Annotate vcf with no records #5
Description
Hello- It seems that CAVA throws an exception if the input VCF file has no records. This is what I get:
cava.py -i in.vcf -c cava.config
-----------------------------------------------------------------------
CAVA (Clinical Annotation of VAriants) v1.2.2 is now running.
Started: 2017-08-14 09:25:16.991644
Configuration file: cava.config
Input file (VCF): in.vcf
Output file (VCF): output.vcf
Log file: output.log
Input file contains 0 records to annotate.
Traceback (most recent call last):
File "/home/db291g/applications/cava/CAVA/cava.py", line 420, in <module>
breaks = findFileBreaks(copts.input, copts.threads)
File "/home/db291g/applications/cava/CAVA/cava.py", line 134, in findFileBreaks
delta = int((counter - first + 1) / threads)
UnboundLocalError: local variable 'first' referenced before assignment
I think a vcf with no records is a legitimate input so I fixed this on my local copy by adding this check just after https://github.com/RahmanTeam/CAVA/blob/master/cava.py#L416 :
if numOfRecords == 0:
sys.stderr.write('Done. Nothing to be annotated.\n')
sys.exit(0)
In this way cava writes out the VCF header and exits clean.
Maybe it should be fixed in the master as well?