6674
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Ran 28 Aug 2018 02:34PM UTC

Jobs 2

Files 41

Run time 10min

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Build # 6674

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travis-ci

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Commit Message

add metagenomics.py::filter_bam_to_taxa (#883)

* add metagenomics.py::filter_bam_to_taxa

add the CLI function filter_bam_to_taxa to metagenomics.py (and two basic unit tests). This function filters an input bam file to include only reads that have been mapped to specified taxonomic IDs or scientific names. This requires a classification TSV file, as produced by tools such as Kraken, as well as the NCBI taxonomy database. The column numbers of the tax ID and read ID can be specified, allowing use beyond kraken-format read classification files, however the relationship is assumed to be bijective. Closes #875

* add WDL for filter_bam_to_taxa

* add pre/post read counts as WDL output in filter_bam_to_taxa task

* correction for extract_tarball command

* revisions following code review by @yesimon

* allow WDL task filter_bam_to_taxa to pass --without-children boolean

Run Details

390 of 2647 branches covered (14.73%)

64 of 64 new or added lines in 1 file covered. (100.0%)

2068 of 6421 relevant lines covered (32.21%)

1.03 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
5	6674.5 (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 --cov file_utils")	28 Aug 2018 02:43PM UTC	0	73.11	Travis Job 6674.5
6	6674.6 (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 --cov file_utils")	28 Aug 2018 02:34PM UTC	0	32.21	Travis Job 6674.6

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