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Ran 05 Dec 2016 09:25PM UTC

Files 41

Run time 22s

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Committed 05 Dec 2016 09:07PM UTC coverage: 72.165% (+0.02%) from 72.141%

Job # 3296.2

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

remove reads with leading or trailing indels prior to V-Phaser2 (#537)

* add SamtoolsTool.filterByCigarString(); filter v-phaser input to remove leading and trailing indels

Add a function, filterByCigarString(), that uses two samtools processes
to filter a bam file based on a regex applied to each aligned read’s
cigar string. The initial use case (included in this commit) is to
remove reads with leading and trailing indels, which would otherwise
cause v-phaser2 to crash. A unit test is also added for
SamtoolsTool.filterByCigarString().

* remove leading_or_trailing_indels_removed bam file

remove leading_or_trailing_indels_removed bam file after it is no
longer needed

* remove expected sam output file, do not redirect stderr to stdout

remove expected sam output file, do not redirect stderr to stdout

Coverage Stats

5512 of 7638 relevant lines covered (72.17%)

0.72 hits per line

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master: 23%

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