Comments (2)
@mcshane and I think that this is "technically" fine, in that the BAM/SAM spec allows this behavior. However, it is true that it is confusing and may cause problems downstream if tools don't first check if the read is mapped or unmapped before handling it.
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I think we just need to clear out path_pos around here:
Lines 4446 to 4456 in 2e6be77
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