search

ekg / seqwish

alignment to variation graph inducer
MIT License
143 stars 18 forks source link

raised a warning when PAF files have no CIGAR strings #61 #64

Closed AndreaGuarracino closed 4 years ago

AndreaGuarracino commented 4 years ago

In this way users are warned if, for example, they use minimap2 without its -c option.

seqwish -s example.fasta -p example.nocigar.paf:0,example.cigar.paf:0 -g graph.gfa

[seqwish] WARNING: input alignment file example.nocigar.paf does not have CIGAR strings. The resulting graph will only represent the input sequences.

ekg commented 4 years ago

This is good. It will work when none of the records have a cigar. That's probably the most common error case. Checking every alignment might be overkill. Although someone might find a way to make the mistake of mixing alignments with and without cigars. If that happens we can check every record during alignment parsing.