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broadinstitute / viral-ngs / 5350
23%

Build:
DEFAULT BRANCH: master
Ran 23 Jan 2018 06:19PM UTC
Jobs 2
Files 45
Run time 13min
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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

49 of 49 new or added lines in 2 files covered. (100.0%)

6064 of 8549 relevant lines covered (70.93%)

0.94 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
2
100.0
read_utils.py
5
100.0
taxon_filter.py
Jobs
ID Job ID Ran Files Coverage
5 5350.5 (TRAVIS_JOB=test_py36 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]) 23 Jan 2018 06:25PM UTC 0
70.87
Travis Job 5350.5
6 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]) 23 Jan 2018 06:19PM UTC 0
33.78
Travis Job 5350.6
Source Files on build 5350
Detailed source file information is not available for this build.
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