[med-svn] [gmap] branch master updated (ba960d9 -> 988d7b7)

[Alex Mestiashvili]

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

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

      from  ba960d9   Upload to unstable
       new  8d06e3b   Repack and compress with xz the source
       new  d5f07a3   Imported Upstream version 2016-05-25
       new  980038f   Merge tag 'upstream/2016-05-25'
       new  80cbd64   Update d/copyright
       new  6dd0b19   Merge copyright stanzas with the same license
       new  872b14e   Update copyright, upload to unstable
       new  ab78374   Add links to binaries for specific CPU instruction sets (ssse4.1 and nosimd)
       new  011f0e2   Override lintian warnings for missing man pages
       new  dc88157   Imported Upstream version 2016-06-03
       new  d2ebf94   Merge tag 'upstream/2016-06-03'
       new  b6a846e   Import new upstream version, update changelog
       new  8ab5509   Imported Upstream version 2016-06-09
       new  a14b749   Merge tag 'upstream/2016-06-09'
       new  e560fae   Import new upstream version, update changelog
       new  90b3af5   Don't run test in parallel
       new  988d7b7   Update changelog, upload to unstable

The 16 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 +-
 debian/changelog                |    17 +
 debian/copyright                |     7 +-
 debian/gmap.lintian-overrides   |     4 +
 debian/rules                    |    10 +-
 debian/watch                    |     1 +
 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 +-
 60 files changed, 41620 insertions(+), 40926 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
 create mode 100644 debian/gmap.lintian-overrides

-- 
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