This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository fitgpc.
commit 5f4a37d77cc42e5993460027cc41053d0bd67539 Author: Andreas Tille <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fitgpc.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
