VariantEval Error if output file does not pre-exist

[kloot]

Bug Report

Affected tool(s) or class(es)

VariantEval, -O, --output

Affected version(s)

• Latest public release version [4.1.0.0]
• Latest master branch as of [date of test?]

Description

Program starts then terminates with error:
***********************************************************************
A USER ERROR has occurred: Couldn't read file file:///[.....]/X034.eval.grp. Error was: It doesn't exist.
***********************************************************************

Note: The error is not thrown, and VariantEval completes successfully, if a zero-byte file with the name passed with the -o or --output arguments is created before executing VariantEval
For this example: touch X034.eval.grp

Steps to reproduce

Command line:
gatk VariantEval -R $ref -L autosomes.list --eval W034.raw.annotated.vcf.gz --dbsnp dbsnp.vcf.gz -O X034.eval.grp

Expected behavior

Expect the program to create its own output file (as other GATK tools do)

Actual behavior

Terminates with error (above)

---

[cmnbroad]

Yup, thx for the report. Unfortunately our test framework always creates an output file first, so it doesn't catch this. Should be an easy fix.