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GroupReadsByUmi optionally allows inter-contig pairs #648

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merged 2 commits into from
Mar 1, 2021
Merged

GroupReadsByUmi optionally allows inter-contig pairs #648

merged 2 commits into from
Mar 1, 2021

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mjhipp
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@mjhipp mjhipp commented Jan 28, 2021 •
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Closes #634

In order for pairs from different chromosomes to be grouped together, ReadInfo was changed to prioritize the chromosome, and take the lower chromosome of the two reads.

@mjhipp mjhipp marked this pull request as ready for review January 28, 2021 18:56
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mjhipp commented Feb 4, 2021

@nh13 would you rather me make this change optional/experimental?

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nh13 commented Feb 4, 2021

I think an opt-in model would be great, --allow-inter-contig-grouping or some better name than that, but the rest looks great to me!

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mjhipp commented Feb 4, 2021

Thanks @nh13! Updated to make the feature opt-in.

@mjhipp mjhipp changed the title GroupReadsByUmi does not require single contig GroupReadsByUmi optionally allows inter-contig pairs Feb 4, 2021
@mjhipp mjhipp mentioned this pull request Feb 4, 2021
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nh13 requested changes Feb 24, 2021
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I think there's one place where the contig or refIndex wasn't considered, but should be. If you agree, the rest looks good to me.

src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala Outdated Show resolved Hide resolved
src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala Outdated Show resolved Hide resolved
@nh13 nh13 mentioned this pull request Feb 24, 2021
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@mjhipp mjhipp requested a review from nh13 March 1, 2021 19:47
@nh13 nh13 merged commit 1a98c85 into fulcrumgenomics:master Mar 1, 2021
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nh13 commented Mar 1, 2021

Thank-you @mjhipp this is great!

@nh13 nh13 mentioned this pull request Mar 1, 2021
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@mjhipp mjhipp deleted the mh_inter_chrom_group_umi branch March 17, 2021 23:59
@nh13 nh13 mentioned this pull request Aug 19, 2021
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Accepting discordant pairs in GroupReadsByUmi
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@mjhipp @nh13