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zeeev / wham

Structural variant detection and association testing
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WHAM taking too long to run #36

Closed abolia closed 8 years ago

abolia commented 8 years ago

Hi Zev,

Sorry for re-posting this. I posted it on a closed issue so re-posting this.

" I am trying to run WHAM for some single end data. But its been more than 10 hours and it still says "INFO: gathering stats for each bam file." I have already removed this https://github.com/zeeev/wham/blob/master/src/bin/multi-wham-testing.cpp#L622 so it does not throw out error and is still running. Moreover, there are only 84 @SQ tags in the header file and its a pretty small BAM file with about ~ 71000 reads.

Do you think it might be coz its single end data. Please let me know.

Thank you for all your help. "

Thanks, Ashini

zeeev commented 8 years ago

WHAM was designed for paired end data.

abolia commented 8 years ago

Okay, got you. Thanks.

Ashini