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
In the case of 0 matches and 0 mismatches,
guidescan enumerate --format csvfails to produce any output line corresponding to the kmer.guidescan enumerate --format samproduces a line, but it is truncated and does not have all expected columns.For example, the kmer file:
processed against
hg38.indexproduces the sam line:This is the case regardless of
--mode succinctor--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