[med-svn] [gmap] branch upstream updated (04146bd -> 8ab5509)

[Alex Mestiashvili]

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

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

      from  04146bd   Imported Upstream version 2016-05-01
       new  d5f07a3   Imported Upstream version 2016-05-25
       new  dc88157   Imported Upstream version 2016-06-03
       new  8ab5509   Imported Upstream version 2016-06-09

The 3 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                       |    88 +
 INSTALL                         |    19 +-
 Makefile.in                     |   420 +-
 VERSION                         |     2 +-
 acinclude.m4                    |     7 +-
 aclocal.m4                      |   740 +-
 config/asm-bsr.m4               |     2 +-
 config/ax_cpuid_intel.m4        |    51 +
 config/ax_cpuid_non_intel.m4    |   156 +
 config/ax_ext.m4                |   273 +-
 config/ax_gcc_x86_avx_xgetbv.m4 |    79 -
 config/ax_gcc_x86_cpuid.m4      |    79 -
 config/builtin-popcount.m4      |    67 +
 config/compile                  |   232 +-
 config/config.guess             |   564 +-
 config/config.sub               |   306 +-
 config/depcomp                  |   531 +-
 config/install-sh               |   385 +-
 config/libtool.m4               |  4187 ++--
 config/ltmain.sh                |  8139 +++++---
 config/ltoptions.m4             |   147 +-
 config/ltsugar.m4               |     7 +-
 config/ltversion.m4             |    14 +-
 config/lt~obsolete.m4           |    17 +-
 config/missing                  |   461 +-
 config/test-driver              |   148 +
 configure                       | 22362 ++++++++------------
 configure.ac                    |    80 +-
 src/Makefile.am                 |    62 +-
 src/Makefile.in                 | 41374 +++++++++++++++++++-------------------
 src/config.h.in                 |    19 +-
 src/cpuid.c                     |    54 +-
 src/dynprog_simd.c              |    70 +-
 src/gmap.c                      |    43 +-
 src/gmap_select.c               |    22 +-
 src/gmapl_select.c              |    22 +-
 src/gsnap.c                     |     8 +-
 src/gsnap_select.c              |    22 +-
 src/gsnapl_select.c             |    22 +-
 src/iit-read-univ.c             |     4 +-
 src/indexdb.c                   |    17 +-
 src/pair.c                      |     8 +-
 src/sam_sort.c                  |     5 +-
 src/sarray-read.c               |    10 +-
 src/splice.c                    |    87 +-
 src/splicetrie.c                |     4 +-
 src/stage1hr.c                  |   188 +-
 src/stage2.c                    |     6 +-
 src/stage3.c                    |    56 +-
 src/stage3.h                    |     4 +-
 src/stage3hr.c                  |    54 +-
 src/stage3hr.h                  |     8 +-
 src/uniqscan.c                  |     6 +-
 tests/Makefile.in               |   593 +-
 util/Makefile.in                |   176 +-
 55 files changed, 41588 insertions(+), 40919 deletions(-)
 create mode 100644 config/ax_cpuid_intel.m4
 create mode 100644 config/ax_cpuid_non_intel.m4
 delete mode 100644 config/ax_gcc_x86_avx_xgetbv.m4
 delete mode 100644 config/ax_gcc_x86_cpuid.m4
 create mode 100644 config/builtin-popcount.m4
 mode change 100755 => 100644 config/ltmain.sh
 create mode 100755 config/test-driver

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