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broadinstitute / viral-ngs / 3296
23%

Build:
DEFAULT BRANCH: master
Ran 05 Dec 2016 09:21PM UTC
Jobs 3
Files 41
Run time 6min
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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

5527 of 7638 relevant lines covered (72.36%)

2.16 hits per line

Jobs
ID Job ID Ran Files Coverage
1 3296.1 05 Dec 2016 09:21PM UTC 0
71.77
Travis Job 3296.1
2 3296.2 05 Dec 2016 09:25PM UTC 0
72.17
Travis Job 3296.2
3 3296.3 05 Dec 2016 09:28PM UTC 0
71.76
Travis Job 3296.3
Source Files on build 3296
Detailed source file information is not available for this build.
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