Commit 3cc51e72 authored by Andreas Tille's avatar Andreas Tille

New upstream version 2.0

parent b0f78643
This diff is collapsed.
##
## INSTRUCTIONS TO INSTALL GFF2APLOT v2.0
##
##
## $Id: INSTALL,v 1.1 2003/03/17 17:58:46 jabril Exp $
##
GFF2APLOT v2.0
a program to visualize the alignment of two genomic sequences
together with their annotations. From GFF-format input files
it produces PostScript figures for that alignment.
Copyright (C) 1999-2003 - Josep Francesc ABRIL FERRANDO
Thomas WIEHE
Roderic GUIGO SERRA
-------------------------------------------------------------------------------
Installing GFF2APLOT v2.0
-------------------------------------------------------------------------------
+ PROGRAM's PRE-REQUISITES:
gff2aplot needs the following Perl modules installed in your system,
we used those available from the standard Perl distribution. Those
that are not in the standard distribution are marked with an '(*)',
although this will change from one installation to another. In such
cases make sure that you already have downloaded them from
CPAN (http://www.perl.com/CPAN) and get them installed.
"Getopt::Long" - processing command-line options.
"Benchmark" - checking and comparing running times of code.
"Data::Dumper" - pretty printing data structures for debugging (*?).
+ INSTALLING SOFTWARE:
You will find a Makefile in the distribution directory that you may need
to edit in order to install GFF2APLOT. In principle, you only need to
modify the INSTALLDIR variable, although you can achieve the same effect
from command-line, as shown latter in this document.
Depending on the system, you may also have to modify/update the ali2gff
Makefile that can be found at the src/ali2gff directory.
GFF2APLOT Makefiles were developed and tested on a Red Hat Linux box
running GNU Make version 3.79.1.
Once you have set up the makefile, just type:
make
and then:
make install
By default, the latter command will move all the scripts to /usr/local/bin
but if you want to place all the exec files into another directory, just
define the new installation path as follows:
make INSTALLDIR=/your/path/bin install
Another way of doing that is modifying that variable on the Makefile
accordingly to your needs.
Our apologies but there is not a 'make test' yet...
Thanks for using GFF2APLOT, we hope you will enjoy it and it will
be useful for your research.
+ SETTING ENVIRONMENT VARIABLES:
There are two environmental variables that can be set by users to their
preferences:
+ You can specify the path where gff2aplot can find the default
files with the shell variable "GFF2APLOT_CUSTOMPATH". Default
value is the path where you are running gff2aplot.
+ You can also define the default custom filename you will like
with the variable "GFF2APLOT_CUSTOMFILE", program default filename
for custom file is ".gff2aplotrc".
+ Now gff2aplot does not need to write any temporary file, so that
previous versions default temporary directory path variable
("GFF2APLOT_TMP") is no longer used.
+ Setting those vars in Bourne-shell and C-shell:
o Using a Bourne-Shell (e.g. bash):
export GFF2APLOT_CUSTOMPATH="path"
export GFF2APLOT_CUSTOMFILE="file_name"
o Using a C-Shell:
setenv GFF2APLOT_CUSTOMPATH "path"
setenv GFF2APLOT_CUSTOMFILE "file_name"
-------------------------------------------------------------------------------
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
# INSTALLING GFF2APLOT FILES
#
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
# The following Makefile was developed
# on a Red Hat Linux box running on GNU Make version 3.79.1
#
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
# Copyright (C) 1999-2003 - Josep Francesc ABRIL FERRANDO
# Thomas WIEHE
# Roderic GUIGO SERRA
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
#
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
# $Id: dist_Makefile,v 1.1 2003/03/17 17:58:46 jabril Exp $
#
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
# INSTALLDIR is the only variable that should be modified
# (unless you were not using GNUmake, of course, because in such
# case you must fix all the GNUmake specific commands... ;^D).
#
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
### PATHS
BBIN = /bin
UBIN = /usr/bin
LBIN = /usr/local/bin
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# REMEMBER: INSTALLDIR is the only variable that should be modified
INSTALLDIR = $(LBIN)
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#
### MAKE VARS
.PHONY : clean cleanall forceall
.DEFAULT : all
.PRECIOUS : %.sh %.awk %.pl %.pm %.ps %.tgz %.gz \
%.rc %.gff %.gb %.fa README
.SECONDARY :
.SUFFIXES :
#
### INTERPRETERS
DATE = $(shell date)
USER = $(shell whoami)
GAWK = $(firstword $(shell which gawk))
GAWKV = $(shell $(GAWK) --version | \
$(GAWK) '$$0 ~ /^GNU Awk/ { print $$0; }')
BASH = $(firstword $(shell which bash))
BASHV = $(shell $(BASH) --version | \
$(GAWK) '$$0 ~ /^GNU bash/ { print $$0; }')
PERL = $(firstword $(shell which perl))
PERLV = $(shell $(PERL) --version | \
$(GAWK) '$$0 ~ /^This/ { \
gsub(/^This is perl,[ \t]+/,"",$$0); \
print $$0; \
}') #'
#
### COMMANDS
# You can update the following paths to your system settings
V = -v
RM = $(firstword $(shell which rm )) $(V)
RD = $(firstword $(shell which rmdir)) $(V)
CP = $(firstword $(shell which cp )) $(V)
MV = $(firstword $(shell which mv )) $(V)
LN = $(firstword $(shell which ln )) $(V)
MD = $(firstword $(shell which mkdir)) $(V)
CHM = $(firstword $(shell which chmod)) -c
CHO = $(firstword $(shell which chown)) -c
#
### LOCAL PATHS
WORK = .
SRC = $(WORK)/src
BIN = $(WORK)/bin
#
### LOCAL VARS
BINEXT = .sh .awk .pl .pm
GFF2APLOT = gff2aplot.pl
PARSEBLAST = parseblast.pl
BLAT2GFF = blat2gff.pl
SIM2GFF = sim2gff.pl
ALI2GFF = ali2gff
ALI2GFFD = $(SRC)/ali2gff
SRCCODE = $(GFF2APLOT) $(PARSEBLAST) \
$(BLAT2GFF) $(SIM2GFF) $(ALI2GFF)
BINCODE = $(addprefix $(BIN)/, $(SRCCODE))
#
### MAKE RULES
all: header main trailer
test :
@echo "### SORRY !!! Tests were not implemented yet...";
install : header installbin trailer
forceall : header cleanbin main trailer
clean : header cleanbin trailer
cleanall : header cleanbin trailer
cleanbin :
-@$(RM) -f $(wildcard $(BIN)/*);
main : $(BINCODE)
@$(CHM) 755 $^;
installbin : $(BINCODE)
@echo "### COPYING BIN FILES TO $(INSTALLDIR)...";
@$(CP) -p $^ $(INSTALLDIR)/;
#
### FINISHING CODE
$(addprefix $(BIN)/, $(ALI2GFF)) : $(addprefix $(ALI2GFFD)/, $(ALI2GFF))
@${CP} $(addprefix $(ALI2GFFD)/, $(ALI2GFF)) \
$(addprefix $(BIN)/, $(ALI2GFF))
$(addprefix $(ALI2GFFD)/, $(ALI2GFF)) : $(addprefix $(addprefix $(ALI2GFFD)/, $(ALI2GFF)), .h .c)
@echo "### Making ALI2GFF..."
@cd $(ALI2GFFD); \
$(MAKE) -f ./Makefile;
$(addprefix $(BIN)/, %.sh) : $(addprefix $(SRC)/, %.sh)
@echo "### Finishing BASH script from \"$<\" -> \"$@\"" ;
@( echo "#!$(BASH)"; cat $< ) > $@;
$(addprefix $(BIN)/, %.awk) : $(addprefix $(SRC)/, %.awk)
@echo "### Finishing GAWK script from \"$<\" -> \"$@\"" ;
@( echo "#!$(GAWK) -f"; cat $< ) > $@;
$(addprefix $(BIN)/, %.pl) : $(addprefix $(SRC)/, %.pl)
@echo "### Finishing PERL script from \"$<\" -> \"$@\"" ;
@( echo "#!$(PERL) -w"; cat $< ) > $@;
$(addprefix $(BIN)/, %.pm) : $(addprefix $(SRC)/, %.pm)
@echo "### Finishing PERL module from \"$<\" -> \"$@\"" ;
@$(CP) -u $< $@ ;
isexec : $(BINCODE)
@$(CHM) 755 $<;
#
### INFO RULES
info : header getinfo trailer
getinfo :
@echo "### BASH ### $(BASH) ### $(BASHV)";
@echo "### GAWK ### $(GAWK) ### $(GAWKV)";
@echo "### PERL ### $(PERL) ### $(PERLV)";
header :
@echo "###";
@echo "### RUNNING MAKEFILE";
@echo "###";
@echo "### $(DATE) -- $(USER)";
@echo "###";
trailer :
@echo "###";
@echo "### MAKEFILE DONE...";
@echo "###";
##
## README FOR GFF2APLOT v2.0
##
##
## $Id: README,v 1.1 2003/03/17 17:58:46 jabril Exp $
##
Dear User:
This file contains important program information. Please read
these tips through carefully, before beginning to work with GFF2APLOT.
See INSTALL file for further tips on how to install the program
and related scripts on your system.
-------------------------------------------------------------------------------
License Terms
-------------------------------------------------------------------------------
GFF2APLOT v2.0
a program to visualize the alignment of two genomic sequences
together with their annotations. From GFF-format input files
it produces PostScript figures for that alignment.
Copyright (C) 1999-2003 - Josep Francesc ABRIL FERRANDO
Thomas WIEHE
Roderic GUIGO SERRA
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version (http://www.gnu.org).
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-------------------------------------------------------------------------------
Author's Address
-------------------------------------------------------------------------------
Josep Francesc ABRIL FERRANDO
GENOME BIOINFORMATICS LAB
GRIB --- IMIM / UPF / CRG
Passeig Maritim de la Barceloneta, 37-49.
08003 - Barcelona, Catalonia, Spain.
Phone: +34 93 2240302
Fax: +34 93 2240875
e-mail: jabril@imim.es
URL: http://genome.imim.es/~jabril
-------------------------------------------------------------------------------
Listing Files for Current Distribution
-------------------------------------------------------------------------------
You can retrieve the latests files from the following FTP address:
ftp://genome.imim.es/pub/gff_tools/gff2aplot/
The current distribution tarball contains the following files
and subdirectories:
README This file...
GNU-GPL The GNU General Public License Version 2.
INSTALL Instructions on how to prepare
the GFF2APLOT scripts to run them
in your system.
Please, take a look at it...
Makefile Well, you know... ;^D
src/
GFF2APLOT and related scripts.
src/gff2aplot.pl
The main program, which converts GFF input
into alignment PostScript plots.
src/parseblast.pl
A parser for the standard output
from most of the BLAST programs available
(NCBI-Blast/WashU-Blast/WebBlast/MegaBlast).
src/blat2gff.pl
Filtering BLAT output into GFF.
src/sim2gff.pl
Converting SIM output into GFF.
src/ali2gff
C program that parses SIM/Mummer output
and produces GFF records for the alignment.
bin/
It is empty until you make
the executables for the distribution.
doc/
Contains documentation for gff2aplot,
initially the "User's Manual".
examples/ A set of three examples,
in separate directories, each containing
GFF data, customization files and
PostScript output obtained with gff2aplot.
See the corresponding README file to see
how the figures were generated.
examples/wublast/
examples/mhcregion/
examples/splice_sites/
-------------------------------------------------------------------------------
Reporting Bugs and Suggestions
-------------------------------------------------------------------------------
+ GFF2APLOT author's e-mail adress: jabril@imim.es
+ HELP:
If you need help after reading manual pages you are free to send an e-mail
to authors. It will help to filter your mail properly if you start your
subject string with "[GFF2APLOT] HELP:".
You will get a reply as soon as possible.
+ BUGS:
If you find any bug or something is not plotted properly, you can send a bug
report which subject string may start with "[GFF2APLOT] BUG:".
+ SUGGESTIONS:
We thank any helpful suggestion for improving our program. Message
subject string will start with "[GFF2APLOT] SUGGEST:".
-------------------------------------------------------------------------------
Acknowledgements
-------------------------------------------------------------------------------
We would like to thank Matthias Platzer, at IMB, Jena, for helpful
comments while developing the program prototype. We would like to
thank the colleagues at Genome Bioinformatics Lab within the GRIB
for their extensive testing of GFF2APLOT.
We would also thank users that will cite the paper on GFF2APLOT,
or at least it's web-site URL. Paper is currently submitted,
so you may cite GFF2APLOT as:
http://genome.imim.es/software/gfftools/GFF2APLOT.html
-------------------------------------------------------------------------------
.TH ALI2GFF 1 "Mon, 21 Mar 2005 21:44:15 -0300"
.SH NAME
ali2gff \- Module to translate a MUMmer output files into gff formatted output.
.SH SYNOPSIS
.B ali2gff
.RI "[-r] [-t <.|0|1|2>] [-x <name>] [-y <name>] [-H] [-f] [-h] <MUMmer_output_file>"
.br
.SH OPTIONS
.TP
.B \-h, \-\-help
Show summary of options.
.TP
.B \-r
Interchange the order of sequences (sequence 1 on y-axis, sequence 2 on x-axis).
.TP
.B \-t <.|0|1|2>
Put label 'frame' in gff output.
.TP
.B \-x <name>
Specify the species name for species1 (default: "Seq1").
.TP
.B \-y <name>
Specify the species name for species2 (default: "Seq2").
.TP
.B \-i
Ignore full sequence identities.
.TP
.B \-f
Write output to file.
.SH SEE ALSO
.BR blat2gff (1),
.BR gff2aplot (1),
.BR parseblast (1),
.BR sim2gff (1).
.br
.SH AUTHOR
ali2gff was written by Steffi Gebauer-Jung.
.PP
This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>,
for the Debian project (but may be used by others).
.TH BLAT2GFF 1 "Mon, 21 Mar 2005 21:44:15 -0300"
.SH NAME
blat2gff \- Converts BLAT output files to GFF formatted files
.SH SYNOPSIS
.B blat2gff
.RI " < inputfile > outputfile"
.br
.SH SEE ALSO
.BR ali2gff (1),
.BR gff2aplot (1),
.BR parseblast (1),
.BR sim2gff (1).
.br
.SH AUTHOR
blat2gff was written by Josep Francesc ABRIL FERRANDO <jabril@imim.es>.
.PP
This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>,
for the Debian project (but may be used by others).
gff2aplot (2.0-8) unstable; urgency=medium
* Moved debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
* spelling
* Fix Mayhem bug
Closes: #715627
-- Andreas Tille <tille@debian.org> Sun, 13 Dec 2015 21:17:30 +0100
gff2aplot (2.0-7) unstable; urgency=low
* debian/upstream: Added citation information
* debian/control:
- Standards-Version: 3.9.3 (no changes needed)
- Fixed Vcs-Svn
- Removed cdbs+quilt from Build-Depends
* debian/copyright: Rewritten to DEP5
* debian/patches/use-dpkg-buildflags.patch: Use build flags from environment
to enable hardening
* debhelper 9 (control+compat)
-- Andreas Tille <tille@debian.org> Tue, 01 May 2012 22:37:01 +0200
gff2aplot (2.0-6) unstable; urgency=low
* debian/control
- Added myself as Uploader
- Standards-Version: 3.9.1 (no changes needed)
- debhelper 7 (actually >= 7.1)
- Fixed Spelling of Debian Med team
- Build-Depends: removed cdbs, added quilt
* debian/source/format: 3.0 (quilt)
* debian/rules: rewritten to use dh
* debian/patches: use quilt
* debian/patches/01-makefile.diff: Removed because unneeded
with current packaging
* debian/{examples,install,manpages}: added
-- Andreas Tille <tille@debian.org> Tue, 25 Jan 2011 13:32:41 +0100
gff2aplot (2.0-5) unstable; urgency=low
* Updated Standards-Version;
* Changed Maintainer to the Debian-Med Packaging Team;
* Added new Homepage field;
* Added Vcs-* fields.
-- Nelson A. de Oliveira <naoliv@debian.org> Sun, 24 Feb 2008 00:25:43 -0300
gff2aplot (2.0-4) unstable; urgency=low
* Updated patches/01-makefile.diff, so ali2gff doesn't get stripped when
using DEB_BUILD_OPTIONS=nostrip (Closes: #436975);
* Updated maintainer email;
* Updated Standards-Version to 3.7.2;
* Updated compat version to 5;
* Updated watch file.
-- Nelson A. de Oliveira <naoliv@debian.org> Thu, 09 Aug 2007 17:16:13 -0300
gff2aplot (2.0-3) unstable; urgency=low
* Not using DEB_AUTO_UPDATE_DEBIAN_CONTROL of CDBS anymore;
* Updated Standards-Version to 3.6.1.1 (no modifications needed).
-- Nelson A. de Oliveira <naoliv@gmail.com> Thu, 2 Jun 2005 20:26:19 -0300
gff2aplot (2.0-2) unstable; urgency=low
* debian/rules: fix DEB_AUTO_UPDATE_DEBIAN_CONTROL position;
* debian/control: changed ps-viewer to postscript-viewer on Suggests field;
* debian/control: corrected indentation of description;
* Included watch file.
-- Nelson A. de Oliveira <naoliv@gmail.com> Tue, 12 Apr 2005 14:16:53 -0300
gff2aplot (2.0-1) unstable; urgency=low
* Initial Release (Closes: #300828)
-- Nelson A. de Oliveira <naoliv@gmail.com> Mon, 21 Mar 2005 20:30:45 -0300
Source: gff2aplot
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Nelson A. de Oliveira <naoliv@debian.org>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9)
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/gff2aplot/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/gff2aplot/trunk/
Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html
Package: gff2aplot
Architecture: any
Depends: ${shlibs:Depends},
${perl:Depends},
${misc:Depends}
Suggests: postscript-viewer,
gff2ps
Description: pair-wise alignment-plots for genomic sequences in PostScript
A program to visualize the alignment of two genomic sequences together with
their annotations. From GFF-format input files it produces PostScript figures
for that alignment.
The following menu lists many features of gff2aplot:
* Comprehensive alignment plots for any GFF-feature. Attributes are defined
separately so you can modify only whatsoever attributes for a given file or
share same customization across different data-sets.
* All parameters are set by default within the program, but it can be also
fully configured via gff2ps-like flexible customization files. Program can
handle several of such files, summarizing all the settings before producing
the corresponding figure. Moreover, all customization parameters can be set
via command-line switches, which allows users to play with those parameters
before adding any to a customization file.
* Source order is taken from input files, if you swap file order you can
visualize alignment and its annotation with the new input arrangement.
* All alignment scores can be visualized in a PiP box below gff2aplot area,
using grey-color scale, user-defined color scale or score-dependent
gradients.
* Scalable fonts, which can also be chosen among the basic PostScript default
fonts. Feature and group labels can be rotated to improve readability in
both annotation axes.
* The program is still defined as a Unix filter so it can handle data from
files, redirections and pipes, writing output to standard-output and
warnings to standard error.
* gff2aplot is able to manage many physical page formats (from A0 to A10, and
more -see available page sizes in its manual-), including user-defined ones.
This allows, for instance, the generation of poster size genomic maps, or
the use of a continuous-paper supporting plotting device, either in portrait
or landscape.
* You can draw different alignments on same alignment plot and distinguish
them by using different colors for each.
* Shape dictionary has been expanded, so that further feature shapes are now
available (see manual).
* Annotation projections through alignment plots (so called ribbons) emulate
transparencies via complementary color fill patterns. This feature allows
one to show color pseudo-blending when horizontal and vertical ribbons
overlap.
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: GFF2APLOT
Upstream-Contact: Josep Francesc ABRIL FERRANDO <jabril@imim.es>
Source: http://genome.imim.es/software/gfftools/GFF2APLOT.html
Files: *
Copyright: 1999-2003 Josep Francesc ABRIL FERRANDO <jabril@imim.es>
Thomas WIEHE <rguigo@imim.es>
Roderic GUIGO SERRA <twiehe@zedat.fu-berlin.de>
License: GPL-2+
Files: debian/*
Copyright: 2005-2008 Nelson A. de Oliveira <naoliv@gmail.com>
2011-2012 Andreas Tille <tille@debian.org>
License: GPL-2+
License: GPL-2+
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any later version..
.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
along with this package; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
.
On Debian systems, the complete text of the GNU General
Public License can be found in `/usr/share/common-licenses/GPL'.
README
doc/GFF2APLOT_MANUAL.ps.gz
.TH GFF2APLOT 1 "Mon, 21 Mar 2005 21:44:15 -0300"
.SH NAME
gff2aplot \- Converting GFF files for pairwise alignments to PostScript.
.SH SYNOPSIS
.B gff2aplot
.RI "[options] <GFF_files|STDIN>"
.br
.SH DESCRIPTION
This manual page documents briefly the
.B gff2aplot
command.
.PP
\fBgff2aplot\fP is a program that draws color-filled alignment plots from GFF files for that alignment and two sequences annotations.
.SH OPTIONS
A double dash on itself "--" signals end of the options and start of file names (if present). You can use a single dash "-" as STDIN placeholder. Available options and a short description are listed here:
.TP
.B \-h, \-\-help
Show summary of options.
.TP
.B \-\-version
Shows current version and exits.
.TP
.B \-v, \-\-verbose
Verbose mode, a full report is sent to standard error (default is set to showing only WARNINGS).
.TP
.B \-V, \-\-logs-filename <filename>
Report is written to a log file.
.TP
.B \-q, \-\-quiet
Quiet mode, do not show any message/warning to standard error (reporting only ERRORS).
.TP
.B \-p, \-\-page-size <format_name>
Setting a page size among pre-defined ones see below for a list of available page formats).
.TP
.B \-\-margin-left <length>
.TP
.B \-\-margin-right <length>
.TP
.B \-\-margin-top <length>
.TP
.B \-\-margin-bottom <length>