.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
.TH GETCOUNTS.PY "1" "September 2019" "getCounts.py 0.7.5+dfsg" "User Commands"
.SH NAME
getCounts.py \- generate read counts for each input file
.SH SYNOPSIS
.B getCounts.py
[\fI\,options\/\fR] [\fI\,<inputFile.thetaMeans>\/\fR]\fI\,+\/\fR
.SH DESCRIPTION
.IP
This program reads supplied .thetaMeans files and using either information from .prob files or Nmap option generates read counts for each input file provided.
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-o\fR OUT, \fB\-\-outFile\fR=\fI\,OUT\/\fR
Output file
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Verbose output
.TP
\fB\-p\fR PROBDIR, \fB\-\-probDir\fR=\fI\,PROBDIR\/\fR
Directory with .prob files. The program will look in
here for files with same name except fot extension
\&.prob in order to find out total\-aligned\-read counts
for each experiment.
.TP
\fB\-n\fR NMAP, \fB\-\-Nmap\fR=\fI\,NMAP\/\fR
Comma separated list of total aligned\-read\-counts for
each experiment.