Multiple crashes when using convert2bed

[hongxuchen]

When feeding convert2bed with some crafted files, it may abort or cause segfault. Details can be seen from gdb.

Aborted                 ./convert2bed -i gvf -o bed --do-not-sort < c00.gvf > /dev/null
Aborted                 ./convert2bed -i gvf -o bed --do-not-sort < c01.gvf > /dev/null
Aborted                 ./convert2bed -i gff -o bed --do-not-sort < c00.gff > /dev/null
Aborted                 ./convert2bed -i gtf -o bed --do-not-sort < c00.gtf > /dev/null
Segmentation fault      ./convert2bed -i rmsk -o bed --do-not-sort < c00.out > /dev/null
Aborted                 ./convert2bed -i wig -o bed --do-not-sort < c00.wig > /dev/null
Aborted                 ./convert2bed -i wig -o bed --do-not-sort < c01.wig > /dev/null

Proof-of-Crash files are attached.
bedops-report.zip

[alexpreynolds]

Thanks, I'll look into what I can do to test for malformed input for a subsequent version. I do make some assumptions that the input follows specification.

I'll keep this open for now — depending on what my bandwidth allows, there might be fixes in the next version.

[alexpreynolds]

Patches in commit 727d981 for GVF, GFF, GTF, Wiggle and RepeatMasker conversion on malformed inputs.