#45 Non-existant exclude file does not cause program to terminate with non-zero status

[Steve Chervitz]

To reproduce: specify a non-existant file with --exclude.

The issue: vcftools prints an error message to STDOUT about the file problem but exits with a status of 0, making it appear to have executed successfully when it did not. If you are using a --recode option, the recoded VCF does not get created.

Example command:

vcftools_0.1.11/bin/vcftools --vcf data.vcf --out data --recode --exclude ./foo-exclude.txt

Output:

VCFtools - v0.1.11
(C) Adam Auton 2009

Parameters as interpreted:
--vcf data.vcf
--out data
--recode
--exclude ./foo-exclude.txt

Reading Index file.
File contains 332666 entries and 3 individuals.
Applying Required Filters.
Excluding sites by user-supplied list
Error:Could not open SNPs to Exclude file./foo-exclude.txt

[Adam Auton]

Actually appears to be an issue with all reported errors. Will be fixed in the next release.