Estimates "split" or "spliced" alignments.
last-split [\,options\/] \,LAST-alignments.maf\/
Read alignments of query sequences to a genome, and estimate the genomic source of each part of each query, allowing different parts of one query to come from different parts of the genome.
-h, --help
show this help message and exit
-g, --genome=\,NAME\/
lastdb genome name
-d, --direction=\,D\/
RNA direction: 0=reverse, 1=forward, 2=mixed (default=1)
-c, --cis=\,PROB\/
cis-splice probability per base (default=0.004)
-t, --trans=\,PROB\/
trans-splice probability per base (default=1e-05)
-M, --mean=\,MEAN\/
mean of ln[intron length] (default=7)
-S, --sdev=\,SDEV\/
standard deviation of ln[intron length] (default=1.7)
-m, --mismap=\,PROB\/
maximum mismap probability (default=0.01)
-s, --score=\,INT\/
minimum alignment score (default=e OR e+t*ln[1000])
-n, --no-split
write original, not split, alignments
-v, --verbose
be verbose
-V, --version
show version information and exit