Closed jelber2 closed 2 years ago
Hi @jelber2,
thank's for notifying about this. I was able to reproduce this behavior and will have at look at it.
I found the bug which should be fixed in PR https://github.com/rust-bio/rust-bio-tools/pull/241.
The error did not occur due to soft clips but due to empty sequences set by minimap2.
Applying the -Y
causes minimap2 to annotate the full sequence to each record which is why the subcommand worked fine.
Nevertheless, this should be fixed in the next release of rust-bio-tools.
thanks @FelixMoelder!
Hi,
For the sequence in the link below aligned to the reference in the link below, bam-anonymize throws an error that I guess means there is no soft clipping for a supplementary alignment when using minimap2. My suggestion might be to produce an error message that might suggest turning on soft clipping for supplementary alignments in the aligner if the goal is to output all sequences from the BAM file later (i.e., I would not suggest changing bam-anonymize to ignore such a sequence).
get sequence and reference
map read to reference with minimap2 without the
-Y
option-Y use soft clipping for supplementary alignments
run bam-anonymize - returns error
map read to reference with minimap2 with the
-Y
optionrun bam-anonymize - runs without error using
-Y
with minimap2Rust-Bio-Tools version