broadinstitute / viral-ngs
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master: 23%

LAST BUILD BRANCH: ct-krakenuniq-summary-kmer-filter
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LAST BUILD ON BRANCH ct-multialign
branch: ct-multialign
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travis-ci

tomkinsc 
changed string interpolation back to % syntax since the logging module doesn't support format-style {} substitutions

3 of 3 new or added lines in 1 file covered. (100.0%)

2745 of 4697 relevant lines covered (58.44%)

1.16 hits per line

Relevant lines Covered
4697 RELEVANT LINES 2745 COVERED LINES
1.16 HITS PER LINE
Source Files on ct-multialign
Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
1044 ct-multialign changed string interpolation back to % syntax since the logging module doesn't support format-style {} substitutions push tomkinsc travis-ci pending completion  
1042 ct-multialign Merge branch 'ct-multialign' of https://github.com/broadinstitute/viral-ngs into ct-multialign push dpark01 travis-ci pending completion  
1041 ct-multialign commented out threads parameter from GATK tool since IndelRealigner does not yet support parallel execution push tomkinsc travis-ci pending completion  
1038 ct-multialign typecasting of thread count to int in gatk and trinity tools push tomkinsc travis-ci pending completion  
1036 ct-multialign moved NCBI fetching tests from unit/ to integration/ Since the NCBI-fetching tests hit a third-party API, there is a chance that they will fail when the server is down. The NCBI fetching functions themselves are straightforward, so the tests are ... push tomkinsc travis-ci pending completion  
1034 ct-multialign removed debug statements, changed ncbi.py author line push tomkinsc travis-ci pending completion  
1028 ct-multialign The optional argument --threads can now be specified for a few more of the tools, and is passed through to the tools used under the hood. In the snakemake rules, the number of cores is similarly specified for rules calling the modified tools, in t... push tomkinsc travis-ci pending completion  
1027 ct-multialign accession parsing function in intrahost.py has been adjusted to be more flexible, used by merge_to_vcf(). old alt allele-related code block in parse_ann has been fully removed (was previously commented out) added lines to UGER cluster-submitter.p... push tomkinsc travis-ci pending completion  
1026 ct-multialign changed UGER queues from short to long where they were previously four-hour short queues on LSF (UGER short is two nours, and things were timing out) push tomkinsc travis-ci pending completion  
1025 ct-multialign fixed annot_transfer snakemake rule, changed lastal_db build so accession file is now optional in config file (defaults to reference accessions), changed job script to import virtual env push tomkinsc travis-ci pending completion  
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