Feature Request: Conversion from BioAlignments to SAM.Record

[MillironX]

Previously seen on Slack

It would be great if there was some way to convert an alignment into a SAM/BAM.Record so that it could be exported to the filesystem for future use. Note that I will only refer to SAM.Record from here on, but the same would be expected for BAM.Record, along the lines of #25.

Expected Behavior

Ideally, this would simply be a new method for the SAM.Record constructor. Something like

XAM.SAM.Record(aln::PairwiseAlignment, kwargs...)

There would need to be other information (possibly with defaults?) added, as a SAM.Record contains more fields than

Current Behavior

There is no such behavior.

Possible Solution / Implementation

The challenge here is that SAM.Records store more information than PairwiseAlignments. Here's a map of what I think could be inferred vs. what needs to be passed as an argument.

Column	Field name	PairwiseAlignment accessor	Possible default
1	QNAME	N/A	N/A
2	FLAG	N/A*	N/A
3	RNAME	N/A	N/A
4	POS	N/A	1**
5	MAPQ	unknown	255
6	CIGAR	cigar(aln.a.aln)	N/A
7	RNEXT	N/A	N/A***
8	PNEXT	N/A	N/A***
9	TLEN	length(aln.a.seq)	N/A
10	SEQ	aln.a.seq	N/A
11	QUAL	N/A	"*"
12	NM****	count_mismatches(aln)	N/A

Notes

*

It might be possible to compute some of the flags based on the sequence, but I don't know how to do so.

**

In my experience, BioAlignments.cigar generates an alignment that always starts at position 1, and then pads it with deletions.

***

These fields are context-sensitive. Maybe generating records should be stateful 🤷?

****

Technically, the Number of Mismatches field is optional, but it is included in the recommended practices, and some tools fail if it isn't included.

Context

I was working on generating very specific alignments for variant calling purposes, and found that I couldn't export the result to another tool. Having this functionality would remedy that.