gff3-ffetch segfaults

[pjotrp]

wget ftp://ftp.wormbase.org/pub/wormbase/species/celegans/sequence/genomic/c elegans.WS232.genomic.fa.gz wget ftp://ftp.wormbase.org/pub/wormbase/species/celegans/sequence/genomic/c elegans.WS232.genomic.fa.gz gzip -d *.gz

gff3-ffetch mRNA c_elegans.WS232.annotations.gff3 c_elegans.WS232.genomic.fa Segmentation fault

[lomereiter]

(one of Pjotr's links must be ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/gff/c_elegans.WS232.annotations.gff3.gz)

I think I've found where the issue comes from. First, Pjotr did specify files in the wrong order, and gff3-ffetch didn't even notice whereas it clearly states in usage information that FASTA should come first. So what happens is the following:

• gff3-ffetch tries to get FASTA from the end of first file
• there's no FASTA at the end of the file, and get_fasta_range() returns null
• however, if we look back at bio/gff3/conv/fasta.d, we see that the result is not checked for null, and property all is accessed. Here's where the segfault is likely to occur. (I haven't checked, though.)

[mamarjan]

Thanks Artem, I'll fix that right away.