SamUtils PairOrientation is confusingly ambiguous about paired reads needing to map to the same contig #1709
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…) pertains only to reads on the same contig. - Now getPairOrientation will throw an exception if thrown when the two reads are mapped to different contigs - Added tests to verify that the exception is thrown in the 4 cases specified.
lbergelson
reviewed
Jul 2, 2024
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@yfarjoun There's a typo. This seems like a good improvement otherwise though. Does this require corresponding changes in Picard to avoid hitting the new error case?
An alternate solution would be to add a new state that captures cross chromosome pairs.
| * @return PairOrientation of the given SAMRecord. | ||
| * @throws IllegalArgumentException If the record is not a paired read, or | ||
| * one or both reads are unmapped. | ||
| * one or both reads are unmapped, or is the two records do are not mapped to the |
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typo here: "or is the two records do are not"
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