6
23%
master: 23%

Ran 23 Jan 2018 06:19PM UTC

Files 39

Run time 10min

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Committed 23 Jan 2018 06:05PM UTC coverage: 33.784% (-0.06%) from 33.843%

Job # TRAVIS_JOB=test_snakemake PYTEST_ADDOPTS="-rsxX -n 2 --durations=25 --fixture-durations=10 --junit-xml=pytest.xml --cov-report= --cov broad_utils --cov illumina --cov assembly --cov interhost --cov intrahost --cov metagenomics --cov ncbi --cov read_utils --cov reports --cov taxon_filter --cov tools --cov util" BUNDLE_SECRET=[secure]

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

option in depletion to revert tags in aligned files (#751)

* clear additional attributes when calling RevertSam as part of depletion

The desire is to revert the bam to unaligned state. Tags from
representative bams listed via: samtools view input.bam | cut -f 12- |
tr '\t' '\n' | cut -d ':' -f 1 | awk '{ if(!x[$1]++) { print }}'

* make tag clearing optional, add to deplete_taxa WDL task

* change optional format

the DX web interface does not seem to render a UI element for
Array[String]?

* allow default tags (only pass specified tags if non-zero length

* fix help text for tag list argument

* add default tag list of tags to clear from input bam in RevertBam

* hopefully allow tags_to_clear_space_separated to be passed through

* bugfix for multipart blast database prefix; parallelize mvicuna rmdup by library

* add log statements

* Remove debug line

Run Details

1948 of 5766 relevant lines covered (33.78%)

0.34 hits per line

Source Files on job 5350.6 (TRAVIS_JOB=test_snakemake PYTEST_ADDOPTS="-rsxX -n 2 --durations=25 --fixture-durations=10 --junit-xml=pytest.xml --cov-report= --cov broad_utils --cov illumina --cov assembly --cov interhost --cov intrahost --cov metagenomics --cov ncbi --cov read_utils --cov reports --cov taxon_filter --cov tools --cov util" BUNDLE_SECRET=[secure])

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