[med-svn] [mapdamage] 04/05: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository mapdamage.

commit b657dd79e017d406ffc4717c33547be2d0cbd26a
Author: Andreas Tille <tille at debian.org>
Date:   Tue Aug 2 09:47:20 2016 +0200

    Add manpage
---
 debian/manpages    |   1 +
 debian/mapDamage.1 | 164 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 165 insertions(+)

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
diff --git a/debian/mapDamage.1 b/debian/mapDamage.1
new file mode 100644
index 0000000..0cdca2c
--- /dev/null
+++ b/debian/mapDamage.1
@@ -0,0 +1,164 @@
+.TH MAPDAMAGE "1" "August 2016" "mapDamage 2.0.6" "User Commands"
+.SH NAME
+mapDamage \- tracking and quantifying damage patterns in ancient DNA sequences
+.SH SYNOPSIS
+.B mapDamage
+[\fI\,options\/\fR] \fI\,-i BAMfile -r reference.fasta\/\fR
+.SH DESCRIPTION
+MapDamage is a computational framework written in Python and R, which
+tracks and quantifies DNA damage patterns among ancient DNA sequencing
+reads generated by Next-Generation Sequencing platforms.
+.SH OPTIONS
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.IP
+Input files:
+.TP
+\fB\-i\fR FILENAME, \fB\-\-input\fR=\fI\,FILENAME\/\fR
+SAM/BAM file, must contain a valid header, use '\-' for
+reading a BAM from stdin
+.TP
+\fB\-r\fR REF, \fB\-\-reference\fR=\fI\,REF\/\fR
+Reference file in FASTA format
+.IP
+General options:
+.TP
+\fB\-n\fR DOWNSAMPLE, \fB\-\-downsample\fR=\fI\,DOWNSAMPLE\/\fR
+Downsample to a randomly selected fraction of the
+reads (if 0 < DOWNSAMPLE < 1), or a fixed number of
+randomly selected reads (if DOWNSAMPLE >= 1). By
+default, no downsampling is performed.
+.TP
+\fB\-\-downsample\-seed\fR=\fI\,DOWNSAMPLE_SEED\/\fR
+Seed value to use for downsampling. See documentation
+for py module 'random' for default behavior.
+.TP
+\fB\-\-merge\-reference\-sequences\fR
+Ignore referece sequence names when tabulating reads
+(using '*' instead). Useful for alignments with a
+large number of reference sequnces, which may
+otherwise result in excessive memory or disk usage due
+to the number of tables generated.
+.TP
+\fB\-l\fR LENGTH, \fB\-\-length\fR=\fI\,LENGTH\/\fR
+read length, in nucleotides to consider [70]
+.TP
+\fB\-a\fR AROUND, \fB\-\-around\fR=\fI\,AROUND\/\fR
+nucleotides to retrieve before/after reads [10]
+.TP
+\fB\-Q\fR MINQUAL, \fB\-\-min\-basequal\fR=\fI\,MINQUAL\/\fR
+minimun base quality Phred score considered, Phred\-33
+assumed [0]
+.TP
+\fB\-d\fR FOLDER, \fB\-\-folder\fR=\fI\,FOLDER\/\fR
+folder name to store results [results_FILENAME]
+.TP
+\fB\-f\fR, \fB\-\-fasta\fR
+Write alignments in a FASTA file
+.TP
+\fB\-\-plot\-only\fR
+Run only plotting from a valid result folder
+.TP
+\fB\-q\fR, \fB\-\-quiet\fR
+Disable any output to stdout
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Display progression information during parsing
+.TP
+\fB\-\-mapdamage\-modules\fR=\fI\,MAPDAMAGE_MODULES\/\fR
+Override the system wide installed mapDamage module
+.IP
+Options for graphics:
+.TP
+\fB\-y\fR YMAX, \fB\-\-ymax\fR=\fI\,YMAX\/\fR
+graphical y\-axis limit for nucleotide misincorporation
+frequencies [0.3]
+.TP
+\fB\-m\fR READPLOT, \fB\-\-readplot\fR=\fI\,READPLOT\/\fR
+read length, in nucleotides, considered for plotting
+nucleotide misincorporations [25]
+.TP
+\fB\-b\fR REFPLOT, \fB\-\-refplot\fR=\fI\,REFPLOT\/\fR
+the number of reference nucleotides to consider for
+ploting base composition in the region located
+upstream and downstream of every read [10]
+.TP
+\fB\-t\fR TITLE, \fB\-\-title\fR=\fI\,TITLE\/\fR
+title used for plots []
+.IP
+Options for the statistical estimation:
+.TP
+\fB\-\-rand\fR=\fI\,RAND\/\fR
+Number of random starting points for the likelihood
+optimization  [30]
+.TP
+\fB\-\-burn\fR=\fI\,BURN\/\fR
+Number of burnin iterations  [10000]
+.TP
+\fB\-\-adjust\fR=\fI\,ADJUST\/\fR
+Number of adjust proposal variance parameters
+iterations  [10]
+.TP
+\fB\-\-iter\fR=\fI\,ITER\/\fR
+Number of final MCMC iterations  [50000]
+.TP
+\fB\-\-forward\fR
+Using only the 5' end of the seqs  [False]
+.TP
+\fB\-\-reverse\fR
+Using only the 3' end of the seqs  [False]
+.TP
+\fB\-\-var\-disp\fR
+Variable dispersion in the overhangs  [False]
+.TP
+\fB\-\-jukes\-cantor\fR
+Use Jukes Cantor instead of HKY85  [False]
+.TP
+\fB\-\-diff\-hangs\fR
+The overhangs are different for 5' and 3'  [False]
+.TP
+\fB\-\-fix\-nicks\fR
+Fix the nick frequency vector (Only C.T from the 5'
+end and G.A from the 3' end)  [False]
+.TP
+\fB\-\-use\-raw\-nick\-freq\fR
+Use the raw nick frequency vector without smoothing
+[False]
+.TP
+\fB\-\-single\-stranded\fR
+Single stranded protocol [False]
+.TP
+\fB\-\-theme\-bw\fR
+Use black and white theme in post. pred. plot [False]
+.TP
+\fB\-\-seq\-length\fR=\fI\,SEQ_LENGTH\/\fR
+How long sequence to use from each side [12]
+.TP
+\fB\-\-stats\-only\fR
+Run only statistical estimation from a valid result
+folder
+.TP
+\fB\-\-rescale\fR
+Rescale the quality scores in the BAM file using the
+output from the statistical estimation
+.TP
+\fB\-\-rescale\-only\fR
+Run only rescaling from a valid result folder
+.TP
+\fB\-\-rescale\-out\fR=\fI\,RESCALE_OUT\/\fR
+Write the rescaled BAM to this file
+.TP
+\fB\-\-no\-stats\fR
+Disabled statistical estimation, active by default
+.TP
+\fB\-\-check\-R\-packages\fR
+Check if the R modules are working
+.SH BUGS
+Report bugs to aginolhac at snm.ku.dk, MSchubert at snm.ku.dk or
+jonsson.hakon at gmail.com
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

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