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MarkIlluminaAdapters - why does it only accept query-sorted BAM files?
Hi, MarkIlluminaAdapters only accepts query-sorted BAM files. This limitation shouldn't exist because there are many times where one might want to analyze a coordinate sorted BAM file for Illumina adapter content. There's no reason the exact same code couldn't run on any sorted or unsorted BAM. Illumina adapters are analyzed one read at a time...