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xa2multi.pl outputs RNEXT w.r.t. original alignment #390

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tsnorri opened this issue Apr 26, 2023 · 1 comment · May be fixed by #391
Open

xa2multi.pl outputs RNEXT w.r.t. original alignment #390

tsnorri opened this issue Apr 26, 2023 · 1 comment · May be fixed by #391

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@tsnorri
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tsnorri commented Apr 26, 2023

If an alignment record has = for RNEXT and the XA tag lists an alternative alignment to some other reference for the segment, then xa2multi.pl will copy the = to the RNEXT field of the record generated for the alternative alignment. To make the new record refer to the next segment as listed in the original record, the value in the RNAME field of the original record should be copied instead unless it matches the RNAME of the new record.
@tsnorri tsnorri linked a pull request Apr 26, 2023 that will close this issue
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@tsnorri
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tsnorri commented Aug 10, 2023

Hello, have you considered merging the PR?

@jmarshall jmarshall mentioned this issue Mar 18, 2024
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Fix RNEXT output in xa2multi.pl tsnorri/bwa
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