[med-svn] [sambamba] branch upstream updated (0056226 -> 7d9214a)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository sambamba.

      from  0056226   New upstream version 0.6.5
       new  7d9214a   New upstream version 0.6.6

The 1 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:
 .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(-)
 create mode 100644 Makefile.guix
 create mode 100644 bioconda_push.sh
 create mode 100755 gen_ldc_version_info.py
 create mode 100644 man/README.md

-- 
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