[med-svn] [gmap] branch upstream updated (4645328 -> c510225)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository gmap.

      from  4645328   Imported Upstream version 2014-07-28
       new  c510225   Imported Upstream version 2014-10-09

The 1 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 ++-
 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 +-
 106 files changed, 19282 insertions(+), 7877 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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