Set MAPQ=0 for secondary alignments

ksahlin / strobealign

Aligns short reads using dynamic seed size with strobemers

MIT License

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Closed marcelm closed 6 months ago

marcelm commented 6 months ago

This follows recomended best practice: "No alignments should be assigned mapping quality 255." according to the SAM specification.

Using MAPQ=0 follows what BWA-MEM does for secondary alignments.

Closes #212

ksahlin commented 6 months ago

Approved.