[med-svn] r15570 - trunk/packages/primer3/trunk/debian
Andreas Tille
tille at moszumanska.debian.org
Thu Dec 19 10:41:12 UTC 2013
Author: tille
Date: 2013-12-19 10:41:12 +0000 (Thu, 19 Dec 2013)
New Revision: 15570
Added:
trunk/packages/primer3/trunk/debian/ntthal.1
Removed:
trunk/packages/primer3/trunk/debian/ntdpal.1.xml
trunk/packages/primer3/trunk/debian/oligotm.1.xml
trunk/packages/primer3/trunk/debian/primer3_core.1.xml
Modified:
trunk/packages/primer3/trunk/debian/changelog
trunk/packages/primer3/trunk/debian/primer3.install
trunk/packages/primer3/trunk/debian/primer3.manpages
Log:
New executable: ntthal (including manpage); Removed *.xml variants of manpages to reduce redundancy
Modified: trunk/packages/primer3/trunk/debian/changelog
===================================================================
--- trunk/packages/primer3/trunk/debian/changelog 2013-12-19 10:38:54 UTC (rev 15569)
+++ trunk/packages/primer3/trunk/debian/changelog 2013-12-19 10:41:12 UTC (rev 15570)
@@ -16,7 +16,9 @@
instead of /opt/primer3_config/
Closes: #702693
* Verified that new upstream
- Closes: #716151, #716213.
+ Closes: #716151, #716213
+ * New executable: ntthal (including manpage)
+ * Removed *.xml variants of manpages to reduce redundancy
-- Andreas Tille <tille at debian.org> Thu, 19 Dec 2013 09:58:19 +0100
Deleted: trunk/packages/primer3/trunk/debian/ntdpal.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2013-12-19 10:38:54 UTC (rev 15569)
+++ trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2013-12-19 10:41:12 UTC (rev 15570)
@@ -1,222 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<?xml-stylesheet type="text/xsl"
- href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
- "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
- <!ENTITY dhfirstname "<firstname>Charles</firstname>">
- <!ENTITY dhsurname "<surname>Plessy</surname>">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>plessy at debian.org</email>">
- <!ENTITY dhusername "Charles Plessy">
- <!ENTITY dhtitle "Primer3 User Manuals">
- <!ENTITY dhucpackage "<refentrytitle>NTDPAL</refentrytitle>">
- <!ENTITY dhpackage "ntdpal">
- <!ENTITY dhrelease "1.1.4">
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
-]>
-
-<refentry>
- <refentryinfo>
- <title>&dhtitle;</title>
- <productname>&dhpackage;</productname>
- <releaseinfo role="version">&dhrelease;</releaseinfo>
- <address>
- &dhemail;
- </address>
- <!-- <author>
- &dhfirstname;
- &dhsurname;
- </author> -->
- <copyright>
- <year>1996,1997,1998,1999,2000,2001,2004,2006,2007,2008</year>
- <holder>Whitehead Institute for Biomedical Research</holder>
- <holder>Steve Rozen (http://jura.wi.mit.edu/rozen)</holder>
- <holder>Helen Skaletsky</holder>
- </copyright>
-
- <legalnotice>
- <para>All rights reserved. On Debian-based systems, please consult <filename>/usr/share/doc/primer3/copyright</filename> to read the licence of &dhpackage;.</para>
- </legalnotice>
-
- <legalnotice>
- <para>This manual page was written by &dhusername; <&dhemail;> for
- the &debian; system (but may be used by others). Permission is
- granted to copy, distribute and/or modify this document under
- the same terms as oligotm itself.<!-- This also applies to this source document --></para>
- </legalnotice>
- </refentryinfo>
-
- <refmeta>
- &dhucpackage;
- &dhsection;
- </refmeta>
-
- <refnamediv>
- <refname>&dhpackage;</refname>
-
- <refpurpose>Provides Primer3's alignment functionality</refpurpose>
- </refnamediv>
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="opt">
- -g <replaceable class="parameter">gval</replaceable>
- </arg>
- <arg choice="opt">
- -l <replaceable class="parameter">lval</replaceable>
- </arg>
- <arg choice="opt">
- -m <replaceable class="parameter">mval</replaceable>
- </arg>
- <arg choice="opt">-f1, f2, f3</arg>
- <arg choice="opt">-p</arg>
- <arg choice="opt">-s</arg>
- <arg choice="opt">-e</arg>
- <arg choice="req">
- <replaceable class="parameter">seq1</replaceable>
- </arg>
- <arg choice="req">
- <replaceable class="parameter">seq2</replaceable>
- </arg>
- <arg choice="req"><replaceable class="parameter">mode</replaceable></arg>
- </cmdsynopsis>
- </refsynopsisdiv>
- <refsect1>
- <title>DESCRIPTION</title>
-
- <para>
- Ntdpal (NucleoTide Dynamic Programming ALignment) is a stand-alone program
- that provides Primer3's alignment functionality (local, a.k.a.
- Smith-Waterman, global, a.k.a. Needleman-Wunsch, plus "half global").
- </para>
- </refsect1>
-
- <refsect1>
- <title>OPTIONS</title>
-
- <variablelist>
- <varlistentry>
- <term>
- <option>-g</option> <parameter>gval</parameter>
- </term>
- <listitem>
- <para><parameter>gval</parameter> is a (positive) float (.01 precision) specifying penalty for creating a gap respectively (the penalties are subtracted from the output score)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-l</option> <parameter>val</parameter>
- </term>
- <listitem>
- <para><parameter>lval</parameter> is a (positive) float (.01 precision) specifying penalty for lengthening a gap respectively (the penalties are subtracted from the output score)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-a</option>
- </term>
- <listitem>
- <para>Causes the scoring matrix to be modified by dpal_set_ambiguity_codes.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-e</option>
- </term>
- <listitem>
- <para>Causes the end position of the alignment in both sequences to be printed. Do not confuse with the 'e' <emphasis>mode</emphasis>.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-f1, -f2, -f3</option>
- </term>
- <listitem>
- <para>Force specific implementations. -f2 forces use an implementation that might provide more informative error messages, possibly at the expense of some speed.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-h</option>
- </term>
- <listitem>
- <para>Use a different scoring matrix: G and C matches = 3, A and T = 2, and mismatches = -0.5. (The default scoring matrix assigns 1 to a match, and -1 to a mismatch.)
- </para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-p</option>
- </term>
- <listitem>
- <para>Causes the alignment to be displayed on stderr.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-s</option>
- </term>
- <listitem>
- <para>causes <emphasis>only</emphasis> the score to printed.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-m</option> <parameter>mval</parameter>
- </term>
- <listitem>
- <para>is the maximum allowed gap (default is 3).</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <replaceable>seq1</replaceable> and <replaceable>seq2</replaceable>
- </term>
- <listitem>
- <para>are the sequences to be aligned.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <replaceable>mode</replaceable>
- </term>
- <listitem>
- <para> is one of <parameter>g</parameter>, <parameter>G</parameter>, <parameter>l</parameter>, or <parameter>L</parameter> specifying a global, global end-anchored, local, or local end-anchored alignment respectively. For backward compatibility <parameter>e</parameter> is equivalent to <parameter>G</parameter>.</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
-
- <refsect1>
- <title>REFERENCE</title>
- <para>
- Please cite Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users and for biologist programmers." In S. Krawetz and S. Misener, eds. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology. Humana Press, Totowa, NJ, 2000, pages 365-386.
- </para>
- </refsect1>
-
- <refsect1>
- <title>SEE ALSO</title>
- <para>
- <citerefentry>
- <refentrytitle>primer3_core</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>
- <citerefentry>
- <refentrytitle>oligotm</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>
- </para>
- </refsect1>
-</refentry>
Added: trunk/packages/primer3/trunk/debian/ntthal.1
===================================================================
--- trunk/packages/primer3/trunk/debian/ntthal.1 (rev 0)
+++ trunk/packages/primer3/trunk/debian/ntthal.1 2013-12-19 10:41:12 UTC (rev 15570)
@@ -0,0 +1,40 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3.
+.TH NTTHAL "1" "December 2013" "2.3.6" "Primer3 User Manuals"
+.SH NAME
+ntthal \- Provides Primer3's alignment functionality based on nearest-neighbor thermodynamical approach
+.SH DESCRIPTION
+\fBntthal\fR is analogous to \fBntdpal\fR. Between two sequences, \fBntthal\fR finds
+alignment/sec structure, that has the highest melting
+temperature. Ntthal is based on nearest-neighbor thermodynamical
+approach.
+.SH SYNOPSIS
+.B ntthal
+\fIOPTIONS\fR oligo
+.SH OPTIONS
+\fB\-mv\fR monovalent_conc \- concentration of monovalent cations in mM, by default 50 mM
+.PP
+\fB\-dv\fR divalent_conc \- concentration of divalent cations in mM, by default 0 mM
+.PP
+\fB\-n\fR dNTP_conc \- concentration of deoxynycleotide triphosphate in mM, by default 0 mM
+.PP
+\fB\-d\fR dna_conc \- concentration of DNA strands in nM, by default 50 nM
+.PP
+\fB\-a\fR mode \- alignment type, END1, END2, ANY and HAIRPIN, by default ANY (when duplex)
+.PP
+\fB\-t\fR temp \- temperature at which duplex is calculated, by default 37C
+.PP
+\fB\-r\fR \- causes the alignment NOT to be displayed on stderr, _only_ Tm is printed
+.PP
+\fB\-maxloop\fR size \- the maximum size of secondary structures loops.
+.IP
+Default is 30 (this is maximum allowed length, currently).
+.PP
+\fB\-path\fR <path> \- the path to the thermodynamic parameter files
+.PP
+\fB\-s1\fR DNA_oligomer
+.PP
+\fB\-s2\fR DNA_oligomer
+.SH AUTHORS
+This manual page was created by Andreas Tille <tille at debian.org> using help2man
+for Debian but can be freely used for any other purpose
+
Deleted: trunk/packages/primer3/trunk/debian/oligotm.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/oligotm.1.xml 2013-12-19 10:38:54 UTC (rev 15569)
+++ trunk/packages/primer3/trunk/debian/oligotm.1.xml 2013-12-19 10:41:12 UTC (rev 15570)
@@ -1,189 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<?xml-stylesheet type="text/xsl"
- href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
- "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
- <!ENTITY dhfirstname "<firstname>Charles</firstname>">
- <!ENTITY dhsurname "<surname>Plessy</surname>">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>plessy at debian.org</email>">
- <!ENTITY dhusername "Charles Plessy">
- <!ENTITY dhucpackage "<refentrytitle>OLIGOTM</refentrytitle>">
- <!ENTITY dhtitle "Primer3 User Manuals">
- <!ENTITY dhpackage "oligotm">
- <!ENTITY dhrelease "1.1.4">
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
-]>
-
-<refentry>
- <refentryinfo>
- <title>&dhtitle;</title>
- <productname>&dhpackage;</productname>
- <releaseinfo role="version">&dhrelease;</releaseinfo>
- <address>
- &dhemail;
- </address>
- <!-- <author>
- &dhfirstname;
- &dhsurname;
- </author> -->
- <copyright>
- <year>1996,1997,1998,1999,2000,2001,2004,2006,2007,2008</year>
- <holder>Whitehead Institute for Biomedical Research</holder>
- <holder>Steve Rozen (http://jura.wi.mit.edu/rozen)</holder>
- <holder>Helen Skaletsky</holder>
- </copyright>
-
- <legalnotice>
- <para>All rights reserved. On Debian-based systems, please consult <filename>/usr/share/doc/primer3/copyright</filename> to read the licence of &dhpackage;.</para>
- </legalnotice>
-
- <legalnotice>
- <para>This manual page was written by &dhusername; <&dhemail;> for
- the &debian; system (but may be used by others). Permission is
- granted to copy, distribute and/or modify this document under
- the same terms as oligotm itself.<!-- This also applies to this source document --></para>
- </legalnotice>
- </refentryinfo>
-
- <refmeta>
- &dhucpackage;
- &dhsection;
- </refmeta>
-
- <refnamediv>
- <refname>&dhpackage;</refname>
- <refpurpose>Prints oligo's melting temperature on stdout</refpurpose>
- </refnamediv>
-
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="opt">OPTIONS</arg>
- <arg choice="req">oligo</arg>
- </cmdsynopsis>
- <para>where oligo is a DNA sequence of between 2 and 36 bases</para>
- </refsynopsisdiv>
-
- <refsect1 id="description">
- <title>DESCRIPTION</title>
- <para>
- <command>&dhpackage;</command> prints the melting temperature of a given deoxyribonucleotide on the standard output. It is part of the oligotm library.
- </para>
- </refsect1>
-
- <refsect1 id="options">
- <title>OPTIONS</title>
- <variablelist>
- <varlistentry>
- <term>
- <option>-mv</option> <parameter>monovalent_conc</parameter>
- </term>
- <listitem>
- <para>Concentration of monovalent cations in mM, by default 50 mM.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-dv</option> <parameter>divalent_conc</parameter>
- </term>
- <listitem>
- <para>Concentration of divalent cations in mM, by default 0 mM.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-n</option> <parameter>dNTP_conc</parameter>
- </term>
- <listitem>
- <para>Concentration of deoxynucleotide triphosphate in mM, by default 0 mM.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-d</option> <parameter>dna_conc</parameter>
- </term>
- <listitem>
- <para>Concentration of DNA strands in nM, by default 50 nM.</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-tp</option> <parameter>[0|1]</parameter>
- </term>
- <listitem>
- <para>Specifies the table of thermodynamic parameters and
- the method of melting temperature calculation:</para>
- <itemizedlist>
- <listitem>
- <para><parameter>0</parameter> Breslauer et al., 1986 and Rychlik et al., 1990 (used by primer3 up to and including release 1.1.0). This is the default, but <emphasis>not</emphasis> the recommended value.</para>
- </listitem>
- <listitem>
- <para><parameter>1</parameter> Use nearest neighbor parameter from SantaLucia 1998. <emphasis>This is the recommended value</emphasis>.</para>
- </listitem>
- </itemizedlist>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-sc</option> <parameter>[0..2]</parameter>
- </term>
- <listitem>
- <para>Specifies salt correction formula for the melting temperature calculation:</para>
- <itemizedlist>
- <listitem>
- <para><parameter>0</parameter> Schildkraut and Lifson 1965, used by primer3 up to and including release 1.1.0. This is the default, but <emphasis>not</emphasis> the recommended value.</para>
- </listitem>
- <listitem>
- <para><parameter>1</parameter> SantaLucia 1998. <emphasis>This is the recommended value</emphasis>.</para>
- </listitem>
- <listitem>
- <para><parameter>2</parameter> Owczarzy et al., 2004.</para>
- </listitem>
- </itemizedlist>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-i</option>
- </term>
- <listitem>
- <para>prints references to publications which were used for thermodynamic calculations.</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
-
- <refsect1 id="reference">
- <title>REFERENCE</title>
- <para>
- Please cite Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users
- and for biologist programmers." In S. Krawetz and
- S. Misener, eds. Bioinformatics Methods and Protocols in
- the series Methods in Molecular Biology. Humana Press,
- Totowa, NJ, 2000, pages 365-386.
- </para>
- </refsect1>
-
- <refsect1 id="see_also">
- <title>SEE ALSO</title>
- <para>
- <citerefentry>
- <refentrytitle>primer3_core</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>
- <citerefentry>
- <refentrytitle>ntdpal</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>
- </para>
- </refsect1>
-</refentry>
Modified: trunk/packages/primer3/trunk/debian/primer3.install
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.install 2013-12-19 10:38:54 UTC (rev 15569)
+++ trunk/packages/primer3/trunk/debian/primer3.install 2013-12-19 10:41:12 UTC (rev 15570)
@@ -1,5 +1,6 @@
src/primer3_core usr/bin
src/ntdpal usr/bin
+src/ntthal usr/bin
src/oligotm usr/bin
#src/long_seq_tm_test usr/bin
src/primer3_config etc
Modified: trunk/packages/primer3/trunk/debian/primer3.manpages
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.manpages 2013-12-19 10:38:54 UTC (rev 15569)
+++ trunk/packages/primer3/trunk/debian/primer3.manpages 2013-12-19 10:41:12 UTC (rev 15570)
@@ -1,3 +1 @@
-debian/ntdpal.1
-debian/primer3_core.1
-debian/oligotm.1
+debian/*.1
Deleted: trunk/packages/primer3/trunk/debian/primer3_core.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3_core.1.xml 2013-12-19 10:38:54 UTC (rev 15569)
+++ trunk/packages/primer3/trunk/debian/primer3_core.1.xml 2013-12-19 10:41:12 UTC (rev 15570)
@@ -1,153 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<?xml-stylesheet type="text/xsl"
- href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
- "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
- <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
- <!ENTITY dhsurname "<surname>Moeller</surname>">
- <!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhtitle "Primer3 User Manuals">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>moeller at debian.org</email>">
- <!ENTITY dhusername "Steffen Moeller">
- <!ENTITY dhucpackage "<refentrytitle>PRIMER3_CORE</refentrytitle>">
- <!ENTITY dhpackage "primer3_core">
- <!ENTITY dhrelease "1.1.4">
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
-]>
-
-<refentry>
- <refentryinfo>
- <title>&dhtitle;</title>
- <productname>&dhpackage;</productname>
- <releaseinfo role="version">&dhrelease;</releaseinfo>
- <address>
- &dhemail;
- </address>
-<!-- <author>
- &dhfirstname;
- &dhsurname;
- </author> -->
- <copyright>
- <year>1996,1997,1998,1999,2000,2001,2004,2006,2007,2008</year>
- <holder>Whitehead Institute for Biomedical Research</holder>
- <holder>Steve Rozen (http://jura.wi.mit.edu/rozen)</holder>
- <holder>Helen Skaletsky</holder>
- </copyright>
-
- <legalnotice>
- <para>All rights reserved. On Debian-based systems, please consult <filename>/usr/share/doc/primer3/copyright</filename> to read the licence of &dhpackage;.</para>
- </legalnotice>
-
- <legalnotice>
- <para>This manual page was written by &dhusername; &dhemail; for
- the &debian; system (but may be used by others). Permission is
- granted to copy, distribute and/or modify this document under
- the same terms as &dhpackage; itself.<!-- This also applies to this source document --></para>
- </legalnotice>
- </refentryinfo>
- <refmeta>
- &dhucpackage;
-
- &dhsection;
- </refmeta>
- <refnamediv>
- <refname>&dhpackage;</refname>
-
- <refpurpose>Designs primers for PCR</refpurpose>
- </refnamediv>
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage;</command>
- <arg choice="opt">-format_output</arg>
- <!-- <arg choice="opt">-2x_compat</arg> -->
- <arg choice="opt">-strict_tags</arg>
- <arg choice="opt">< <replaceable>input_file</replaceable></arg>
- </cmdsynopsis>
- </refsynopsisdiv>
-
- <refsect1>
- <title>DESCRIPTION</title>
-
- <para>
- &dhpackage; picks primers for PCR reactions, considering as criteria oligonucleotide melting temperature, size, GC content and primer-dimer possibilities, PCR product size, positional constraints within the source sequence, and miscellaneous other constraints.
- </para>
- <para>
- By default, &dhpackage; accepts input and produces output in Boulder-io format, a pre-XML text-based input/output format for program-to-program data interchange format. The Boulder-io format and the commands that &dhpackage; understands are described in the <filename>README</filename> file, which on Debian systems can be found in <filename class="directory">/usr/share/doc/primer3/</filename>.
- </para>
- </refsect1>
-
- <refsect1>
- <title>OPTIONS</title>
-
- <variablelist>
- <varlistentry>
- <term>
- <option>-format_output</option>
- </term>
- <listitem>
- <para> Prints a more user-oriented report for each sequence.</para>
- </listitem>
- </varlistentry>
-<!--
- <varlistentry>
- <term>
- <option>-2x_compat</option>
- </term>
- <listitem>
- <para>Print the output using Primer v2 compatible tag names.</para>
- </listitem>
- </varlistentry>
--->
- <varlistentry>
- <term>
- <option>-strict_tags</option>
- </term>
- <listitem>
- <para>
- &dhpackage; echoes and ignores any tags it does not recognize, unless the <option>-strict_tags</option> flag is set on the command line, in which case &dhpackage; prints an error in the PRIMER_ERROR output tag, and prints additional information on stdout; this option can be useful for debugging systems that incorporate primer.
- </para>
- </listitem>
- </varlistentry>
- </variablelist>
-
- <note><para>The old flag -2x_compat is no longer supported.</para></note>
- </refsect1>
-
- <refsect1>
- <title>EXIT STATUS CODES</title>
- <itemizedlist>
- <listitem><para> 0 on normal operation.</para></listitem>
- <listitem><para>-1 under the following conditions: illegal command-line arguments, unable to fflush stdout, unable to open (for writing and creating) a .for, .rev or .int file (probably due to a protection problem).</para></listitem>
- <listitem><para>-2 on out-of-memory.</para></listitem>
- <listitem><para>-3 empty input.</para></listitem>
- <listitem><para>-4 error in a "Global" input tag (message in PRIMER_ERROR).</para></listitem>
- </itemizedlist>
- </refsect1>
-
- <refsect1>
- <title>REFERENCE</title>
- <para>
- Please cite Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users and for biologist programmers." In S. Krawetz and S. Misener, eds. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology. Humana Press, Totowa, NJ, 2000, pages 365-386.
- </para>
- </refsect1>
-
- <refsect1>
- <title>SEE ALSO</title>
- <para>
- <citerefentry>
- <refentrytitle>ntdpal</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>
-
- <citerefentry>
- <refentrytitle>oligotm</refentrytitle>
- <manvolnum>1</manvolnum>
- </citerefentry>
- </para>
- </refsect1>
-
-</refentry>
-
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