.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH BAM-READ "1" "July 2018" "bam-read version 1.0.0" "User Commands"
.SH NAME
bam-read \- Parse bam files after multi-mapping reads have been assigned and aggregate read mapping information by contig.
.SH SYNOPSIS
Currently captured:

 - name
 - bases mapped
 - edit distance
 - bridges
 - length
 - reads mapped
 - both mapped
 - proper pair
 - good
 - uncovered bases
 - mean mapq
 - probability of coverage not being segmented
.SH DESCRIPTION
bam\-read version 1.0.0
Usage:
bam\-read <bam_file> <output_csv> <nullprior (optional)>
.PP
example:
bam\-read in.bam out.csv 0.95
.PP
Usage:
bam\-read <bam_file> <output_csv> <nullprior (optional)>
.PP
example:
bam\-read in.bam out.csv 0.95