VCFFilter fails with segmentation fault when negative values included in filter

Question

VCFFilter fails with segmentation fault when negative values included in filter

Closed this issue 6 years ago · 1 comments

Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1.0

This query works: -g " GL = 1 "

This query fails with a segmentation fault: -g " GL = -1 "

Quoting or escaping problem?

Fatal error: Exit code 139 ()
/galaxy-repl/main/jobdir/XXX/XXX/XXX/tool_script.sh: line 9: 16344 Segmentation fault (core dumped) vcffilter -g " GL = -1 " input1.vcf.gz > "/galaxy-repl/main/files/018/482/dataset_18482698.dat"

cc @galaxyproject/guac

Answer 1 · 2018-07-24T23:05:29.000Z

The tool has been updated to wrapper version 1.0.0_rc1+galaxy1.

The query structure is differs from the prior wrapper, but it works (pos + neg filter).