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Ran 28 Mar 2020 12:06AM UTC

Files 43

Run time 3s

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Committed 28 Mar 2020 12:01AM UTC coverage: 23.262%. Remained the same

Job # CACHE_DIR="$HOME/misc_cache" MINICONDA_DIR="$HOME/miniconda" PIP_DIR="$HOME/virtualenv" GATK_PATH="$CACHE_DIR" PYTHONIOENCODING=UTF8 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 kmer_utils --cov reports --cov taxon_filter --cov tools --cov util --cov file_utils" DOCKER_REGISTRY="quay.io" DOCKER_REPO_PROD="quay.io/broadinstitute/viral-ngs" DOCKER_REPO_DEV="quay.io/broadinstitute/viral-ngs-dev" DOCKER_REGISTRY_MIRROR="docker.io" DOCKER_REPO_PROD_MIRROR="broadinstitute/viral-ngs" BOTO_CONFIG=/dev/null _JAVA_OPTIONS="-Xmx3g" TRAVIS_JOB=test_snakemake

Build Type

Pull #1008

travis-ci-com

Committed by

web-flow

Commit Message

Update read_utils.py

The old mvicuna post-processing code expects read IDs to have a /1 mate suffix, and only includes those that do, which single-end reads do not have (nor interleaved fastqs, but that's a separate issue and we're generating the fastqs for this internal function ourselves so interleaving should not be an issue). So no single-end IDs were preserved. This ensures single-end read IDs make it through this post-processing.

Pull Request Pull Request #1008: do not discard read IDs for single-end reads after running mvicuna

Run Details

309 of 2707 branches covered (11.41%)

1452 of 6242 relevant lines covered (23.26%)

0.23 hits per line

Source Files on job 1225.5 (CACHE_DIR="$HOME/misc_cache" MINICONDA_DIR="$HOME/miniconda" PIP_DIR="$HOME/virtualenv" GATK_PATH="$CACHE_DIR" PYTHONIOENCODING=UTF8 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 kmer_utils --cov reports --cov taxon_filter --cov tools --cov util --cov file_utils" DOCKER_REGISTRY="quay.io" DOCKER_REPO_PROD="quay.io/broadinstitute/viral-ngs" DOCKER_REPO_DEV="quay.io/broadinstitute/viral-ngs-dev" DOCKER_REGISTRY_MIRROR="docker.io" DOCKER_REPO_PROD_MIRROR="broadinstitute/viral-ngs" BOTO_CONFIG=/dev/null _JAVA_OPTIONS="-Xmx3g" TRAVIS_JOB=test_snakemake)

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