index out of bounds: the len is 0 but the index is 0'

[hsiehph]

Hey Mitchell,

Here is the error I encountered when I used the following command. I am using rustybam 0.1.29 on linux

$ rustybam liftover --bed <(printf "chrX\t51683493\t51720362\n") chrX.paf | rb invert | rb trim-paf
Processing contig chrX 1/1
thread 'main' panicked at 'index out of bounds: the len is 0 but the index is 0', src/paf.rs:227:25
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

It seems to me it occurs in the function trim-paf when there is no sequence lifted. I am including the paf file so you can reproduce the error yourself.

Thanks,
PingHsun(Benson)

chrX.paf.gz

[adadiehl]

We are having the same issue, with paf alignments generated with minimap2 and GSAlign. We have not manipulated the output files in any way prior to running rb. Error output is identical from releases 0.1.29 and 0.1.30.

[mrvollger]

@adadiehl I think that this commit I just pushed fixes this, can you install from source and test your file.

[adadiehl]

@mrvollger This seems to have resolved our issue. Thank you!