.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.9.
.TH LAST-PAIR-PROBS.PY "1" "May 2012" "last-pair-probs.py 199" "User Commands"
.SH NAME
last-pair-probs.py \- Read alignments of paired DNA reads to a genome
.SH DESCRIPTION
.SS "Usage:"
.IP
last\-pair\-probs.py \fB\-\-help\fR
last\-pair\-probs.py [options] alignments1 alignments2
.PP
Read alignments of paired DNA reads to a genome, and estimate the probability
that each alignment represents the genomic source of the read.
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-r\fR, \fB\-\-rna\fR
specifies that the reads are from potentially\-spliced
RNA
.TP
\fB\-m\fR M, \fB\-\-mismap\fR=\fIM\fR
don't write alignment pairs with mismap probability >
M (default: 0.01)
.TP
\fB\-f\fR BP, \fB\-\-fraglen\fR=\fIBP\fR
mean fragment length in bp
.TP
\fB\-s\fR BP, \fB\-\-sdev\fR=\fIBP\fR
standard deviation of fragment length
.TP
\fB\-g\fR BP, \fB\-\-genome\fR=\fIBP\fR
haploid genome size in bp
.TP
\fB\-d\fR PROB, \fB\-\-disjoint\fR=\fIPROB\fR
prior probability of disjoint mapping (default: 0.02
if \fB\-r\fR, else 0.01)
.TP
\fB\-c\fR CHROM, \fB\-\-circular\fR=\fICHROM\fR
specifies that chromosome CHROM is circular (default:
chrM)