[med-svn] [gmap] 02/04: Merge tag 'upstream/2014-10-09'

[Andreas Tille]

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tille pushed a commit to branch master
in repository gmap.

commit 03c34e7545dfdf3ef6705509b6f60a810f205071
Merge: fe772e8 c510225
Author: Andreas Tille <tille at debian.org>
Date:   Sat Oct 11 08:17:18 2014 +0200

    Merge tag 'upstream/2014-10-09'
    
    Upstream version 2014-10-09

 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 ++-
 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 +-
 106 files changed, 19282 insertions(+), 7877 deletions(-)

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