SYNOPSIS

last-split [,options/] ,LAST-alignments.maf/

DESCRIPTION

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.

OPTIONS

-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