5
23%
master: 23%

Ran 28 Aug 2018 02:43PM UTC

Files 48

Run time 7s

Badge

Committed 28 Aug 2018 02:20PM UTC coverage: 73.111% (+0.2%) from 72.926%

Job # 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"

Build Type

push

travis-ci

Committed by

web-flow

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

2436 of 4119 branches covered (59.14%)

6849 of 9368 relevant lines covered (73.11%)

0.73 hits per line

Source Files on job 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")

broadinstitute / viral-ngs / 6674 / 5
23%
master: 23%

README BADGES
x

Markdown

Textile

RDoc

HTML

Rst

broadinstitute / viral-ngs / 6674 / 5 23% master: 23%

README BADGES x

Markdown

Textile

RDoc

HTML

Rst

broadinstitute / viral-ngs / 6674 / 5
23%
master: 23%

README BADGES
x