Set samtools wrapper to use mpileup instead of pileup. #35
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Added an error check to the genome coverage function. I considered changing the script file in the mapping pipeline that calls the genome coverage function to run samtools but thought it best to use the sam module. If you want me to add mpileup to the samtools wrapper then I'm happy to do that otherwise I'm happy with the current fix. |
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Identical (cherry-picked) commits just merged into develop. Closing pull request. |
andrewjpage
referenced
this pull request
in andrewjpage/vr-codebase
Nov 22, 2011
Fix to fastq import - delete bams after fastq gzipped.
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I've set the samtools wrapper to run mpileup instead of pileup.
Pileup has been removed from samtools so anything trying to use the wrapper to run samtools pileup on a recent version of samtools will fail.
So saying, I suspect the only thing using the wrapper to run pileup is the genome coverage option in the mapping pipeline. And I'm planning to fix the genome coverage option next week.