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tgen / pegasusPipe

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vcfMerger and mergeVcfAlleleCount #10

Closed tgenahmet closed 7 years ago

tgenahmet commented 7 years ago

@denriquez @PedalheadPHX let me know what you guys think. I'm a little confused by this.

1)vcfMerger 2)mergeVcfAlleleCount If you look at lines 334, 343, and 351 in pbs script 2) you'll see it references pbs script 1).

For example: mv ${MERGERDIR}/${BASENAME}.vcfMergerInQueue ${MERGERDIR}/${BASENAME}.vcfMergerFail I think it should say: mv ${MERGERDIR}/${BASENAME}.vcfMergerACInQueue ${MERGERDIR}/${BASENAME}.vcfMergerACFail

tgenahmet commented 7 years ago

@denriquez @PedalheadPHX I want to make this fix. I'm pretty sure mergeVcfAlleleCount runs after vcfMerger and thus should not be marking the previous job (vcfMerger) as pass or fail. See my code fix above.

denriquez commented 7 years ago

I believe you are correct that definitely looks like a bug in the AC pbs script. That code fix looks right. I looked over those scripts and the shell scripts and I even can't believe we haven't encountered any serious problems with this.