bedannotator not functional in v1.9.2

[Travis Saari]

Hello,

I'm using FlashFry-assembly-1.9.2, and the bedannotator module seems to be nonfunctional. The only result of using it is the displacement of the last column of data. No annotations are created, and no position transformations occur. I first encountered this using my own dataset, but have since confirmed this to be true following the wiki instructions to the letter:

Here's my commands:

java -Xmx4g -jar FlashFry-assembly-1.9.2.jar discover --database hg19_cas9ngg_database --fasta myc_example.fasta --output myc_example.sites
java -Xmx4g -jar FlashFry-assembly-1.9.2.jar score --input myc_example.sites --output myc_example_sites.scored --scoringMetrics doench2014ontarget,doench2016cfd,dangerous,hsu2013,minot,bedannotator --database hg19_cas9ngg_database --inputAnnotationBed ~/turbo/data-public/databases/ENCODE/wgEncodeBroadHmmGm12878HMM.bed --transformPositions myc_example.bed

#Viewing myc_example_sites.scored shows that the results from the last column, otCount, have been shifted to the right by one column (except for the header). No translations or annotations are apparent.

#Comparing without using bedannotator, can get equivalent files by just reordering the columns
java -Xmx4g -jar FlashFry-assembly-1.9.2.jar score --input myc_example.sites --output myc_example_sites_noannotate.scored --scoringMetrics doench2014ontarget,doench2016cfd,dangerous,hsu2013,minot --database hg19_cas9ngg_database
cut -f1-15,17 myc_example_sites.scored | tail -n +2 > myc_example_sites_2compare.scored
tail -n +2 myc_example_sites_noannotate.scored > myc_example_sites_noannotate_2compare.scored
#After removing the header and shifting the columns, the outputs are now identical
diff myc_example_sites_noannotate_2compare.scored myc_example_sites_2compare.scored

[Aaron McKenna]

Hi twsaari,

sorry about the delay here; I was moving cross-country. I totally messed up the BedAnnotator when I moved over to the new command line argument system. I've fixed and tested this in 1.9.3. I'm just about to update the documentation as well (some things changed at UCSC, so I've checked-in the sample BED files), but let me know if this fixes things for you.

[Aaron McKenna]

I'm going to close this for now unless the update doesn't work for you. Thanks again for trying out FlashFry!