[med-svn] [express] 07/08: include manpage

[Michael Crusoe]

This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a commit to branch master
in repository express.

commit d75b8a793d4d5f555afa7cc6358f20f48f5ba23a
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date:   Wed Feb 11 18:50:26 2015 -0500

    include manpage
---
 debian/express.1        | 113 ++++++++++++++++++++++++++++++++++++++++++++++++
 debian/express.manpages |   1 +
 2 files changed, 114 insertions(+)

diff --git a/debian/express.1 b/debian/express.1
new file mode 100644
index 0000000..1365658
--- /dev/null
+++ b/debian/express.1
@@ -0,0 +1,113 @@
+.TH EXPRESS "1" "February 2015" "express 1.5.1" "User Commands"
+.SH NAME
+express \- Streaming quantification for high-throughput sequencing
+.SH DESCRIPTION
+File Usage:  express [options] <target_seqs.fa> <hits.(sam/bam)>
+Piped Usage: bowtie [options] \fB\-S\fR <index> <reads.fq> | express [options] <target_seqs.fa>
+.SS "Required arguments:"
+.TP
+<target_seqs.fa>
+target sequence file in fasta format
+.TP
+<hits.(sam/bam)>
+read alignment file in SAM or BAM format
+.SS "Standard Options:"
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+produce help message
+.TP
+\fB\-o\fR [ \fB\-\-output\-dir\fR ] arg (=.)
+write all output files to this directory
+.TP
+\fB\-D\fR [ \fB\-\-preprocess\fR ]
+run preprocess script for eXpressD
+.TP
+\fB\-m\fR [ \fB\-\-frag\-len\-mean\fR ] arg (=200)
+prior estimate for average fragment
+length
+.TP
+\fB\-s\fR [ \fB\-\-frag\-len\-stddev\fR ] arg (=80)
+prior estimate for fragment length std
+deviation
+.TP
+\fB\-H\fR [ \fB\-\-haplotype\-file\fR ] arg
+path to a file containing haplotype pairs
+.TP
+\fB\-B\fR [ \fB\-\-additional\-batch\fR ] arg (=0)
+number of additional batch EM rounds
+after initial online round
+.TP
+\fB\-O\fR [ \fB\-\-additional\-online\fR ] arg (=0) number of additional online EM rounds
+after initial online round
+.TP
+\fB\-L\fR [ \fB\-\-max\-read\-len\fR ] arg (=250)
+maximum allowed length of a read
+.TP
+\fB\-\-output\-align\-prob\fR
+output alignments (sam/bam) with
+probabilistic assignments
+.TP
+\fB\-\-output\-align\-samp\fR
+output alignments (sam/bam) with sampled
+assignments
+.TP
+\fB\-\-fr\-stranded\fR
+accept only forward\->reverse alignments
+(second\-stranded protocols)
+.TP
+\fB\-\-rf\-stranded\fR
+accept only reverse\->forward alignments
+(first\-stranded protocols)
+.TP
+\fB\-\-f\-stranded\fR
+accept only forward single\-end alignments
+(second\-stranded protocols)
+.TP
+\fB\-\-r\-stranded\fR
+accept only reverse single\-end alignments
+(first\-stranded protocols)
+.TP
+\fB\-\-no\-update\-check\fR
+disables automatic check for update via
+web
+.TP
+\fB\-\-logtostderr\fR
+prints all logging messages to stderr
+.SS "Advanced Options:"
+.TP
+\fB\-f\fR [ \fB\-\-forget\-param\fR ] arg (=0.84999999999999998)
+sets the 'forgetting factor' parameter
+(0.5 < c <= 1)
+.TP
+\fB\-\-library\-size\fR arg
+specifies library size for FPKM instead
+of calculating from alignments
+.TP
+\fB\-\-max\-indel\-size\fR arg (=10)
+sets the maximum allowed indel size,
+affecting geometric indel prior
+.TP
+\fB\-\-calc\-covar\fR
+calculate and output covariance matrix
+.TP
+\fB\-\-expr\-alpha\fR arg (=0.0050000000000000001)
+sets the strength of the prior, per bp
+.TP
+\fB\-\-stop\-at\fR arg (=0)
+sets the number of fragments to
+process, disabled with 0
+.TP
+\fB\-\-burn\-out\fR arg (=5000000)
+sets number of fragments after which to
+stop updating auxiliary parameters
+.TP
+\fB\-\-no\-bias\-correct\fR
+disables bias correction
+.TP
+\fB\-\-no\-error\-model\fR
+disables error modelling
+.TP
+\fB\-\-aux\-param\-file\fR arg
+path to file containing auxiliary
+parameters to use instead of learning
+
diff --git a/debian/express.manpages b/debian/express.manpages
new file mode 100644
index 0000000..fd29734
--- /dev/null
+++ b/debian/express.manpages
@@ -0,0 +1 @@
+debian/express.1

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