.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
.TH SGA-BAM2DE "1" "December 2019" "sga-bam2de 0.10.15" "User Commands"
.SH NAME
sga-bam2de \- Make a distance estimate file from a bam file of reads aligned to contigs
.SH DESCRIPTION
sga\-bam2de.pl \- Make a distance estimate file from a bam file of reads aligned to contigs
sga\-bam2de.pl \fB\-n\fR N \fB\-\-prefix\fR lib300 lib300.bam
Options:
.TP
\fB\-n\fR N
Minimum number of pairs required to consider two contigs linked
.TP
\fB\-m\fR LEN
Only find links between contigs with length at least LEN bp (default: 200)
.TP
\fB\-t\fR NUM
Use NUM threads for computing the distance estimates
.TP
\fB\-\-prefix\fR NAME
Use NAME as the prefix for the outfiles
.TP
\fB\-\-mind\fR D
Set the minimum distance estimate to test to be D. This should be a negative
number if contigs are expected to overlap. Defaults to \fB\-99bp\fR.
.TP
\fB\-\-mina\fR N
Set the minimum alignment length to be N.
.TP
\fB\-\-help\fR
This help output.