[med-svn] [sambamba] 03/04: Merge tag 'upstream/0.6.6'

[Andreas Tille]

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tille pushed a commit to branch master
in repository sambamba.

commit 54cf2bb916fc8e7a51138b55ad433bee89d3f50d
Merge: 5cdcdc7 7d9214a
Author: Andreas Tille <tille at debian.org>
Date:   Sun Mar 5 13:11:54 2017 +0100

    Merge tag 'upstream/0.6.6'
    
    Upstream version 0.6.6

 .gitignore                                    |   2 +
 .test_suite.sh                                |   7 +-
 .travis.yml                                   |  12 ++-
 Makefile                                      |  37 +++++--
 Makefile.guix                                 |  83 +++++++++++++++
 README.md                                     |  65 +++++++++---
 bioconda_push.sh                              |  14 +++
 bioconda_yaml_gen.py                          |   3 +-
 cram/reader.d                                 |   5 +-
 cram/wrappers.d                               |  28 ++---
 cram/writer.d                                 |   4 +-
 gen_ldc_version_info.py                       |  22 ++++
 main.d                                        |  13 +++
 man/README.md                                 |  18 ++++
 man/sambamba-index.1                          |  24 ++---
 man/sambamba-index.1.ronn                     |  10 +-
 sambamba-ldmd-debug.rsp                       |   2 +-
 sambamba-ldmd-release.rsp                     |   2 +-
 sambamba/depth.d                              |   4 +-
 sambamba/index.d                              |   2 +-
 sambamba/markdup.d                            |   2 +-
 sambamba/merge.d                              |   4 +-
 sambamba/pileup.d                             | 142 +++++++++++++++-----------
 sambamba/slice.d                              |  30 +++---
 sambamba/sort.d                               |  18 ++--
 sambamba/utils/common/bed.d                   |   5 +-
 sambamba/utils/common/file.d                  |   4 +-
 sambamba/utils/common/filtering.d             |  35 +++++--
 sambamba/utils/view/alignmentrangeprocessor.d |   8 +-
 sambamba/view.d                               |  22 ++++
 utils/lz4.d                                   |   4 +-
 utils/strip_bcf_header.d                      |   2 +-
 utils/version_.d                              |   2 +-
 33 files changed, 451 insertions(+), 184 deletions(-)

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