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 escape-sample-names
branch: escape-sample-names
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1571

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travis-ci

tomkinsc 
sanitize additional fields

previously only sample IDs (and the sample part of library) were
sanitized to be filename-compatible, now sample, library, and run are
all sanitized

4 of 4 new or added lines in 1 file covered. (100.0%)

4077 of 6158 relevant lines covered (66.21%)

1.98 hits per line

Relevant lines Covered
6158 RELEVANT LINES 4077 COVERED LINES
1.98 HITS PER LINE
Source Files on escape-sample-names
Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
1571 escape-sample-names sanitize additional fields previously only sample IDs (and the sample part of library) were sanitized to be filename-compatible, now sample, library, and run are all sanitized push tomkinsc travis-ci pending completion  
1564 escape-sample-names Merge branch 'master' into escape-sample-names push tomkinsc travis-ci pending completion  
1563 escape-sample-names attempting to isolate whether problem is lastal conda package, travis environment, or viral-ngs push tomkinsc travis-ci pending completion  
1562 escape-sample-names specify python for maf-convert, more flexibility on travis python version for conda install version check push tomkinsc travis-ci pending completion  
1561 escape-sample-names added python --version to travis install-pip.sh push tomkinsc travis-ci pending completion  
1558 escape-sample-names Merge branch 'master' into escape-sample-names push tomkinsc travis-ci pending completion  
1554 escape-sample-names declared encoding in test_illumina push tomkinsc travis-ci pending completion  
1552 escape-sample-names fix? push tomkinsc travis-ci pending completion  
1549 escape-sample-names added unicode to samplesheet name test It looks like samtools passes through latin-1 but not utf-8. specified the encoding in samtools.py getHeader() as "latin-1" and we can at least load "Sénégal" now. Added unicode to the test case push tomkinsc travis-ci pending completion  
1546 escape-sample-names added unit test for bad sample names sample names in the sample sheet can contain characters that are illegal in filenames, causing Picard to fail when trying to write files. a sanitization function (util.file.string_to_file_name()) is now applie... push tomkinsc travis-ci pending completion  
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