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Lancet changes to sync with other pipelines #374

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merged 1 commit into from
Aug 27, 2020

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bryce-turner
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These are changes I'm confident were made previously, but I don't see anything in the commit history. These changes are required in suncity and coyote, but not as much of an effect in phoenix. However it is a cleaner approach than what we have currently, slightly faster as well.

These are changes I'm confident were made previously, but I don't see anything in the commit history. These changes are required in suncity and coyote, but not as much of an effect in phoenix. However it is a cleaner approach than what we have currently, slightly faster as well.
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Agree this is a better solution, is there any other tool with the same issue of not collecting the contig header lines from the input BAM used for calling?

@PedalheadPHX PedalheadPHX merged commit 11657b1 into master Aug 27, 2020
@bryce-turner bryce-turner deleted the potential-lancet-changes branch August 27, 2020 16:52
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Lancet was the only case as specific as this one. Octopus had similar issues, but applying the reheader along with sorting caused issues in suncity/coyote. However, applying a sort after the concatenation was able to solve the issues in that case.

These octopus changes have already been made across all pipelines. No further pull-requests needed.

@PedalheadPHX PedalheadPHX restored the potential-lancet-changes branch August 27, 2020 17:29
@bryce-turner bryce-turner deleted the potential-lancet-changes branch September 1, 2020 16:15
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2 participants