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SamUtils PairOrientation is confusingly ambiguous about paired reads needing to map to the same contig #1709

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SamUtils PairOrientation is confusingly ambiguous about paired reads needing to map to the same contig #1709

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Commits on May 15, 2024

  1. - Improved documentation to clarify that PairOrientation (in SamUtils… 

    …) 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.
    @yfarjoun
    yfarjoun committed May 15, 2024
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