bedtools fails to read CRAM 3.1 files produced by HTSlib ≥1.22 #1137
Description
Description
bedtools fails to read CRAM files produced by HTSlib 1.22 or later, which now defaults to CRAM version 3.1 output.
Error Message
bedtools merge -i example.cram
Error: line number 1 of file example.cram has 1 fields, but 0 were expected.
Similar errors occur with other bedtools commands that accept BAM/CRAM input.
Root Cause
As noted in the https://github.com/samtools/htslib/releases/tag/1.22:
Note this release changes the default output CRAM version from 3.0 to 3.1. HTSlib and SAMtools have been able to read CRAM 3.1 since version 1.12, however other tools may not yet be able to cope.
CRAM 3.1 has been readable by HTSlib since version 1.12 (released 2021), but bedtools appears to not support it yet.