Variant in truth set outside confident region not marked UNK

[anands-repo]

Hello, I had a question about bed file usage - the output from hap.py doesn't conform to my understanding of how the confident region bed file is treated.

I ran hap.py passing the confident region bed file via the -f option.

The following are the relevant lines in the bed file:

18  553162  554090    
18  554191  556182    
18  559076  559227    
18  559371  560092    
18  560204  565232    

As may be seen, the location 557512 is not contained in this bed file, and is separated by more than a thousand bases from another confident region. However, a record in the truth set pertaining to this site isn't marked UNK:
18 557512 . C CAAAAA 50 . BS=557512;Regions=CONF,TS_contained GT:BD:BK:BI:BVT:BLT:QQ 0|1:FN:.:i1_5:INDEL:het:. ./.:.:.:.:NOCALL:nocall:0
This line is taken from ${OUT}.vcf.gz file output by hap.py (please refer to the run command below to see definition of $OUT). In addition, since this location is far removed from the adjacent confident regions in the bed file, it is not easy to see how this may be the product of padding a confident region.

The complete command used is as follows:
python ~/hap.py-install/bin/hap.py $TRUTH $QUERY -f $BED -o $OUT -r $REF

Happy version is Hap.py v0.3.10-2-gfd67904

Thanks for any clarification!

[anands-repo]

Apologies from my side. There was a problem with the bed file being unsorted.

Closing the issue.