Commit 42965fb6 authored by Julien Y. Dutheil's avatar Julien Y. Dutheil

New upstream version 1.3.1+dfsg

parent 4bf43ea1
......@@ -23,7 +23,7 @@ IF(NOT BUILD_STATIC)
FORCE)
ENDIF()
IF(BUILD_STATIC)
MESSAGE("-- Static linkage requested.")
MESSAGE(STATUS "Static linkage requested.")
SET (CMAKE_CXX_FLAGS "-static -static-libgcc ${CMAKE_CXX_FLAGS}")
ENDIF()
......@@ -50,7 +50,8 @@ else ()
# Generate command line args (always add -c to output compressed file to stdout)
if (${COMPRESS_PROGRAM} STREQUAL "gzip")
# -n for no timestamp in files (reproducible builds)
set (COMPRESS_ARGS -c -n)
# -9 for maximum compression (lintian error)
set (COMPRESS_ARGS -c -n -9)
else ()
set (COMPRESS_ARGS -c)
endif ()
......@@ -152,10 +153,10 @@ ADD_SUBDIRECTORY(man)
# Packager
SET(CPACK_PACKAGE_NAME "maffilter")
SET(CPACK_PACKAGE_VENDOR "Julien Y. Dutheil")
SET(CPACK_PACKAGE_VERSION "1.3.0")
SET(CPACK_PACKAGE_VERSION "1.3.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "1")
SET(CPACK_PACKAGE_VERSION_MINOR "3")
SET(CPACK_PACKAGE_VERSION_PATCH "0")
SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Filtering of genome alignment in the Multiple Alignment Format (MAF)")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/LICENSE")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS")
......
......@@ -133,7 +133,7 @@ void help()
(*ApplicationTools::message << " ... param=option_file").endLine();
(*ApplicationTools::message).endLine();
(*ApplicationTools::message << " Refer to the MafFilter Manual for a list of available options.").endLine();
(*ApplicationTools::message << " Online version: http://biopp.univ-montp2.fr/manual/html/maffilter/").endLine();
(*ApplicationTools::message << " Online version: https://jydu.github.io/maffilter/Manual/index.html").endLine();
(*ApplicationTools::message << " Or type 'info maffilter' in a terminal.").endLine();
(*ApplicationTools::message << "__________________________________________________________________________").endLine();
}
......@@ -141,9 +141,9 @@ void help()
int main(int args, char** argv)
{
cout << "******************************************************************" << endl;
cout << "* MAF Filter, version 1.3.0 *" << endl;
cout << "* MAF Filter, version 1.3.1 *" << endl;
cout << "* Author: J. Dutheil Created on 10/09/10 *" << endl;
cout << "* Last Modif. 09/03/18 *" << endl;
cout << "* Last Modif. 18/08/18 *" << endl;
cout << "******************************************************************" << endl;
cout << endl;
......@@ -1617,7 +1617,7 @@ int main(int args, char** argv)
ApplicationTools::displayResult("-- Reference sequence", reference);
bool map3 = ApplicationTools::getBooleanParameter("map3", cmdArgs, false);
ApplicationTools::displayBooleanResult("-- Ouput map3 file", map3);
ApplicationTools::displayBooleanResult("-- Output map3 file", map3);
bool recodeChr = ApplicationTools::getBooleanParameter("recode_chr", cmdArgs, false);
ApplicationTools::displayBooleanResult("-- Recode chromosomes", recodeChr);
......
#! /bin/sh
arch=`uname -m`
version=1.1.99-1
version=1.3.0-1
strip MafFilter/maffilter
tar cvzf maffilter-${arch}-bin-static-${version}.tar.gz MafFilter/maffilter
......
......@@ -13,7 +13,7 @@ find_program (MAKEINFO NAMES makeinfo texi2any DOC "makeinfo doc generator progr
if (NOT MAKEINFO)
message (STATUS "makeinfo program not found: 'info' and 'html' target disabled (builds info/html doc)")
else (NOT MAKEINFO)
message (STATUS "Found makeinfo as '${MAKEINFO}': 'info' and 'html' target enabled (builds info/html doc)")
message (STATUS "Found ${MAKEINFO}: 'info' and 'html' target enabled (builds info/html doc)")
set (input ${CMAKE_CURRENT_SOURCE_DIR}/maffilter.texi)
......@@ -58,6 +58,19 @@ else (NOT MAKEINFO)
)
add_custom_target (html DEPENDS ${output})
# Also provide a "html-multipages" target that builds html doc (not installed, and not part of "all").
set (output ${CMAKE_CURRENT_BINARY_DIR}/html/)
set (makeinfo-css "http://www.w3.org/StyleSheets/Core/Steely")
add_custom_command (
OUTPUT ${output}
COMMAND ${MAKEINFO} --html --no-headers --css-ref=${makeinfo-css} -o ${output} ${input}
DEPENDS ${input}
COMMENT "Generating html (multipages) doc"
VERBATIM
)
add_custom_target (html-multipages DEPENDS ${output})
# Provide a "pdf" target that builds pdf doc (not installed, not part of "all").
find_program (TEXIDVI NAMES texi2dvi)
if (TEXIDVI)
......
\input texinfo @c -*-texinfo-*-
@c %**start of header
@setfilename maffilter.info
@settitle MafFilter Manual 1.3.0
@settitle MafFilter Manual 1.3.1
@c @documentencoding UTF-8
@afourpaper
@dircategory Science Biology Genetics
......@@ -12,7 +12,7 @@
@copying
This is the manual of MafFilter, version 1.3.0.
This is the manual of MafFilter, version 1.3.1.
Copyright @copyright{} 2018 Julien Y. Dutheil
@end copying
......
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<!-- This is the manual of MafFilter, version 1.3.1.
Copyright (C) 2018 Julien Y. Dutheil -->
<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
<head>
<title>MafFilter Manual 1.3.1: AlnFilter</title>
<meta name="description" content="MafFilter Manual 1.3.1: AlnFilter">
<meta name="keywords" content="MafFilter Manual 1.3.1: AlnFilter">
<meta name="resource-type" content="document">
<meta name="distribution" content="global">
<meta name="Generator" content="makeinfo">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<link href="index.html#Top" rel="start" title="Top">
<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
<link href="Cleaning.html#Cleaning" rel="up" title="Cleaning">
<link href="AlnFilter2.html#AlnFilter2" rel="next" title="AlnFilter2">
<link href="RemoveEmptySequences.html#RemoveEmptySequences" rel="prev" title="RemoveEmptySequences">
<style type="text/css">
<!--
a.summary-letter {text-decoration: none}
blockquote.indentedblock {margin-right: 0em}
blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
blockquote.smallquotation {font-size: smaller}
div.display {margin-left: 3.2em}
div.example {margin-left: 3.2em}
div.lisp {margin-left: 3.2em}
div.smalldisplay {margin-left: 3.2em}
div.smallexample {margin-left: 3.2em}
div.smalllisp {margin-left: 3.2em}
kbd {font-style: oblique}
pre.display {font-family: inherit}
pre.format {font-family: inherit}
pre.menu-comment {font-family: serif}
pre.menu-preformatted {font-family: serif}
pre.smalldisplay {font-family: inherit; font-size: smaller}
pre.smallexample {font-size: smaller}
pre.smallformat {font-family: inherit; font-size: smaller}
pre.smalllisp {font-size: smaller}
span.nolinebreak {white-space: nowrap}
span.roman {font-family: initial; font-weight: normal}
span.sansserif {font-family: sans-serif; font-weight: normal}
ul.no-bullet {list-style: none}
-->
</style>
<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
</head>
<body lang="en">
<a name="AlnFilter"></a>
<div class="header">
<p>
Next: <a href="AlnFilter2.html#AlnFilter2" accesskey="n" rel="next">AlnFilter2</a>, Previous: <a href="RemoveEmptySequences.html#RemoveEmptySequences" accesskey="p" rel="prev">RemoveEmptySequences</a>, Up: <a href="Cleaning.html#Cleaning" accesskey="u" rel="up">Cleaning</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
</div>
<a name="Alignment-filtering"></a>
<h4 class="subsection">2.2.5 Alignment filtering</h4>
<p>Split alignment blocks by removing regions with ambiguous alignments.
The local uncertainty in the alignment is determined through a sliding window based approach.
For each window, the number of gap characters and the total entropy are computed. Any window
for which both the entropy and number of gaps exceed the given thresholds will be removed from
the alignment, and the corresponding block split accordingly.
</p>
<a name="Synopsis_003a-13"></a>
<h3 class="heading">Synopsis:</h3>
<table class="cartouche" border="1"><tr><td>
<div class="example">
<pre class="example">maf.filter= \
[...],
AlnFilter( \
species=(species1,species2,etc), \
window.size=10, \
window.step=1, \
max.gap=9, \
max.ent=0.2, \
missing_as_gap=yes, \
relative=no, \
file=data.trash_aln.maf.gz, \
compression=gzip), \
[...]
</pre></div>
</td></tr></table>
<a name="Arguments_003a-12"></a>
<h3 class="heading">Arguments:</h3>
<dl compact="compact">
<dt><code>species=(species1, species2, etc)</code></dt>
<dd><p>A coma separated, within parentheses, list of species. All calculations will be performed on the sub-alignment corresponding to these species only.
</p>
</dd>
<dt><code>window.size={int&gt;0}</code></dt>
<dd><p>The width, in bp, of the sliding window.
</p>
</dd>
<dt><code>window.step={int&gt;0}</code></dt>
<dd><p>The step by which the window is moved, in bp.
</p>
</dd>
<dt><code>relative={boolean}</code></dt>
<dd><p>Tell if maximum amount of gap is relative (that is, as a proportion of the total amount of character in each window).
</p>
</dd>
<dt><code>max.gap={int&gt;0|1&gt;double&gt;0}</code></dt>
<dd><p>The maximum number of gaps allowed in each window (if relative is set to no), or the maximum proportion of gaps (if relative is set to yes)
</p>
</dd>
<dt><code>max.ent={float}</code></dt>
<dd><p>The maximum entropy allowed in each window.
</p>
</dd>
<dt><code>missing_as_gap={yes/no}</code></dt>
<dd><p>Tell if missing sequences should be considered as gaps.
</p>
</dd>
<dt><code>file={none|{path}}</code></dt>
<dd><p>An optional file were removed alignment parts will be stored, in the MAF format.
This can be helpful for visual inspection and fine tuning of the filter parameters.
</p>
</dd>
<dt><code>compression={none|gzip|zip|bzip2}</code></dt>
<dd><p>Compression format for output file (if file != none).
</p>
</dd>
</dl>
</body>
</html>
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<!-- This is the manual of MafFilter, version 1.3.1.
Copyright (C) 2018 Julien Y. Dutheil -->
<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
<head>
<title>MafFilter Manual 1.3.1: AlnFilter2</title>
<meta name="description" content="MafFilter Manual 1.3.1: AlnFilter2">
<meta name="keywords" content="MafFilter Manual 1.3.1: AlnFilter2">
<meta name="resource-type" content="document">
<meta name="distribution" content="global">
<meta name="Generator" content="makeinfo">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<link href="index.html#Top" rel="start" title="Top">
<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
<link href="Cleaning.html#Cleaning" rel="up" title="Cleaning">
<link href="EntropyFilter.html#EntropyFilter" rel="next" title="EntropyFilter">
<link href="AlnFilter.html#AlnFilter" rel="prev" title="AlnFilter">
<style type="text/css">
<!--
a.summary-letter {text-decoration: none}
blockquote.indentedblock {margin-right: 0em}
blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
blockquote.smallquotation {font-size: smaller}
div.display {margin-left: 3.2em}
div.example {margin-left: 3.2em}
div.lisp {margin-left: 3.2em}
div.smalldisplay {margin-left: 3.2em}
div.smallexample {margin-left: 3.2em}
div.smalllisp {margin-left: 3.2em}
kbd {font-style: oblique}
pre.display {font-family: inherit}
pre.format {font-family: inherit}
pre.menu-comment {font-family: serif}
pre.menu-preformatted {font-family: serif}
pre.smalldisplay {font-family: inherit; font-size: smaller}
pre.smallexample {font-size: smaller}
pre.smallformat {font-family: inherit; font-size: smaller}
pre.smalllisp {font-size: smaller}
span.nolinebreak {white-space: nowrap}
span.roman {font-family: initial; font-weight: normal}
span.sansserif {font-family: sans-serif; font-weight: normal}
ul.no-bullet {list-style: none}
-->
</style>
<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
</head>
<body lang="en">
<a name="AlnFilter2"></a>
<div class="header">
<p>
Next: <a href="EntropyFilter.html#EntropyFilter" accesskey="n" rel="next">EntropyFilter</a>, Previous: <a href="AlnFilter.html#AlnFilter" accesskey="p" rel="prev">AlnFilter</a>, Up: <a href="Cleaning.html#Cleaning" accesskey="u" rel="up">Cleaning</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
</div>
<a name="Alignment-filtering-2"></a>
<h4 class="subsection">2.2.6 Alignment filtering 2</h4>
<p>This is another algorithm for cleaning alignment blocks (see AlnFilter), using sliding windows.
The number of gaps in each alignment column in the window is counted, and the column is masked if it contains more than a given threshold of gaps. consecutive patterns in the window are only counted ones. In the follwing 10nt window:
</p><pre class="verbatim">AATCGGGCGT
AA---GCGGA
AA---CGGGT
CA---CGGGA
</pre><p>positions 3, 4 and 5 will be masked if the maximum number of gaps allowed is 2 or less. The three columns will however count as only one indel event.
The window is then discarded if it contains more than a given number of indel events.
</p>
<a name="Synopsis_003a-14"></a>
<h3 class="heading">Synopsis:</h3>
<table class="cartouche" border="1"><tr><td>
<div class="example">
<pre class="example">maf.filter= \
[...],
AlnFilter2( \
species=(species1,species2,etc), \
window.size=10, \
window.step=1, \
max.gap=1, \
max.pos=1, \
relative=no, \
missing_as_gap=yes, \
file=data.trash_aln.maf.gz, \
compression=gzip), \
[...]
</pre></div>
</td></tr></table>
<a name="Arguments_003a-13"></a>
<h3 class="heading">Arguments:</h3>
<dl compact="compact">
<dt><code>species=(species1, species2, etc)</code></dt>
<dd><p>A coma separated, within parentheses, list of species. All calculations will be performed on the sub-alignment corresponding to these species only.
</p>
</dd>
<dt><code>window.size={int&gt;0}</code></dt>
<dd><p>The width, in bp, of the sliding window.
</p>
</dd>
<dt><code>window.step={int&gt;0}</code></dt>
<dd><p>The step by which the window is moved, in bp.
</p>
</dd>
<dt><code>relative={boolean}</code></dt>
<dd><p>Tell if maximum amount of gap is relative (that is, as a proportion of the total amount of character in each site).
</p>
</dd>
<dt><code>max.gap={int&gt;0|1&gt;double&gt;0}</code></dt>
<dd><p>The maximum number of gaps allowed in each site (if relative is set to no), or the maximum proportion of gaps (if relative is set to yes)
</p>
</dd>
<dt><code>max.pos={int&gt;0}</code></dt>
<dd><p>The maximum number of positions with gaps (&ldquo;indel events&rdquo;).
</p>
</dd>
<dt><code>missing_as_gap={yes/no}</code></dt>
<dd><p>Tell if missing sequences should be considered as gaps.
</p>
</dd>
<dt><code>file={none|{path}}</code></dt>
<dd><p>An optional file were removed alignment parts will be stored, in the MAF format.
This can be helpful for visual inspection and fine tuning of the filter parameters.
</p>
</dd>
<dt><code>compression={none|gzip|zip|bzip2}</code></dt>
<dd><p>Compression format for output file (if file != none).
</p>
</dd>
</dl>
</body>
</html>
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<!-- This is the manual of MafFilter, version 1.3.1.
Copyright (C) 2018 Julien Y. Dutheil -->
<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
<head>
<title>MafFilter Manual 1.3.1: AlnScore</title>
<meta name="description" content="MafFilter Manual 1.3.1: AlnScore">
<meta name="keywords" content="MafFilter Manual 1.3.1: AlnScore">
<meta name="resource-type" content="document">
<meta name="distribution" content="global">
<meta name="Generator" content="makeinfo">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<link href="index.html#Top" rel="start" title="Top">
<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
<link href="Descriptive.html#Descriptive" rel="up" title="Descriptive">
<link href="BlockCounts.html#BlockCounts" rel="next" title="BlockCounts">
<link href="SequenceLength.html#SequenceLength" rel="prev" title="SequenceLength">
<style type="text/css">
<!--
a.summary-letter {text-decoration: none}
blockquote.indentedblock {margin-right: 0em}
blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
blockquote.smallquotation {font-size: smaller}
div.display {margin-left: 3.2em}
div.example {margin-left: 3.2em}
div.lisp {margin-left: 3.2em}
div.smalldisplay {margin-left: 3.2em}
div.smallexample {margin-left: 3.2em}
div.smalllisp {margin-left: 3.2em}
kbd {font-style: oblique}
pre.display {font-family: inherit}
pre.format {font-family: inherit}
pre.menu-comment {font-family: serif}
pre.menu-preformatted {font-family: serif}
pre.smalldisplay {font-family: inherit; font-size: smaller}
pre.smallexample {font-size: smaller}
pre.smallformat {font-family: inherit; font-size: smaller}
pre.smalllisp {font-size: smaller}
span.nolinebreak {white-space: nowrap}
span.roman {font-family: initial; font-weight: normal}
span.sansserif {font-family: sans-serif; font-weight: normal}
ul.no-bullet {list-style: none}
-->
</style>
<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
</head>
<body lang="en">
<a name="AlnScore"></a>
<div class="header">
<p>
Next: <a href="BlockCounts.html#BlockCounts" accesskey="n" rel="next">BlockCounts</a>, Previous: <a href="SequenceLength.html#SequenceLength" accesskey="p" rel="prev">SequenceLength</a>, Up: <a href="Descriptive.html#Descriptive" accesskey="u" rel="up">Descriptive</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
</div>
<a name="Alignment-score"></a>
<h4 class="subsubsection">2.3.1.4 Alignment score</h4>
<p>The <code>AlnScore</code> statistics reports the alignment score associated to the block, if any.
</p>
<p>(No argument)
</p>
</body>
</html>
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<!-- This is the manual of MafFilter, version 1.3.1.
Copyright (C) 2018 Julien Y. Dutheil -->
<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
<head>
<title>MafFilter Manual 1.3.1: Analyzing</title>
<meta name="description" content="MafFilter Manual 1.3.1: Analyzing">
<meta name="keywords" content="MafFilter Manual 1.3.1: Analyzing">
<meta name="resource-type" content="document">
<meta name="distribution" content="global">
<meta name="Generator" content="makeinfo">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<link href="index.html#Top" rel="start" title="Top">
<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
<link href="Filters.html#Filters" rel="up" title="Filters">
<link href="Descriptive.html#Descriptive" rel="next" title="Descriptive">
<link href="FeatureFilter.html#FeatureFilter" rel="prev" title="FeatureFilter">
<style type="text/css">
<!--
a.summary-letter {text-decoration: none}
blockquote.indentedblock {margin-right: 0em}
blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
blockquote.smallquotation {font-size: smaller}
div.display {margin-left: 3.2em}
div.example {margin-left: 3.2em}
div.lisp {margin-left: 3.2em}
div.smalldisplay {margin-left: 3.2em}
div.smallexample {margin-left: 3.2em}
div.smalllisp {margin-left: 3.2em}
kbd {font-style: oblique}
pre.display {font-family: inherit}
pre.format {font-family: inherit}
pre.menu-comment {font-family: serif}
pre.menu-preformatted {font-family: serif}
pre.smalldisplay {font-family: inherit; font-size: smaller}
pre.smallexample {font-size: smaller}
pre.smallformat {font-family: inherit; font-size: smaller}
pre.smalllisp {font-size: smaller}
span.nolinebreak {white-space: nowrap}
span.roman {font-family: initial; font-weight: normal}
span.sansserif {font-family: sans-serif; font-weight: normal}
ul.no-bullet {list-style: none}
-->
</style>
<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
</head>
<body lang="en">
<a name="Analyzing"></a>
<div class="header">
<p>
Next: <a href="Exporting.html#Exporting" accesskey="n" rel="next">Exporting</a>, Previous: <a href="Cleaning.html#Cleaning" accesskey="p" rel="prev">Cleaning</a>, Up: <a href="Filters.html#Filters" accesskey="u" rel="up">Filters</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
</div>
<a name="Statistical-analysis"></a>
<h3 class="section">2.3 Statistical analysis</h3>
</body>
</html>
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<!-- This is the manual of MafFilter, version 1.3.1.
Copyright (C) 2018 Julien Y. Dutheil -->
<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
<head>
<title>MafFilter Manual 1.3.1: BlockCounts</title>
<meta name="description" content="MafFilter Manual 1.3.1: BlockCounts">
<meta name="keywords" content="MafFilter Manual 1.3.1: BlockCounts">
<meta name="resource-type" content="document">
<meta name="distribution" content="global">
<meta name="Generator" content="makeinfo">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<link href="index.html#Top" rel="start" title="Top">
<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
<link href="Descriptive.html#Descriptive" rel="up" title="Descriptive">
<link href="PairwiseDivergence.html#PairwiseDivergence" rel="next" title="PairwiseDivergence">
<link href="AlnScore.html#AlnScore" rel="prev" title="AlnScore">
<style type="text/css">
<!--
a.summary-letter {text-decoration: none}
blockquote.indentedblock {margin-right: 0em}
blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
blockquote.smallquotation {font-size: smaller}
div.display {margin-left: 3.2em}
div.example {margin-left: 3.2em}
div.lisp {margin-left: 3.2em}
div.smalldisplay {margin-left: 3.2em}
div.smallexample {margin-left: 3.2em}
div.smalllisp {margin-left: 3.2em}
kbd {font-style: oblique}
pre.display {font-family: inherit}
pre.format {font-family: inherit}
pre.menu-comment {font-family: serif}
pre.menu-preformatted {font-family: serif}
pre.smalldisplay {font-family: inherit; font-size: smaller}
pre.smallexample {font-size: smaller}
pre.smallformat {font-family: inherit; font-size: smaller}
pre.smalllisp {font-size: smaller}
span.nolinebreak {white-space: nowrap}
span.roman {font-family: initial; font-weight: normal}
span.sansserif {font-family: sans-serif; font-weight: normal}
ul.no-bullet {list-style: none}
-->
</style>
<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
</head>
<body lang="en">
<a name="BlockCounts"></a>
<div class="header">
<p>
Next: <a href="PairwiseDivergence.html#PairwiseDivergence" accesskey="n" rel="next">PairwiseDivergence</a>, Previous: <a href="AlnScore.html#AlnScore" accesskey="p" rel="prev">AlnScore</a>, Up: <a href="Descriptive.html#Descriptive" accesskey="u" rel="up">Descriptive</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
</div>
<a name="Character-frequencies"></a>
<h4 class="subsubsection">2.3.1.5 Character frequencies</h4>
<p>The <code>BlockCounts</code> statistics reports the count of each character found in the block.
</p>
<p>Note: this statistics does not work in case of duplicated sequences (multiple hits from the same chromosome / scaffold / contig).
</p>
<a name="Arguments_003a-20"></a>
<h3 class="heading">Arguments:</h3>
<dl compact="compact">
<dt><code>species={list}</code></dt>
<dd><p>A list of species to be considered in the counts calculations. If no species is given, all sequences are used.
</p></dd>
<dt><code>suffix={string}</code></dt>
<dd><p>An (optional) suffix to append to the statistics name. Useful in case the statistics should be computed for several species independently.
</p></dd>
</dl>
</body>
</html>
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<!-- This is the manual of MafFilter, version 1.3.1.
Copyright (C) 2018 Julien Y. Dutheil -->
<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
<head>
<title>MafFilter Manual 1.3.1: BlockLength</title>
<meta name="description" content="MafFilter Manual 1.3.1: BlockLength">
<meta name="keywords" content="MafFilter Manual 1.3.1: BlockLength">
<meta name="resource-type" content="document">
<meta name="distribution" content="global">
<meta name="Generator" content="makeinfo">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<link href="index.html#Top" rel="start" title="Top">
<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
<link href="Descriptive.html#Descriptive" rel="up" title="Descriptive">
<link href="SequenceLength.html#SequenceLength" rel="next" title="SequenceLength">
<link href="BlockSize.html#BlockSize" rel="prev" title="BlockSize">
<style type="text/css">
<!--
a.summary-letter {text-decoration: none}
blockquote.indentedblock {margin-right: 0em}
blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
blockquote.smallquotation {font-size: smaller}
div.display {margin-left: 3.2em}
div.example {margin-left: 3.2em}
div.lisp {margin-left: 3.2em}
div.smalldisplay {margin-left: 3.2em}
div.smallexample {margin-left: 3.2em}
div.smalllisp {margin-left: 3.2em}
kbd {font-style: oblique}
pre.display {font-family: inherit}
pre.format {font-family: inherit}
pre.menu-comment {font-family: serif}
pre.menu-preformatted {font-family: serif}
pre.smalldisplay {font-family: inherit; font-size: smaller}
pre.smallexample {font-size: smaller}
pre.smallformat {font-family: inherit; font-size: smaller}
pre.smalllisp {font-size: smaller}
span.nolinebreak {white-space: nowrap}
span.roman {font-family: initial; font-weight: normal}
span.sansserif {font-family: sans-serif; font-weight: normal}
ul.no-bullet {list-style: none}
-->
</style>
<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
</head>
<body lang="en">
<a name="BlockLength"></a>
<div class="header">
<p>
Next: <a href="SequenceLength.html#SequenceLength" accesskey="n" rel="next">SequenceLength</a>, Previous: <a href="BlockSize.html#BlockSize" accesskey="p" rel="prev">BlockSize</a>, Up: <a href="Descriptive.html#Descriptive" accesskey="u" rel="up">Descriptive</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
</div>
<a name="Length-of-alignment-blocks"></a>
<h4 class="subsubsection">2.3.1.2 Length of alignment blocks</h4>
<p>The <code>BlockLength</code> statistics reports the number of sites in the block.
</p>
<p>(No argument)
</p>
</body>
</html>
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<!-- This is the manual of MafFilter, version 1.3.1.
Copyright (C) 2018 Julien Y. Dutheil -->
<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
<head>
<title>MafFilter Manual 1.3.1: BlockSize</title>
<meta name="description" content="MafFilter Manual 1.3.1: BlockSize">
<meta name="keywords" content="MafFilter Manual 1.3.1: BlockSize">