[med-svn] [fitgpc] 02/02: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository fitgpc.

commit 5f4a37d77cc42e5993460027cc41053d0bd67539
Author: Andreas Tille <tille at debian.org>
Date:   Wed Feb 12 09:12:56 2014 +0100

    Add manpage
---
 debian/control        |  4 ++-
 debian/createmanpages |  3 +++
 debian/fitgcp.1       | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/manpages       |  1 +
 4 files changed, 74 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 762a670..29892e4 100644
--- a/debian/control
+++ b/debian/control
@@ -16,8 +16,10 @@ Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${python:Depends},
+         python,
          python-scipy,
-         python-numpy
+         python-numpy,
+         python-pysam
 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
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..c67da30
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,3 @@
+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
diff --git a/debian/fitgcp.1 b/debian/fitgcp.1
new file mode 100644
index 0000000..92191b9
--- /dev/null
+++ b/debian/fitgcp.1
@@ -0,0 +1,67 @@
+.TH FITGCP "1" "February 2014" "fitgcp 2013-04-18" "User Commands"
+.SH NAME
+fitgcp \- fit mixtures of probability distributions to genome coverage profiles
+.SH SYNOPSIS
+.B fitgcp 
+[\fIoptions\fR] \fBNAME\fR
+.SH DESCRIPTION
+Fits mixtures of probability distributions to genome coverage profiles using an
+EM\-like iterative algorithm.
+.PP
+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.
+.PP
+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.
+.SH OPTIONS
+\fBNAME\fR: Name of SAM file to analyze.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\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
+.TP
+\fB\-i\fR STEPS, \fB\-\-iterations\fR=\fISTEPS\fR
+Maximum number of iterations. Default: 50
+.TP
+\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
+.TP
+\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
+.TP
+\fB\-p\fR, \fB\-\-plot\fR
+Create a plot of the fitted mixture model. Default:
+False
+.TP
+\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.
+.TP
+\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
+distributions.
+.TP
+\fB\-l\fR, \fB\-\-log\fR
+Enable logging. Default: False
+.TP
+\fB\-\-view\fR
+Only view the GCP. Do not fit any distribution.
+Respects cutoff (\fB\-c\fR). Default: False
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1

-- 
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