broadinstitute / viral-core
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coverage: 70.6% (+0.1%) from 70.494%
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Merge pull request #158 from broadinstitute/perf-hybrid-v2

Optimize filter_bam_by_ids: 13% faster with samtools pipes + SQLite batching

54 of 65 new or added lines in 1 file covered. (83.08%)

4625 of 6551 relevant lines covered (70.6%)

0.71 hits per line

Relevant lines Covered
6551 RELEVANT LINES 4625 COVERED LINES
0.71 HITS PER LINE
Source Files on master

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Builds Branch Commit Type Ran Committer Via Coverage
20865354925 master Merge pull request #158 from broadinstitute/perf-hybrid-v2 Optimize filter_bam_by_ids: 13% faster with samtools pipes + SQLite batching push web-flow github
70.6
20829376976 master Merge pull request #157 from broadinstitute/dp-bbnorm Add rmdup_bbnorm_bam for alignment-free read deduplication using BBNorm push web-flow github
70.49
20804880677 master Merge pull request #155 from broadinstitute/dp-rmdup Migrate rmdup_cdhit_bam from Picard FastqToSam to samtools import push web-flow github
69.83
20632685309 master Merge pull request #154 from broadinstitute/dp-downsample Fix memory allocation in downsample_bams when processing fewer files than CPUs push web-flow github
69.98
20554313081 master Merge pull request #153 from broadinstitute/dp-fix-mvicuna-error-swallow Fix rmdup_mvicuna_bam silently swallowing mvicuna failures push web-flow github
70.0
20464036027 master Merge pull request #152 from broadinstitute/dp-demux Add metadata output to splitcode_demux_fastqs and make samplesheet optional push web-flow github
70.01
20447147980 master Merge pull request #151 from broadinstitute/dp-demux Add --append_run_id parameter to illumina_metadata command push web-flow github
69.66
20391150536 master Merge pull request #149 from broadinstitute/dp-minimap Add threading to bam2fq_pipe and auto-compression to idxstats output push web-flow github
69.65
20387940973 master Merge pull request #148 from broadinstitute/dp-minimap Add Minimap2.idxstats() with PAF-based streaming for faster read counting push web-flow github
69.79
20231469723 master Merge pull request #143 from broadinstitute/dp-fastq-performance Replace Picard FastqToSam with samtools import for faster FASTQ to BAM conversion push web-flow github
69.34
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