Change how markdup looks for single reads.#2119
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Due to changes to fixmate in 1.21 markdup no longer recognised single reads that would have normally have been part of a pair. This change adds a function to look for unset (-1 in bam1_t) mate reference (RNEXT) and mate position (PNEXT) to indicate the missing part of a pair.
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Due to changes to fixmate in 1.21 markdup no longer recognised single reads that would have normally have been part of a pair. This change adds a function to look for unset (-1 in bam1_t) mate reference (RNEXT) and mate position (PNEXT) to indicate the missing part of a pair.
There are other samtools commands that use the paired flag. We should probably review them.
Fixes #2117.