[med-svn] [paleomix] branch upstream updated (346af03 -> 1067366)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository paleomix.

      from  346af03   New upstream version 1.2.7
       new  1067366   New upstream version 1.2.12

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 +
 CHANGES.md                                      | 109 +++++-
 INSTALL.rst                                     |   4 +
 README.rst                                      |  16 +-
 docs/bam_pipeline/requirements.rst              |   6 +-
 docs/conf.py                                    |  28 +-
 docs/index.rst                                  |  14 +-
 docs/yaml.rst                                   | 164 ++++++++-
 docs/zonkey_pipeline/index.rst                  |  11 +-
 paleomix/__init__.py                            |   2 +-
 paleomix/atomiccmd/builder.py                   |  81 +++--
 paleomix/atomiccmd/command.py                   |   8 +-
 paleomix/atomiccmd/pprint.py                    | 102 +++---
 paleomix/common/formats/fasta.py                |  16 +-
 paleomix/common/makefile.py                     |  20 ++
 paleomix/common/testing.py                      |   6 +-
 paleomix/common/vcffilter.py                    |   3 +-
 paleomix/common/vcfwrap.py                      |  15 +-
 paleomix/common/versions.py                     |  77 +++--
 paleomix/main.py                                |   4 +
 paleomix/node.py                                | 100 +++---
 paleomix/nodes/bowtie2.py                       |  31 +-
 paleomix/nodes/bwa.py                           |  41 +--
 paleomix/nodes/commands.py                      |  73 ++--
 paleomix/nodes/mapdamage.py                     |  38 +-
 paleomix/nodes/picard.py                        | 233 ++++++-------
 paleomix/nodes/samtools.py                      |  27 +-
 paleomix/nodes/validation.py                    | 252 ++++++++------
 paleomix/pipeline.py                            |   4 +-
 paleomix/tools/bam_pipeline/makefile.py         | 105 +++---
 paleomix/tools/bam_pipeline/mkfile.py           |   6 +-
 paleomix/tools/bam_pipeline/nodes.py            |  73 ++--
 paleomix/tools/bam_pipeline/parts/lane.py       |   9 +-
 paleomix/tools/bam_pipeline/parts/library.py    |  40 ++-
 paleomix/tools/bam_pipeline/parts/prefix.py     | 102 ++++--
 paleomix/tools/bam_pipeline/parts/statistics.py |  20 +-
 paleomix/tools/bam_pipeline/pipeline.py         |  46 ++-
 paleomix/tools/bam_stats/common.py              |   2 +-
 paleomix/tools/cleanup.py                       |  42 ++-
 paleomix/tools/dupcheck.py                      |  93 +++++
 paleomix/tools/rmdup_collapsed.py               | 315 ++++++++++-------
 paleomix/tools/zonkey/config.py                 |  18 +-
 paleomix/tools/zonkey/pipeline.py               |  17 +-
 paleomix/ui.py                                  |  10 +-
 setup.py                                        |   2 +-
 tests/.coveragerc                               |  11 +
 tests/README.md                                 |   4 +
 tests/atomiccmd_test/builder_test.py            |  75 +++-
 tests/atomiccmd_test/command_test.py            | 213 +++++++-----
 tests/atomiccmd_test/pprint_test.py             | 439 ++++++++++++++----------
 tests/atomiccmd_test/sets_test.py               |  18 +-
 tests/common_tests/fileutils_test.py            |  10 +-
 tests/common_tests/makefile_test.py             | 216 ++++++++++--
 tests/common_tests/versions_tests.py            | 118 +++++--
 tests/run                                       |  27 --
 tests/setup.sh                                  |  15 +
 tox.ini                                         |   4 +-
 57 files changed, 2286 insertions(+), 1251 deletions(-)
 create mode 100644 INSTALL.rst
 create mode 100644 paleomix/tools/dupcheck.py
 create mode 100644 tests/.coveragerc
 create mode 100644 tests/README.md
 delete mode 100755 tests/run
 create mode 100755 tests/setup.sh

-- 
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