Commit 5f4a37d7 authored by Andreas Tille's avatar Andreas Tille

Add manpage

parent 2313c276
......@@ -16,8 +16,10 @@ Architecture: any
Depends: ${shlibs:Depends},
Description: fitting genome coverage distributions with mixture models
Genome coverage, the number of sequencing reads mapped to a position in
a genome, is an insightful indicator of irregularities within sequencing
help2man --no-info --no-discard-stderr \
--name='fit mixtures of probability distributions to genome coverage profiles' \
--version-string="2013-04-18" fitgcp > debian/fitgcp.1
.TH FITGCP "1" "February 2014" "fitgcp 2013-04-18" "User Commands"
fitgcp \- fit mixtures of probability distributions to genome coverage profiles
.B fitgcp
[\fIoptions\fR] \fBNAME\fR
Fits mixtures of probability distributions to genome coverage profiles using an
EM\-like iterative algorithm.
The script uses a SAM file as input and parses the mapping information and
creates a Genome Coverage Profile (GCP). The GCP is written to a file, such that
this step can be skipped the next time.
The user provides a mixture model that is fitted to the GCP. Furthermore, the
user may specify initial parameters for each model.
As output, the script generates a text file containing the final set of fit
parameters and additional information about the fitting process. A log file
contains the the current set of parameters in each step of the iteration. If
requested, a plot of the GCP and the fitted distributions can be created.
\fBNAME\fR: Name of SAM file to analyze.
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
\fB\-d\fR DIST, \fB\-\-distributions\fR=\fIDIST\fR
Distributions to fit. z\->zero; n: nbinom (MOM); N:
nbinom (MLE); p:binom; t: tail. Default: zn
\fB\-i\fR STEPS, \fB\-\-iterations\fR=\fISTEPS\fR
Maximum number of iterations. Default: 50
\fB\-t\fR THR, \fB\-\-threshold\fR=\fITHR\fR
Set the convergence threshold for the iteration. Stop
if the change between two iterations is less than THR.
Default: 0.01
\fB\-c\fR CUTOFF, \fB\-\-cutoff\fR=\fICUTOFF\fR
Specifies a coverage cutoff quantile such that only
coverage values below this quantile are considered.
Default: 0.95
\fB\-p\fR, \fB\-\-plot\fR
Create a plot of the fitted mixture model. Default:
\fB\-m\fR MEAN, \fB\-\-means\fR=\fIMEAN\fR
Specifies the initial values for the mean of each
Poisson or Negative Binomial distribution. Usage: \fB\-m\fR
12.4 \fB\-m\fR 16.1 will specify the means for the first two
non\-zero/tail distributions. The default is calculated
from the data.
\fB\-a\fR ALPHA, \fB\-\-alpha\fR=\fIALPHA\fR
Specifies the initial values for the proportion alpha
of each distribution. Usage: For three distributions
\fB\-a\fR 0.3 \fB\-a\fR 0.3 specifies the proportions 0.3, 0.3 and
0.4. The default is equal proportions for all
\fB\-l\fR, \fB\-\-log\fR
Enable logging. Default: False
Only view the GCP. Do not fit any distribution.
Respects cutoff (\fB\-c\fR). Default: False
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