Ensure samtools sort call on the UR flag keeps paired-end reads together

BimberLab / nimble

nimble — execute lightweight, flexible alignments on arbitrary reference libraries

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Ensure samtools sort call on the UR flag keeps paired-end reads together #55

Closed hextraza closed 1 year ago

hextraza commented 2 years ago

Another option would be to rewrite the paired-end parser for the .bam file process module to use the first_in_pair and second_in_pair flags instead of parsing positionally, at a cost of efficiency

bbimber commented 2 years ago

Can you ask samtools to sort on both UR and read name?