[med-svn] [sambamba] branch master updated (69a3a58 -> f519b7d)

[Andreas Tille]

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

tille pushed a change to branch master
in repository sambamba.

      from  69a3a58   replace rdmd
       new  5cdcdc7   Try some patches to build with Debian tools
       new  7d9214a   New upstream version 0.6.6
       new  54cf2bb   Merge tag 'upstream/0.6.6'
       new  f519b7d   Update to upstream version 0.6.6

The 4 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 +-
 debian/changelog                              |   2 +-
 debian/control                                |   1 +
 debian/patches/guix_makefile.patch            |  86 ++++++++++++++++
 debian/patches/series                         |   3 +-
 debian/patches/use_debian_packaged_libs.patch |  56 +++++++---
 debian/rules                                  |   5 +-
 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 +-
 39 files changed, 588 insertions(+), 200 deletions(-)
 create mode 100644 Makefile.guix
 create mode 100644 bioconda_push.sh
 create mode 100644 debian/patches/guix_makefile.patch
 create mode 100755 gen_ldc_version_info.py
 create mode 100644 man/README.md

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sambamba.git