[med-svn] [augustus] 01/04: remove pregenerated manpage

[Sascha Steinbiss]

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

sascha-guest pushed a commit to branch master
in repository augustus.

commit f663c4d3c645c569fb0b83aa236863c5f647e8fd
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Thu Mar 24 11:52:23 2016 +0000

    remove pregenerated manpage
---
 debian/mansrc/augustus.1 | 180 -----------------------------------------------
 1 file changed, 180 deletions(-)

diff --git a/debian/mansrc/augustus.1 b/debian/mansrc/augustus.1
deleted file mode 100644
index 4e62158..0000000
--- a/debian/mansrc/augustus.1
+++ /dev/null
@@ -1,180 +0,0 @@
-'\" t
-.\"     Title: augustus
-.\"    Author: [see the "AUTHORS" section]
-.\" Generator: Asciidoctor 1.5.4
-.\"      Date: 2016-03-19
-.\"    Manual: \ \&
-.\"    Source: \ \&
-.\"  Language: English
-.\"
-.TH "AUGUSTUS" "1" "2016-03-19" "\ \&" "\ \&"
-.ie \n(.g .ds Aq \(aq
-.el       .ds Aq '
-.ss \n[.ss] 0
-.nh
-.ad l
-.de URL
-\\$2 \(laURL: \\$1 \(ra\\$3
-..
-.if \n[.g] .mso www.tmac
-.LINKSTYLE blue R < >
-.SH "NAME"
-augustus \- a gene prediction tool
-.SH "SYNOPSIS"
-.sp
-\fBaugustus\fP [parameters] \-\-species=SPECIES queryfilename
-.SH "OPTIONS"
-.sp
-The mandatory option \(aqqueryfilename\(aq specifies the filename (including relative path) to the file containing the query sequence(s) in FASTA format.
-.sp
-SPECIES is an identifier for the species. Use \fB\-\-species=help\fP to see a list.
-.SS "Further parameters:"
-.sp
-\fB\-\-strand=both\fP, \fB\-\-strand=forward\fP or \fB\-\-strand=backward\fP
-.RS 4
-define the strand to search on
-.RE
-.sp
-\fB\-\-genemodel=genemodel\fP
-.RS 4
-where genemodel is one of:
-.sp
-.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-partial      \- allow prediction of incomplete genes at the sequence boundaries (default)
-.RE
-.sp
-.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-intronless   \- only predict single\-exon genes like in prokaryotes and some eukaryotes
-.RE
-.sp
-.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-complete     \- only predict complete genes
-.RE
-.sp
-.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-atleastone   \- predict at least one complete gene
-.RE
-.sp
-.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-exactlyone   \- predict exactly one complete gene
-.RE
-.RE
-.sp
-\fB\-\-singlestrand=true\fP
-.RS 4
-predict genes independently on each strand, allow overlapping genes on opposite strands.
-This option is turned off by default.
-.RE
-.sp
-*\-\-hintsfile=hintsfilenam*e
-.RS 4
-When this option is used the prediction considering hints (extrinsic information) is turned on.
-hintsfilename contains the hints in gff format.
-.RE
-.sp
-\fB\-\-AUGUSTUS_CONFIG_PATH=path\fP
-.RS 4
-path to config directory (if not specified as environment variable)
-.RE
-.sp
-\fB\-\-alternatives\-from\-evidence=true/false\fP
-.RS 4
-report alternative transcripts when they are suggested by hints
-.RE
-.sp
-\fB\-\-alternatives\-from\-sampling=true/false\fP
-.RS 4
-report alternative transcripts generated through probabilistic sampling
-.RE
-.sp
-\fB\-\-maxtracks=n\fP
-.RS 4
-For a description of these parameters see section 4 of README.TXT.
-.RE
-.sp
-\fB\-\-proteinprofile=filename\fP
-.RS 4
-When this option is used the prediction will consider the protein profile provided as parameter.
-The protein profile extension is described in section 7 of README.TXT.
-.RE
-.sp
-\fB\-\-progress=true\fP
-.RS 4
-show a progressmeter
-.RE
-.sp
-\fB\-\-gff3=on/off\fP
-.RS 4
-output in gff3 format
-.RE
-.sp
-\fB\-\-predictionStart=A\fP, \fB\-\-predictionEnd=B\fP
-.RS 4
-A and B define the range of the sequence for which predictions should be found.
-.RE
-.sp
-\fB\-\-UTR=on/off\fP
-.RS 4
-predict the untranslated regions in addition to the coding sequence. This currently works only for a subset of species.
-.RE
-.sp
-\fB\-\-noInFrameStop=true/false\fP
-.RS 4
-Do not report transcripts with in\-frame stop codons. Otherwise, intron\-spanning stop codons could occur. Default: false
-.RE
-.sp
-\fB\-\-noprediction=true/false\fP
-.RS 4
-If true and input is in genbank format, no prediction is made. Useful for getting the annotated protein sequences.
-.RE
-.sp
-\fB\-\-uniqueGeneId=true/false\fP
-.RS 4
-If true, output gene identifyers like this: seqname.gN
-.RE
-.sp
-\fB\-\-paramlist\fP
-.RS 4
-Show full list of supported parameters.
-.RE
-.SH "AUTHORS"
-.sp
-AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
-.SH "ADDITIONAL DOCUMENTATION"
-.sp
-An exhaustive description can be found in the file /usr/share/augustus/README.TXT.
\ No newline at end of file

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