terminate called after throwing an instance of 'std::invalid_argument'

[tseemann]

using 1.1 and htslib 1.10.2

% ivar trim -i ivar.bam -b nCoV-2019.scheme.bed -p out

terminate called after throwing an instance of 'std::invalid_argument'
 what():  stoi
Aborted (core dumped)

Maybe it's the BED:

% cut -f1-3 nCoV-2019.scheme.bed > new.bed

ivar trim -i ivar.bam -b nww.bed -p out
Number of references: 1
Reference Name: MN908947
Reference Length: 29903
Using Region: MN908947
Sorted By Coordinate
Sorted By Query Name
Segmentation fault (core dumped)

Any ideas?

[tseemann]

via @drpowell

I think the reason it does on your original bed is because a score is expected in col 5 which you don't have
https://github.com/andersen-lab/ivar/blob/master/src/primer_bed.cpp#L88
(and a strand in col 6)

[tseemann]

See also artic-network/artic-ncov2019#12

[gkarthik]

I think that is the source of the error. I use the BED format from here - https://genome.ucsc.edu/FAQ/FAQformat.html#format1.

The order I followed is,

chrom, chromStart,chromEnd, name, score, strand

It seems to match the default 6 column BED format generated by bedtools bamtobed. I assumed that order was standard (maybe I'm in the wrong there?).

This issue does bring up the lack of checks while reading the BED file. I'll get on it :).

[tseemann]

Yes it seems @scalene has produced invalid BED files.
Some robustness in ivar would be appreciated however :-)

[gkarthik]

Closed #13