3 +-
 src/genomicpos.h      |    6 +-
 src/get-genome.c      |    2 +-
 src/gmap.c            |  220 ++-
 src/gmapindex.c       |  108 +-
 src/gregion.c         |   84 +-
 src/gregion.h         |    4 +-
 src/gsnap.c           |  263 ++-
 src/iit-read-univ.c   |   21 +-
 src/iit-read-univ.h   |    8 +-
 src/indel.c           |   29 +-
 src/intlist.c         |   74 +-
 src/intlist.h         |   14 +-
 src/list.c            |   69 +-
 src/list.h            |    7 +-
 src/mapq.c            |    8 +-
 src/mem.c             |  382 ++--
 src/mem.h             |   71 +-
 src/oligo.c           |   19 +-
 src/oligoindex_hr.c   |   34 +-
 src/outbuffer.c       |  201 ++-
 src/outbuffer.h       |    8 +-
 src/pair.c            |  704 ++++++--
 src/pair.h            |   45 +-
 src/pairpool.c        |  140 +-
 src/pairpool.h        |    6 +-
 src/parserange.c      |   41 +-
 src/sam_sort.c        | 1422 +++++++++++++++
 src/samflags.h        |    3 +-
 src/samheader.c       |   97 +-
 src/samheader.h       |    6 +-
 src/samprint.c        | 1444 ++++++++-------
 src/samprint.h        |   14 +-
 src/samread.c         | 1467 +++++++++++++++
 src/samread.h         |   37 +
 src/sarray-read.c     |  575 +++++-
 src/shortread.c       |  401 +++--
 src/shortread.h       |   15 +-
 src/smooth.c          |   78 +-
 src/spanningelt.c     |  141 +-
 src/spanningelt.h     |   17 +-
 src/splice.c          |  185 +-
 src/splicetrie.c      |   46 +-
 src/stage1.c          |  168 +-
 src/stage1hr.c        | 1155 +++++++-----
 src/stage1hr.h        |    8 +-
 src/stage2.c          | 3290 ++++++++++++++++++++--------------
 src/stage2.h          |   17 +-
 src/stage3.c          |  210 +--
 src/stage3.h          |    4 +-
 src/stage3hr.c        | 1225 +++++++++----
 src/stage3hr.h        |   20 +-
 src/substring.c       |  638 ++++++-
 src/substring.h       |   20 +-
 src/types.h           |   10 +-
 src/uint8list.c       |   31 +-
 src/uint8list.h       |   10 +-
 src/uintlist.c        |   32 +-
 src/uintlist.h        |   10 +-
 src/uinttable.c       |   22 +-
 src/uinttable.h       |    4 +-
 src/uniqscan.c        |   21 +-
 tests/Makefile.in     |  100 +-
 util/Makefile.in      |  108 +-
 util/gmap_build.pl.in |   11 +-
 util/gvf_iit.pl.in    |    2 +-
 109 files changed, 19298 insertions(+), 7885 deletions(-)
 copy NEWS => src/ChangeLog (100%)
 create mode 100644 src/sam_sort.c
 create mode 100644 src/samread.c
 create mode 100644 src/samread.h

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