[med-svn] [gmap] 03/16: Merge tag 'upstream/2016-05-25'

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository gmap.

commit 980038f989f77e911202b3c489573e6ebfe6014c
Merge: 8d06e3b d5f07a3
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu May 26 09:58:42 2016 +0200

    Merge tag 'upstream/2016-05-25'
    
    Upstream version 2016-05-25

 ChangeLog                       |    49 +
 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                |   263 -
 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                       | 22352 ++++++++-------------
 configure.ac                    |    80 +-
 src/Makefile.am                 |    52 +-
 src/Makefile.in                 | 41106 +++++++++++++++++++-------------------
 src/config.h.in                 |    19 +-
 src/cpuid.c                     |    22 +-
 src/dynprog_simd.c              |    70 +-
 src/gmap.c                      |    43 +-
 src/gsnap.c                     |     8 +-
 src/iit-read-univ.c             |     4 +-
 src/pair.c                      |     8 +-
 src/stage1hr.c                  |     8 +-
 src/stage2.c                    |     6 +-
 src/stage3.c                    |    54 +-
 src/stage3.h                    |     4 +-
 src/stage3hr.c                  |     3 +-
 src/uniqscan.c                  |     6 +-
 tests/Makefile.in               |   593 +-
 util/Makefile.in                |   176 +-
 45 files changed, 41072 insertions(+), 40614 deletions(-)

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