[med-svn] samtools 03/03: Update upstream source from tag 'upstream/1.6'

[Andreas Tille]

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tille pushed a commit to branch master
in repository samtools.

commit eec880f99beffff8a1771c41f9fbc77e6b03285c
Merge: 007dfe0 8abd692
Author: Andreas Tille <tille at debian.org>
Date:   Mon Dec 11 15:19:04 2017 +0100

    Update upstream source from tag 'upstream/1.6'
    
    Update to upstream version '1.6'
    with Debian dir 290d6313b34baaaab2f22325cf86f755d204ed21

 .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 +-
 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 +
 test/markdup/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 +
 47 files changed, 1985 insertions(+), 316 deletions(-)

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