Output lines lost in guidescan enumerate for no matches/mismatches
vineetbansal opened this issue · 1 comments
vineetbansal commented
In the case of 0 matches and 0 mismatches, guidescan enumerate --format csv
fails to produce any output line corresponding to the kmer. guidescan enumerate --format sam
produces a line, but it is truncated and does not have all expected columns.
For example, the kmer file:
id,sequence,pam,chromosome,position,sense
GCTAACCCAACGTAGCGACT_1,GCTAACCCAACGTAGCGACT,NGG,unknown,0,+
processed against hg38.index
produces the sam line:
GCTAACCCAACGTAGCGACT_1 0 unknown 0 100 23M * 0 0 GCTAACCCAACGTAGCGACTNGG *
This is the case regardless of --mode succinct
or --mode complete
.
The desired behavior is to still produce the output line with the appropriate values so it is not simply "lost" in processing.
This was tested in guidescan v2.1.6
vineetbansal commented
What should be the specificity value in this case?