[med-svn] samtools branch debian/unstable updated (ae32134 -> 7f525ad)

[Andreas Tille]

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

tille pushed a change to branch debian/unstable
in repository samtools.

      from  ae32134   Close bug, upload to unstable
      adds  8a06c51   New upstream version 1.5
       new  5eef358   Updated version 1.5 from '1.5'
       new  1655d1e   New upstream version
       new  3092088   debhelper 10
       new  d52cd13   Standards-Version: 4.0.0 (no changes needed)
       new  3c0ec5c   Bump versioned Build-Depends: libhts-dev (>= 1.5)
       new  d3b6113   Add recommends to cwl-tool and fix shebang line of cwl scripts
       new  7f525ad   Do not warn about cwl-runner , upload to unstable

The 7 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:
 .gitattributes                                     |  13 -
 .gitignore                                         |  26 --
 .travis.yml                                        |  40 ---
 .travis/clone                                      |  14 -
 Makefile                                           |   3 +-
 NEWS                                               |  15 +
 README                                             |  15 +-
 README.md                                          |  32 --
 bam.h                                              |   2 +-
 bam_sort.c                                         | 237 +++++++++++---
 debian/changelog                                   |  10 +
 debian/compat                                      |   2 +-
 debian/control                                     |   9 +-
 debian/rules                                       |   2 +-
 debian/samtools-faidx.cwl                          |   2 +-
 debian/samtools-index.cwl                          |   2 +-
 debian/samtools-rmdup.cwl                          |   2 +-
 debian/samtools-sort.cwl                           |   2 +-
 debian/samtools-view.cwl                           |   2 +-
 debian/samtools.lintian-overrides                  |   8 +-
 examples/.gitignore                                |   9 -
 misc/wgsim.1                                       |   2 +-
 sam_view.c                                         | 342 ++++++++++++++++-----
 samtools.1                                         |  78 ++++-
 test/bam2fq/6.1.fq.expected                        |  68 ++++
 test/bam2fq/6.2.fq.expected                        |  68 ++++
 test/bam2fq/6.s.fq.expected                        |   8 +
 test/bam2fq/7.1.fq.expected                        |  68 ++++
 test/bam2fq/7.2.fq.expected                        |  68 ++++
 test/bam2fq/7.s.fq.expected                        |   8 +
 test/bam2fq/{4.1.fq.expected => 8.1.fq.expected}   |   6 +-
 test/bam2fq/{4.2.fq.expected => 8.2.fq.expected}   |   6 +-
 test/bam2fq/8.i.fq.expected                        |  12 +
 test/bam2fq/{4.s.fq.expected => 8.s.fq.expected}   |   0
 test/dat/.gitignore                                |   2 -
 test/dat/bam2fq.005.sam                            |   2 +-
 .../dat/{test_input_1_b.sam => test_input_1_d.sam} |  24 +-
 test/merge/.gitignore                              |   5 -
 .../tag.pg.merge.expected.sam}                     |  29 +-
 .../tag.pg.n.merge.expected.sam}                   |  32 +-
 test/mpileup/.gitignore                            |  12 -
 .../name.sort.expected.sam}                        |   8 +-
 .../pos.sort.expected.sam}                         |   2 +-
 .../tag.as.sort.expected.sam}                      |  26 +-
 .../tag.fi.sort.expected.sam}                      |  26 +-
 .../tag.rg.n.sort.expected.sam}                    |  16 +-
 .../tag.rg.sort.expected.sam}                      |  16 +-
 test/split/.gitignore                              |   4 -
 test/test.pl                                       |  38 +++
 49 files changed, 1028 insertions(+), 395 deletions(-)
 delete mode 100644 .gitattributes
 delete mode 100644 .gitignore
 delete mode 100644 .travis.yml
 delete mode 100755 .travis/clone
 delete mode 100644 README.md
 delete mode 100644 examples/.gitignore
 create mode 100644 test/bam2fq/6.1.fq.expected
 create mode 100644 test/bam2fq/6.2.fq.expected
 create mode 100644 test/bam2fq/6.s.fq.expected
 create mode 100644 test/bam2fq/7.1.fq.expected
 create mode 100644 test/bam2fq/7.2.fq.expected
 create mode 100644 test/bam2fq/7.s.fq.expected
 copy test/bam2fq/{4.1.fq.expected => 8.1.fq.expected} (89%)
 copy test/bam2fq/{4.2.fq.expected => 8.2.fq.expected} (89%)
 create mode 100644 test/bam2fq/8.i.fq.expected
 copy test/bam2fq/{4.s.fq.expected => 8.s.fq.expected} (100%)
 delete mode 100644 test/dat/.gitignore
 copy test/dat/{test_input_1_b.sam => test_input_1_d.sam} (57%)
 delete mode 100644 test/merge/.gitignore
 copy test/{dat/test_input_1_b.sam => merge/tag.pg.merge.expected.sam} (50%)
 copy test/{dat/test_input_1_c.sam => merge/tag.pg.n.merge.expected.sam} (50%)
 delete mode 100644 test/mpileup/.gitignore
 copy test/{dat/test_input_1_a.sam => sort/name.sort.expected.sam} (98%)
 copy test/{dat/test_input_1_a.sam => sort/pos.sort.expected.sam} (98%)
 copy test/{dat/test_input_1_b.sam => sort/tag.as.sort.expected.sam} (56%)
 copy test/{dat/test_input_1_b.sam => sort/tag.fi.sort.expected.sam} (56%)
 copy test/{dat/test_input_1_a.sam => sort/tag.rg.n.sort.expected.sam} (98%)
 copy test/{dat/test_input_1_a.sam => sort/tag.rg.sort.expected.sam} (98%)
 delete mode 100644 test/split/.gitignore

-- 
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