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FLAG 256 vs 272 in SAM files
Hi, I would like to understand the difference between the FLAG "256" and "272" in SAM files. I understood that they are both involved in "secondary alignments" (https://github.com/lh3/minimap2/issues/4). However, I could not understand the difference between the two. Is the FLAG "272" a secondary alignment in the reverse orientation? If not, is there a way to know if the secondary alignment is in the reverse orientation compared to the reference?
By the way, I think flagging secondary alignments is a great feature.