[med-svn] [pbgenomicconsensus] 02/05: Merge tag 'upstream/2.0.0+20160420'

[Afif Elghraoui]

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

afif pushed a commit to branch master
in repository pbgenomicconsensus.

commit 98fc374214e738969070df70dde085f20990e144
Merge: 1a935ba 0b4bc9e
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Thu Apr 21 23:05:18 2016 -0700

    Merge tag 'upstream/2.0.0+20160420'
    
    Upstream version 2.0.0+20160420

 CHANGELOG                                          |   3 +
 GenomicConsensus/ResultCollector.py                |   6 +-
 GenomicConsensus/Worker.py                         |   8 +-
 GenomicConsensus/__init__.py                       |   2 +-
 .../{__init__.py => algorithmSelection.py}         |  43 ++-
 GenomicConsensus/{ => arrow}/__init__.py           |   6 +-
 .../{quiver/quiver.py => arrow/arrow.py}           | 138 +++----
 GenomicConsensus/arrow/diploid.py                  | 223 +++++++++++
 GenomicConsensus/arrow/evidence.py                 | 173 +++++++++
 GenomicConsensus/arrow/model.py                    | 109 ++++++
 GenomicConsensus/{quiver => arrow}/utils.py        | 232 ++++++------
 GenomicConsensus/consensus.py                      |  12 +
 GenomicConsensus/main.py                           | 125 ++++---
 GenomicConsensus/options.py                        |  81 ++--
 GenomicConsensus/plurality/plurality.py            |   4 +-
 GenomicConsensus/{ => poa}/__init__.py             |   1 -
 GenomicConsensus/poa/poa.py                        | 413 +++++++++++++++++++++
 GenomicConsensus/quiver/model.py                   |  10 +-
 GenomicConsensus/quiver/quiver.py                  |  21 +-
 GenomicConsensus/quiver/utils.py                   |  44 +--
 GenomicConsensus/reference.py                      |  52 +--
 GenomicConsensus/utils.py                          |  40 +-
 GenomicConsensus/windows.py                        |   3 +
 README.md                                          |  59 ++-
 bin/arrow                                          |   2 +
 bin/gffToBed                                       |  15 +-
 bin/gffToVcf                                       |  17 +-
 bin/poa                                            |   2 +
 bin/summarizeConsensus                             | 130 +++----
 circle.yml                                         |  31 ++
 doc/{QuiverFAQ.rst => FAQ.rst}                     | 174 +++++----
 doc/HowTo.rst                                      | 128 +++++++
 doc/HowToQuiver.rst                                | 161 --------
 doc/VariantCallerFunctionalSpecification.rst       |   9 +-
 doc/params-template.xml                            |  51 +++
 setup.py                                           |  11 +-
 tests/cram/arrow-all4mer.t                         |  38 ++
 tests/cram/bad_input.t                             |   6 +
 tests/cram/best-all4mer.t                          |  23 ++
 tests/cram/internal/alignment_summary_scaling.t    |  25 ++
 tests/cram/internal/arrow-staph.t                  |  32 ++
 tests/cram/internal/quiver-compatibility.t         |   3 +-
 tests/cram/internal/quiver-ecoli.t                 |   2 +-
 tests/cram/internal/quiver-eichler-bac.t           |   2 +-
 tests/cram/internal/quiver-fluidigm-amplicons.t    |   2 +-
 tests/cram/internal/quiver-mruber.t                |  12 +-
 .../internal/quiver-tinyLambda-coverage-islands.t  |   2 -
 tests/cram/plurality-all4mer.t                     |  37 ++
 tests/cram/plurality-hcv.t                         |  55 ---
 tests/cram/plurality-pbcore-lambda.t               |  17 -
 tests/cram/poa-all4mer.t                           |  37 ++
 tests/cram/quiver-all4mer.t                        |  37 ++
 tests/cram/quiver-hcv.t                            |  66 ----
 tests/cram/version.t                               |   2 +-
 tests/data/all4mer/All4mer.V2.01_Insert.fa         |   5 +
 tests/data/all4mer/All4mer.V2.01_Insert.fa.fai     |   1 +
 tests/data/all4mer/README                          |   5 +
 tests/data/all4mer/hole-numbers.txt                |  14 +
 tests/data/all4mer/out.aligned_subreads.bam        | Bin 0 -> 559393 bytes
 tests/data/all4mer/out.aligned_subreads.bam.pbi    | Bin 0 -> 9926 bytes
 tests/data/sanity/empty.subreads.bam               | Bin 0 -> 728 bytes
 tests/data/sanity/empty.subreads.bam.pbi           | Bin 0 -> 67 bytes
 tests/data/sanity/mapped.subreads.bam              | Bin 0 -> 3334 bytes
 tests/data/sanity/mapped.subreads.bam.pbi          | Bin 0 -> 127 bytes
 tests/data/sanity/mixed.alignmentset.xml           |  19 +
 tests/unit/AlignmentHitStubs.py                    |  32 +-
 tests/unit/test_algorithm_selection.py             |  14 +
 tests/unit/test_quiver.py                          |  48 +++
 tests/unit/test_summarize_consensus.py             |  78 ++++
 tests/unit/test_tool_contract.py                   |  17 +-
 70 files changed, 2268 insertions(+), 902 deletions(-)

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