[med-svn] [paleomix] 02/07: Updated version 1.2.12 from 'upstream/1.2.12'

[Andreas Tille]

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

tille pushed a commit to branch master
in repository paleomix.

commit 79935296187b3da5d645e09e24a383cb10c97fba
Merge: b96def7 1067366
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 16 09:33:46 2017 +0100

    Updated version 1.2.12 from 'upstream/1.2.12'
    
    with Debian dir 04c7ca6383af2ebab1d25cff94d213d0b2405c83

 .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(-)

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