[med-svn] samtools branch master updated (2b7a1c6 -> eec880f)

[Andreas Tille]

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tille pushed a change to branch master
in repository samtools.

      from  2b7a1c6   Added references to registries
       new  007dfe0   Switch to default Debian Med repository layout
       new  8abd692   New upstream version 1.6
       new  eec880f   Update upstream source from tag 'upstream/1.6'

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:
 .appveyor.yml                                      |  52 ++
 INSTALL                                            |  36 +
 Makefile                                           |  34 +-
 NEWS                                               |  27 +
 README                                             |   4 +-
 bam.h                                              |   2 +-
 bam_lpileup.c                                      |   1 +
 bam_markdup.c                                      | 844 +++++++++++++++++++++
 bam_mate.c                                         |  50 +-
 bam_plcmd.c                                        |  22 +
 bam_sort.c                                         | 494 +++++++++---
 bamtk.c                                            |  15 +
 bedidx.c                                           |   4 -
 config.h.in                                        |  50 --
 configure.ac                                       |  34 +-
 debian/README.source                               |   4 -
 debian/changelog                                   |   6 +-
 debian/gbp.conf                                    |   6 -
 dict.c                                             |   4 +
 misc/blast2sam.pl                                  |   2 +-
 misc/maq2sam.c                                     |   5 +-
 misc/wgsim.1                                       |   2 +-
 misc/wgsim.c                                       |   6 +-
 padding.c                                          |  31 +-
 phase.c                                            |   1 +
 sam_view.c                                         |  33 +-
 samtools.1                                         |  60 +-
 test/bam2fq/9.1.fq.expected                        |  28 +
 test/bam2fq/9.2.fq.expected                        |  12 +
 test/dat/bam2fq.703.sam                            |  15 +
 .../1_name_sort.expected.sam}                      |   0
 test/markdup/1_name_sort.expected.sam.err          |   1 +
 test/markdup/1_name_sort.sam                       |  18 +
 test/markdup/2_bad_order.expected.sam              |   7 +
 test/markdup/2_bad_order.expected.sam.err          |   1 +
 test/markdup/2_bad_order.sam                       |  19 +
 test/markdup/3_missing_mc.expected.sam             |   2 +
 test/markdup/3_missing_mc.expected.sam.err         |   2 +
 test/markdup/3_missing_mc.sam                      |  18 +
 test/markdup/4_missing_ms.expected.sam             |   2 +
 test/markdup/4_missing_ms.expected.sam.err         |   2 +
 test/markdup/4_missing_ms.sam                      |  18 +
 test/markdup/5_markdup.expected.sam                |  18 +
 test/markdup/5_markdup.sam                         |  18 +
 test/markdup/6_remove_dups.expected.sam            |  12 +
 test/markdup/6_remove_dups.sam                     |  18 +
 test/merge/tag.pg.merge.expected.sam               |  24 +-
 test/mpileup/regression.sh                         |   3 +-
 test/test.pl                                       | 237 ++++--
 version.sh                                         |  13 +
 50 files changed, 1990 insertions(+), 327 deletions(-)
 create mode 100644 .appveyor.yml
 create mode 100644 bam_markdup.c
 delete mode 100644 config.h.in
 delete mode 100644 debian/README.source
 create mode 100644 test/bam2fq/9.1.fq.expected
 create mode 100644 test/bam2fq/9.2.fq.expected
 create mode 100644 test/dat/bam2fq.703.sam
 copy test/{addrprg/1_fixup.sam.expected.err => markdup/1_name_sort.expected.sam} (100%)
 create mode 100644 test/markdup/1_name_sort.expected.sam.err
 create mode 100644 test/markdup/1_name_sort.sam
 create mode 100644 test/markdup/2_bad_order.expected.sam
 create mode 100644 test/markdup/2_bad_order.expected.sam.err
 create mode 100644 test/markdup/2_bad_order.sam
 create mode 100644 test/markdup/3_missing_mc.expected.sam
 create mode 100644 test/markdup/3_missing_mc.expected.sam.err
 create mode 100644 test/markdup/3_missing_mc.sam
 create mode 100644 test/markdup/4_missing_ms.expected.sam
 create mode 100644 test/markdup/4_missing_ms.expected.sam.err
 create mode 100644 test/markdup/4_missing_ms.sam
 create mode 100644 test/markdup/5_markdup.expected.sam
 create mode 100644 test/markdup/5_markdup.sam
 create mode 100644 test/markdup/6_remove_dups.expected.sam
 create mode 100644 test/markdup/6_remove_dups.sam
 create mode 100755 version.sh

-- 
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