.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH LAST-SPLIT "1" "February 2023" "last-split 1447" "User Commands"
.SH NAME
last-split \- Estimates "split" or "spliced" alignments.
.SH SYNOPSIS
.B last-split-plain
[\fI\,options\/\fR] \fI\,LAST-alignments.maf\/\fR
.SH 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.
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-f\fR, \fB\-\-format\fR=\fI\,FMT\/\fR
output format: MAF, MAF+
.TP
\fB\-r\fR, \fB\-\-reverse\fR
reverse the roles of the 2 sequences in each alignment
.TP
\fB\-g\fR, \fB\-\-genome\fR=\fI\,NAME\/\fR
lastdb genome name
.TP
\fB\-d\fR, \fB\-\-direction\fR=\fI\,D\/\fR
RNA direction: 0=reverse, 1=forward, 2=mixed (default: 1)
.TP
\fB\-c\fR, \fB\-\-cis\fR=\fI\,PROB\/\fR
cis\-splice probability per base (default: 0.004)
.TP
\fB\-t\fR, \fB\-\-trans\fR=\fI\,PROB\/\fR
trans\-splice probability per base (default: 1e\-05)
.TP
\fB\-M\fR, \fB\-\-mean\fR=\fI\,MEAN\/\fR
mean of ln[intron length] (default: 7.0)
.TP
\fB\-S\fR, \fB\-\-sdev\fR=\fI\,SDEV\/\fR
standard deviation of ln[intron length] (default: 1.7)
.TP
\fB\-m\fR, \fB\-\-mismap\fR=\fI\,PROB\/\fR
maximum mismap probability (default: 1.0)
.TP
\fB\-s\fR, \fB\-\-score\fR=\fI\,INT\/\fR
minimum alignment score (default: e OR e+t*ln[100])
.TP
\fB\-n\fR, \fB\-\-no\-split\fR
write original, not split, alignments
.TP
\fB\-b\fR, \fB\-\-bytes\fR=\fI\,B\/\fR
maximum memory (default: 8T for split, 8G for spliced)
.TP
\fB\-v\fR, \fB\-\-verbose\fR
be verbose
.TP
\fB\-V\fR, \fB\-\-version\fR
show version information and exit