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last-split - 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

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