[med-svn] [gmap] branch master updated (34b2012 -> 1ff23e8)

[Alex Mestiashvili]

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

      from  34b2012   Update changelog, upload to unstable
       new  d49f40e   New upstream version 2016-11-07
       new  68da9c1   Merge tag 'upstream/2016-11-07'
       new  6450796   Refresh only-do-cpuid-on-amd64-i386.patch
       new  1ff23e8   Update changelog, upload to unstable

The 4 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                                        |  57 +++
 VERSION                                          |   2 +-
 configure                                        |  24 +-
 debian/changelog                                 |   7 +
 debian/patches/only-do-cpuid-on-amd64-i386.patch |   6 +-
 src/bitpack64-access.c                           |  38 +-
 src/bitpack64-incr.c                             |  36 +-
 src/bitpack64-read.c                             | 247 ++++++-----
 src/bitpack64-read.h                             |   3 +
 src/bitpack64-readtwo.c                          |  50 ++-
 src/bitpack64-write.c                            | 144 +++----
 src/cpuid.c                                      |  26 +-
 src/cpuid.h                                      |   5 +-
 src/gmap.c                                       |  10 +-
 src/gmap_select.c                                |   4 +-
 src/gmapl_select.c                               |   4 +-
 src/gsnap.c                                      |   4 +-
 src/gsnap_select.c                               |   4 +-
 src/gsnapl_select.c                              |   4 +-
 src/indexdb-write.c                              |  17 +-
 src/indexdb.c                                    |   3 +-
 src/pair.c                                       | 496 ++++++++++++++++++++++-
 src/pair.h                                       |   4 +-
 src/sam_sort.c                                   |  28 +-
 src/samprint.c                                   | 482 ++++++++++++++++++----
 src/stage1hr.c                                   |   5 +-
 src/stage3hr.c                                   |  33 +-
 src/stage3hr.h                                   |   4 +-
 src/substring.c                                  |  22 +-
 src/substring.h                                  |   5 +-
 src/uniqscan.c                                   |   4 +-
 31 files changed, 1414 insertions(+), 364 deletions(-)

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