Fix small bug when extracting read type from bowtie2 #154
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…t indexes the first element. To fix this, we can grep for all columns with 'YT:Z:' which should only capture the column that we're interested in.
Adding changelog
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@harmonbhasin have you confirmed the samples that were previously failing now run to completion? |
@willbradshaw the pipelline is still running, but yes, the reads don't fail on that step anymore. |
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Updated the regex for a grep such that we don't pull out the wrong column from SAM files.