[med-svn] [gmap] branch upstream updated (11ae4ff -> 88e5821)

[Alex Mestiashvili]

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

      from  11ae4ff   Imported Upstream version 2014-10-22
       new  61cf1e5   Imported Upstream version 2014-11-25
       new  88e5821   Imported Upstream version 2014-12-23

The 2 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 +-
 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 +-
 89 files changed, 10497 insertions(+), 4996 deletions(-)
 delete mode 100644 TODO
 create mode 100755 config/ax_mpi.m4
 delete mode 100644 src/ChangeLog

-- 
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