[med-svn] [pbgenomicconsensus] branch upstream updated (da58626 -> 0b4bc9e)
Afif Elghraoui
afif at moszumanska.debian.org
Fri Apr 22 06:40:15 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository pbgenomicconsensus.
from da58626 Imported Upstream version 2.0.0+20151210
new 0b4bc9e Imported Upstream version 2.0.0+20160420
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:
CHANGELOG | 3 +
GenomicConsensus/ResultCollector.py | 6 +-
GenomicConsensus/Worker.py | 8 +-
GenomicConsensus/__init__.py | 2 +-
.../{io/utils.py => algorithmSelection.py} | 49 ++-
GenomicConsensus/{quiver => arrow}/__init__.py | 4 +-
.../{quiver/quiver.py => arrow/arrow.py} | 138 +++----
GenomicConsensus/{quiver => arrow}/diploid.py | 41 +-
GenomicConsensus/{quiver => arrow}/evidence.py | 70 ++--
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/{plurality => poa}/__init__.py | 0
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, 1920 insertions(+), 968 deletions(-)
copy GenomicConsensus/{io/utils.py => algorithmSelection.py} (55%)
copy GenomicConsensus/{quiver => arrow}/__init__.py (96%)
mode change 100644 => 100755
copy GenomicConsensus/{quiver/quiver.py => arrow/arrow.py} (59%)
mode change 100644 => 100755
copy GenomicConsensus/{quiver => arrow}/diploid.py (90%)
mode change 100644 => 100755
copy GenomicConsensus/{quiver => arrow}/evidence.py (74%)
mode change 100644 => 100755
create mode 100755 GenomicConsensus/arrow/model.py
copy GenomicConsensus/{quiver => arrow}/utils.py (63%)
mode change 100644 => 100755
copy GenomicConsensus/{plurality => poa}/__init__.py (100%)
create mode 100644 GenomicConsensus/poa/poa.py
create mode 100755 bin/arrow
mode change 100755 => 100644 bin/gffToBed
create mode 100755 bin/poa
create mode 100644 circle.yml
rename doc/{QuiverFAQ.rst => FAQ.rst} (70%)
create mode 100644 doc/HowTo.rst
delete mode 100644 doc/HowToQuiver.rst
create mode 100644 doc/params-template.xml
create mode 100644 tests/cram/arrow-all4mer.t
create mode 100644 tests/cram/best-all4mer.t
create mode 100644 tests/cram/internal/alignment_summary_scaling.t
create mode 100644 tests/cram/internal/arrow-staph.t
create mode 100644 tests/cram/plurality-all4mer.t
delete mode 100644 tests/cram/plurality-hcv.t
delete mode 100644 tests/cram/plurality-pbcore-lambda.t
create mode 100644 tests/cram/poa-all4mer.t
create mode 100644 tests/cram/quiver-all4mer.t
delete mode 100644 tests/cram/quiver-hcv.t
create mode 100644 tests/data/all4mer/All4mer.V2.01_Insert.fa
create mode 100644 tests/data/all4mer/All4mer.V2.01_Insert.fa.fai
create mode 100644 tests/data/all4mer/README
create mode 100644 tests/data/all4mer/hole-numbers.txt
create mode 100644 tests/data/all4mer/out.aligned_subreads.bam
create mode 100644 tests/data/all4mer/out.aligned_subreads.bam.pbi
create mode 100644 tests/data/sanity/empty.subreads.bam
create mode 100644 tests/data/sanity/empty.subreads.bam.pbi
create mode 100644 tests/data/sanity/mapped.subreads.bam
create mode 100644 tests/data/sanity/mapped.subreads.bam.pbi
create mode 100644 tests/data/sanity/mixed.alignmentset.xml
create mode 100644 tests/unit/test_algorithm_selection.py
create mode 100644 tests/unit/test_summarize_consensus.py
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