rust-htslib read_pos

[jblachly]

Do we have an equivalent of this?

https://github.com/rust-bio/rust-htslib/blob/622a0996fee4c03674bfcebd16c3876258c28a5b/src/bam/record.rs#L1999-L2008

[charlesgregory]

In a way getAlignedPairs can be subsetted.

dhtslib/source/dhtslib/sam/record.d

Lines 527 to 531 in 11be3de

	/// get a range of aligned read and reference positions
	/// this is meant to recreate functionality from pysam:
	/// https://pysam.readthedocs.io/en/latest/api.html#pysam.AlignedSegment.get_aligned_pairs
	/// range is 0-based half open using chromosomal coordinates
	auto getAlignedPairs(bool withRefSeq)(long start, long end)

It returns a range of AlignedPairs that contain rpos, qpos, cigar op, query base, and potentially reference base (if MD tag is present).

[jblachly]

Interesting that rust-htslib wrote a long function for this; seems useful. keep in back of your mind.