NAME

       last-split5 - Estimates "split" or "spliced" alignments.

SYNOPSIS

       last-split5-plain [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

       -f, --format=FMT
              output format: MAF, MAF+ (default: depends on input)

       -r, --reverse
              reverse the roles of the 2 sequences in each alignment

       -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=1)

       -s, --score=INT
              minimum alignment score (default=e OR e+t*ln[100])

       -n, --no-split
              write original, not split, alignments

       -b, --bytes=B
              maximum memory (default=8T for split, 8G for spliced)

       -v, --verbose
              be verbose

       -V, --version
              show version information and exit