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Option to store the alignments in a non-temporary file #27

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eclarke opened this issue Sep 9, 2015 · 2 comments
Open

Option to store the alignments in a non-temporary file #27

eclarke opened this issue Sep 9, 2015 · 2 comments

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@eclarke
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eclarke commented Sep 9, 2015

The alignments could be useful for downstream debugging. Could there be an option to save the bwa/bowtie SAM file?
@anatolydryga
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i find it useful too. The only one requirement is use BAM not SAM
it saves order of magnitude of disk space

@anatolydryga
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@kylebittinger maybe add --debug option to save all of the intermediate files

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@eclarke @anatolydryga