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samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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EdgeReadIterator (used in Picard's CollectWgsMetrics) doesn't handle intervals correctly #1615

Closed michaelgatzen closed 1 year ago

michaelgatzen commented 2 years ago

When running Picard's CollectWgsMetrics with an IntervalList, only the start and end coordinates of the first interval in that list are considered. This can be traced back to a bug in EdgeReadIterator and AbstractLocusInfo.

michaelgatzen commented 2 years ago

I can't assign this to myself because I'm not a contributor, but I'm working on this issue.

lbergelson commented 1 year ago

closed by #1616