broadinstitute / viral-ngs / 5432 / 5
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coverage: 70.791% (-0.1%) from 70.923%
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]

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add bwa depletion (#762)

* refactor deplete to rename 'deplete_human' to 'deplete', preserving the old name for compatibility

* upgrade picard 2.9.0->2.13, biopython 1.68-1.70, PyYAML 3.11->3.12

* add deplete_bwa_bam() and associated functions, refactor taxon_filter.py

deplete_bwa_bam has been added to taxon_filter.py. Database
extracting/building has been refactored to reduce code duplication in
depletion methods for bwa/blast/bmtagger. In a few places touched by
these changes, lines to create and remove temp files have been replaced
with the util.file.tempfname() context manager

* tempdir as part of extract_build_or_use_database yield

* update test_taxon_filter args

* update test_taxon_filter.py expected output to include bwa and revert bams

* update taxon_filter.wdl to include bwa depletion

* added missing line for bwaDbs to taxon_filter wdl

* add bwaDbs to hs_deplete Snakefile, reorder arg in taxon_filter.py to reflect output file ordering

* remove JVMmemory and chunksize from deplete_bwa and parser

* cruft removal

* refactor threads in Bwa() tool to use newer util.misc.sanitize_thread_count()

* threads rework

* let's try removing a call to Picard SortSam that seems redundant

* have bwa mem write to the outBam directly rather than a temp file

* restore SortSamTool call, add boolean to skip samtools-based sort if specified (sort by default, but not in the case where align_mem_one_rg does it via Picard

* bugfix bwa mem

* remove extra SortSam call

6088 of 8600 relevant lines covered (70.79%)

0.71 hits per line

Source Files on job 5432.5 (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])