broadinstitute / viral-ngs / 4264

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travis-ci

Set a threshold on alignment score when generating spike-in reports (#666)

The spike-in reports uses bwa to align reads to spike-in sequences,
but bwa does not set a threshold on alignment score when reporting
alignments given paired-end data. As a result, many spike-ins can
be reported as hits but are false positives (for example, some
spike-in sequences have a polyA tail and reads with a polyA stretch
can map to these spike-in sequences). Setting a threshold on which
alignments are reported alleviates this problem.

5 of 5 new or added lines in 1 file covered. (100.0%)

5300 of 7951 relevant lines covered (66.66%)

1.99 hits per line