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The groupBy on readname usually works, but sometimes people put a /1,/2 or _1/_2 suffix on the reads for first/second of pair, so you'll want to look out for that.
Actually, the slowness of the FASTQ upload was one of my motivations for doing the cs-bwamem refactor with Fragment!
Question: How to get paired-end alignemntRecord like RDD[AlignmentRecord, AlignmentRecord]?
I want to use it to read mapping.
I try loadPairedFastq and loadFastq:
But it only get AlignmentRecordRDD or RDD[AlignmentRecord], I cann't get paired reads.
Ask for help, thanks, please.
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