Extracting reads overlapping zero-length intervals works on CRAM but not on BAM when -M is set

[acorvelo]

samtools 1.20
htslib 1.20
Linux 3.10.0-1160.71.1.el7.x86_64

Hi,
in samtools view, I'm getting an error when using a BED file containing zero-length intervals (for instance representing the reference span of an insertion) specified by the option -L and using the multi-region iterator -M to extract reads from BAM.

Error:

[E::hts_itr_regions] Failed to create the multi-region iterator!
samtools view: Iterator could not be created. Aborting.

Command:
samtools view -M -L intervals.bed ${BAM}

Example intervals.bed:

chr1	1000000	1000000

The same command works as intended on CRAM. It would be great to have it also working for BAM so that the workflows that depend on it work regardless of the input format.

Thanks!

[whitwham]

Yes, beginning and end being the same point is handled differently in the BAM and CRAM code. Making them the same should be straightforward.