Hey Brad, I saw you had made a commit for GATK 1.3 compatibility, so I installed it and tried to run the tests. Unfortunately the test test_3_empty_fastq gets stuck on a call to GATK. Specifically
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.3-14-g348f2db):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Bad input: Could not find any usable data in the input BAM file(s).
##### ERROR ------------------------------------------------------------------------------------------
The test passes when using GATK 1.2, I think this is due to this point in the changelog:
We now throw an exception when there is no data instead of creating an empty csv file.
Valentine;
Thanks for reporting this. I just pushed fixes that will check for empty files and avoid this issue. Let me know if you run into any other problems.
Hey Brad, I saw you had made a commit for GATK 1.3 compatibility, so I installed it and tried to run the tests. Unfortunately the test
test_3_empty_fastq
gets stuck on a call to GATK. Specificallywill give the error
The test passes when using GATK 1.2, I think this is due to this point in the changelog: