3296
23%

Ran 05 Dec 2016 09:21PM UTC

Jobs 3

Files 41

Run time 6min

Badge

Embed ▾

pending completion

Build # 3296

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

5527 of 7638 relevant lines covered (72.36%)

2.16 hits per line

Jobs

ID	Job ID	Ran	Coverage
1	3296.1	05 Dec 2016 09:21PM UTC	71.77	Travis Job 3296.1
2	3296.2	05 Dec 2016 09:25PM UTC	72.17	Travis Job 3296.2
3	3296.3	05 Dec 2016 09:28PM UTC	71.76	Travis Job 3296.3

Source Files on build 3296

Detailed source file information is not available for this build.

broadinstitute / viral-ngs / 3296
23%

README BADGES
x

Markdown

Textile

RDoc

HTML

Rst

Jobs

Source Files on build 3296

broadinstitute / viral-ngs / 3296 23%

README BADGES x

Markdown

Textile

RDoc

HTML

Rst

Jobs

Source Files on build 3296

broadinstitute / viral-ngs / 3296
23%

README BADGES
x