[med-svn] r122 - in trunk/packages/primer3/branches/upstream/current: . src test test/primer_global_err

[Charles Plessy]

Author: charles-guest
Date: 2006-09-22 14:39:44 +0000 (Fri, 22 Sep 2006)
New Revision: 122

Added:
   trunk/packages/primer3/branches/upstream/current/Copyright.txt
   trunk/packages/primer3/branches/upstream/current/README.primer3_1.0b.txt
   trunk/packages/primer3/branches/upstream/current/how-to-cite.txt
   trunk/packages/primer3/branches/upstream/current/src/long_seq_tm_test_main.c
   trunk/packages/primer3/branches/upstream/current/src/oligotm_main.c
   trunk/packages/primer3/branches/upstream/current/src/release_notes.txt
   trunk/packages/primer3/branches/upstream/current/test/p3-tmpl-mispriming_input
   trunk/packages/primer3/branches/upstream/current/test/p3-tmpl-mispriming_output
   trunk/packages/primer3/branches/upstream/current/test/p3test.pl
   trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_equal.in
   trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_equal.out
   trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_equal.out2
   trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal_equal.in
   trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal_equal.out
   trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal_equal.out2
Removed:
   trunk/packages/primer3/branches/upstream/current/Copyright
   trunk/packages/primer3/branches/upstream/current/README
   trunk/packages/primer3/branches/upstream/current/src/release_notes
   trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no=.in
   trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no=.out
   trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no=.out2
   trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal=.in
   trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal=.out
   trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal=.out2
   trunk/packages/primer3/branches/upstream/current/test/primer_template_mispriming_input
   trunk/packages/primer3/branches/upstream/current/test/primer_template_mispriming_output
   trunk/packages/primer3/branches/upstream/current/test/primer_test.pl
Modified:
   trunk/packages/primer3/branches/upstream/current/src/Makefile
   trunk/packages/primer3/branches/upstream/current/src/boulder_input.c
   trunk/packages/primer3/branches/upstream/current/src/boulder_input.h
   trunk/packages/primer3/branches/upstream/current/src/dpal.c
   trunk/packages/primer3/branches/upstream/current/src/dpal.h
   trunk/packages/primer3/branches/upstream/current/src/format_output.c
   trunk/packages/primer3/branches/upstream/current/src/format_output.h
   trunk/packages/primer3/branches/upstream/current/src/ntdpal_main.c
   trunk/packages/primer3/branches/upstream/current/src/oligotm.c
   trunk/packages/primer3/branches/upstream/current/src/oligotm.h
   trunk/packages/primer3/branches/upstream/current/src/primer3.c
   trunk/packages/primer3/branches/upstream/current/src/primer3.h
   trunk/packages/primer3/branches/upstream/current/src/primer3_main.c
   trunk/packages/primer3/branches/upstream/current/src/primer3_release.h
   trunk/packages/primer3/branches/upstream/current/test/dpal_gen.pl
   trunk/packages/primer3/branches/upstream/current/test/dpal_test.pl
   trunk/packages/primer3/branches/upstream/current/test/long_seq_tm_test.pl
   trunk/packages/primer3/branches/upstream/current/test/primer_boundary1_formatted_output
   trunk/packages/primer3/branches/upstream/current/test/primer_boundary_formatted_output
   trunk/packages/primer3/branches/upstream/current/test/primer_global_err/empty_1.out2
   trunk/packages/primer3/branches/upstream/current/test/primer_internal1_formatted_output
   trunk/packages/primer3/branches/upstream/current/test/primer_internal_formatted_output
   trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary1_formatted_output
   trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary2_formatted_output
   trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_formatted_output
   trunk/packages/primer3/branches/upstream/current/test/primer_must_use_formatted_output
   trunk/packages/primer3/branches/upstream/current/test/primer_position_penalty_formatted_output
   trunk/packages/primer3/branches/upstream/current/test/primer_task_formatted_output
Log:
Load /tmp/tmp.sYMGbl/primer3-1.0b into
trunk/packages/primer3/branches/upstream/current.


Deleted: trunk/packages/primer3/branches/upstream/current/Copyright
===================================================================
--- trunk/packages/primer3/branches/upstream/current/Copyright	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/Copyright	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,44 +0,0 @@
- Copyright (c) 1996,1997,1998,1999,2000,2001,2004
-        Whitehead Institute for Biomedical Research. All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1.      Redistributions must reproduce the above copyright notice, this
-list of conditions and the following disclaimer in the  documentation
-and/or other materials provided with the distribution.  Redistributions of
-source code must also reproduce this information in the source code itself.
-
-2.      If the program is modified, redistributions must include a notice
-(in the same places as above) indicating that the redistributed program is
-not identical to the version distributed by Whitehead Institute.
-
-3.      All advertising materials mentioning features or use of this
-software  must display the following acknowledgment:
-        This product includes software developed by the
-        Whitehead Institute for Biomedical Research.
-
-4.      The name of the Whitehead Institute may not be used to endorse or
-promote products derived from this software without specific prior written
-permission.
-
-We also request that use of this software be cited in publications as 
-
-   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. Code available at
-   http://fokker.wi.mit.edu/primer3/.
-
-THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS'' AND  ANY
-EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE  IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE  ARE
-DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE  FOR ANY
-DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL  DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS  OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)  HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGE.

Added: trunk/packages/primer3/branches/upstream/current/Copyright.txt
===================================================================
--- trunk/packages/primer3/branches/upstream/current/Copyright.txt	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/Copyright.txt	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1,31 @@
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+

Deleted: trunk/packages/primer3/branches/upstream/current/README
===================================================================
--- trunk/packages/primer3/branches/upstream/current/README	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/README	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,1469 +0,0 @@
-
-primer3 release 1.0  (distribution 1.0.0)
-
- Copyright (c) 1996,1997,1998,1999,2000,2001,2004
-        Whitehead Institute for Biomedical Research. All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1.      Redistributions must reproduce the above copyright notice, this
-list of conditions and the following disclaimer in the  documentation
-and/or other materials provided with the distribution.  Redistributions of
-source code must also reproduce this information in the source code itself.
-
-2.      If the program is modified, redistributions must include a notice
-(in the same places as above) indicating that the redistributed program is
-not identical to the version distributed by Whitehead Institute.
-
-3.      All advertising materials mentioning features or use of this
-software  must display the following acknowledgment:
-        This product includes software developed by the
-        Whitehead Institute for Biomedical Research.
-
-4.      The name of the Whitehead Institute may not be used to endorse or
-promote products derived from this software without specific prior written
-permission.
-
-We also request that use of this software be cited in publications as 
-
-   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. Code available at
-   http://fokker.wi.mit.edu/primer3/.
-
-THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS'' AND  ANY
-EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE  IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE  ARE
-DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE  FOR ANY
-DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL  DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS  OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)  HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGE.
-
-INTRODUCTION
-------------
-Primer3 is a complete rewrite of the original PRIMER program
-(Primer 0.5), written by Steve Lincoln, Mark Daly, and Eric
-Lander.  See DIFFERENCES FROM EARLIER VERSIONS for a discussion
-of how Primer3 differs from its predecessors, Primer 0.5 and
-Primer v2.
-
-Primer3 picks primers for PCR reactions, considering as criteria:
-
-o oligonucleotide melting temperature, size, GC content,
-  and primer-dimer possibilities,
-
-o PCR product size,
-
-o positional constraints within the source sequence, and
-
-o miscellaneous other constraints.
-
-All of these criteria are user-specifiable as constraints, and
-some are specifiable as terms in an objective function that
-characterizes an optimal primer pair.  
-
-Whitehead Institute for Biomedical Research provides a web-based
-front end to Primer3 at
-http://fokker.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi
-
-
-INSTALLATION INSTRUCTIONS
--------------------------
-Unzip and untar the distribution.
-
-DO NOT do this on a PC -- primer3_core will not compile if pc
-newlines get inserted into the source files.  Instead, move the
-distribution (primer3_<release>.tar.gz) to Unix, and then
-
-$ unzip primer3_<release>.tar.gz
-$ tar xvf primer3_<release>.tar
-$ cd primer3_<release>/src
-
-If you do not use gcc, modify the makefile to
-  use your (ANSI) C compiler and appropriate 
-  compile and link flags.
-
-$ make primer3_core
-# Warnings about pr_release being unused are harmless.
-$ make ntdpal
-
-$ cd ../test
-$ perl -w primer_test.pl
-$ perl -w dpal_test.pl
-# You should not see 'FAILED' during the tests.
-
-If your perl command is not called perl (for example, if it is
-called perl5) you will have to modify the internals of the test
-scripts).
-
-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").  It is provided
-strictly as is; for further documentation please see the code.
-
-SYSTEM REQUIREMENTS
--------------------
-Primer3 has been successfully installed and tested on the
-following systems
-
-     o Sparc running SunOS 4.1 (gcc 2.7.0)
-     o Alpha running DEC Unix 3.2 (gcc 2.7.0 and DEC cc)
-     o Pentium running Linux 1.2 (Red Hat) (gcc 2.7.0)
-
-Primer3 may well compile and run on other POSIX architectures with
-ANSI C compilers.  Please contact the authors with portability
-suggestions.
-
-
-INPUT AND OUTPUT CONVENTIONS
-----------------------------
-
-By default, Primer3 accepts input and produces output in
-Boulder-io format, a pre-XML text-based input/output format
-for program-to-program data interchange format.  When run
-with the -format_output command-line flag, Primer3 prints a
-more user-oriented report for each sequence.  Additional
-command-line flags include -2x_compat (which causes Primer3
-to print its output using Primer v2 compatible tag names),
-and -strict_tags (both discussed below).  Primer3 exits with
-0 status if it operates correctly.  See EXIT STATUS CODES
-below for additional information.
-
-The syntax of the version of Boulder-io recognized by Primer3 is
-as follows:
-
-  o Input consists of a sequence of RECORDs.
-
-  o A RECORD consists of a sequence of (TAG,VALUE) pairs, each terminated
-    by a newline character (\n). A RECORD is terminated by  '='
-    appearing by itself on a line.
-
-  o A (TAG,VALUE) pair has the following requirements:
-
-        o the TAG must be immediately (without spaces) 
-          followed by '='.
-	o the pair must be terminated by a newline character.
-
-An example of a legal (TAG,VALUE) pair is
-
-PRIMER_SEQUENCE_ID=my_marker
-
-and an example of a BOULDER-IO record is
-
-PRIMER_SEQUENCE_ID=test1
-SEQUENCE=GACTGATCGATGCTAGCTACGATCGATCGATGCATGCTAGCTAGCTAGCTGCTAGC
-=
-
-Many records can be sent, one after another. Below is an example
-of three different records which might be passed through a
-boulder-io stream:
-
-PRIMER_SEQUENCE_ID=test1
-SEQUENCE=GACTGATCGATGCTAGCTACGATCGATCGATGCATGCTAGCTAGCTAGCTGCTAGC
-=
-PRIMER_SEQUENCE_ID=test2
-SEQUENCE=CATCATCATCATCGATGCTAGCATCNNACGTACGANCANATGCATCGATCGT
-=
-PRIMER_SEQUENCE_ID=test3
-SEQUENCE=NACGTAGCTAGCATGCACNACTCGACNACGATGCACNACAGCTGCATCGATGC
-=
-
-Primer3 reads boulder-io on stdin and echos its input and returns
-results in boulder-io format on stdout.  Primer3 indicates many
-user-correctable errors by a value in the PRIMER_ERROR tag (see
-below) and indicates other errors, including system configuration
-errors, resource errors (such out-of-memory errors), and detected
-programming errors by a message on stderr and a non-zero exit
-status.
-
-Below is the list of input tags that Primer3 recognizes.
-Primer3 echos and ignores any tags it does not recognize, unless
-the -strict_tags flag is set on the command line, in which case
-Primer3 prints an error in the PRIMER_ERROR output tag (see
-below), and prints additional information on stdout; this option
-can be useful for debugging systems that incorporate primer.
-
-Except for tags with the type "interval list" each tag is allowed
-only ONCE in any given input record.  This restriction is not
-systematically checked in this beta release: use care.
-
-There are 2 major classes of input tags.  "Sequence" input tags
-describe a particular input sequence to Primer3, and are reset
-after every boulder record.  "Global" input tags describe the
-general parameters that Primer3 should use in its searches, and
-the values of these tags persist between input boulder records
-until or unless they are explicitly reset.  Errors in "Sequence"
-input tags invalidate the current record, but Primer3 will
-continue to process additional records.  Errors in "Global" input
-tags are fatal because they invalidate the basic conditions under
-which primers are being picked.
-
-"Sequence" Input Tags
----------------------
-
-PRIMER_SEQUENCE_ID (string, optional)
-
-(MARKER_NAME is a deprecated synonym maintained for v2
-compatibility.)
-
-An identifier that is reproduced in the output to enable users to
-identify the source of the chosen primers.
-
-This tag must be present if PRIMER_FILE_FLAG is non-zero.
-
-SEQUENCE (nucleotide sequence, REQUIRED)
-
-The sequence from which to choose primers.  The sequence
-must be presented 5' -> 3' (see the discussion of the
-PRIMER_SELF_END argument).  The bases may be upper or lower case.
-No newlines should be inserted into the sequence, because the
-Boulder-IO parser will assume that a line ends at a newline.
-
-INCLUDED_REGION (interval, optional)
-
-A sub-region of the given sequence in which to pick primers.  For
-example, often the first dozen or so bases of a sequence are
-vector, and should be excluded from consideration. The value for
-this parameter has the form
-
-<start>,<length>
-
-where <start> is the index of the first base to consider,
-and <length> is the number of subsequent bases in the
-primer-picking region.
-
-TARGET (interval list, default empty)
-
-If one or more Targets is specified then a legal primer pair must
-flank at least one of them.  A Target might be a simple sequence
-repeat site (for example a CA repeat) or a single-base-pair
-polymorphism.  The value should be a space-separated list of
-
-<start>,<length>
-
-pairs where <start> is the index of the first base of a
-Target, and <length> is its length.
-
-For backward compatibility Primer3 accepts (but ignores)
-a trailing ,<description> for each element of this argument.
-
-EXCLUDED_REGION (interval list, default empty)
-
-Primer oligos may not overlap any region specified in this tag.
-The associated value must be a space-separated list of
-
-<start>,<length>
-
-pairs where <start> is the index of the first base of
-the excluded region, and <length> is its length.  This tag is
-useful for tasks such as excluding regions of low sequence
-quality or for excluding regions containing repetitive elements
-such as ALUs or LINEs.
-
-PRIMER_COMMENT (string, optional)
-
-The value of this tag is ignored.
-
-COMMENT (string, optional)
-
-Deprecated synonym for PRIMER_COMMENT.
-
-PRIMER_SEQUENCE_QUALITY (quality list, default empty)
-
-A list of space separated integers. There must be exactly
-one integer for each base in SEQUENCE if this argument is
-non-empty.  For example, for the sequence ANNTTCA...
-PRIMER_SEQUENCE_QUALITY might be 45 10 0 50 30 34 50 67 ....
-High numbers indicate high confidence in the base called at
-that position and low numbers indicate low confidence in the
-base call at that position.  This parameter is only relevant
-if you are using a base calling program that provides
-quality information (for example phred).
-
-PRIMER_LEFT_INPUT (nucleotide sequence, default empty)
-
-The sequence of a left primer to check and around which to design
-right primers and optional internal oligos.  Must be a substring
-of SEQUENCE.
-
-PRIMER_RIGHT_INPUT (nucleotide sequence, default empty)
-
-The sequence of a right primer to check and around which to
-design left primers and optional internal oligos.  Must be a
-substring of the reverse strand of SEQUENCE.
-
-PRIMER_START_CODON_POSITION (int, default -1000000)
-
-This parameter should be considered EXPERIMENTAL at this point.
-Please check the output carefully; some erroneous inputs might
-cause an error in Primer3.
-
-Index of the first base of a start codon.  This parameter allows
-Primer3 to select primer pairs to create in-frame amplicons
-e.g. to create a template for a fusion protein.  Primer3 will
-attempt to select an in-frame left primer, ideally starting at or
-to the left of the start codon, or to the right if necessary.
-Negative values of this parameter are legal if the actual start
-codon is to the left of available sequence. If this parameter is
-non-negative Primer3 signals an error if the codon at the
-position specified by this parameter is not an ATG.  A value less
-than or equal to -10^6 indicates that Primer3 should ignore this
-parameter.
-
-Primer3 selects the position of the right primer by scanning
-right from the left primer for a stop codon.  Ideally the right
-primer will end at or after the stop codon.
-
-"Global" Input Tags
--------------------
-
-PRIMER_PICK_ANYWAY (boolean, default 0)
-
-If true pick a primer pair even if PRIMER_LEFT_INPUT,
-PRIMER_RIGHT_INPUT, or PRIMER_INTERNAL_OLIGO_INPUT violates
-specific constraints.
-
-PRIMER_MISPRIMING_LIBRARY (string, optional)
-
-The name of a file containing a nucleotide sequence library of
-sequences to avoid amplifying (for example repetitive sequences, or
-possibly the sequences of genes in a gene family that should
-not be amplified.)  The file must be in (a slightly restricted)
-FASTA format (W. B. Pearson and D.J. Lipman, PNAS 85:8 pp
-2444-2448 [1988]); we briefly discuss the organization of this
-file below.  If this parameter is specified then Primer3 locally
-aligns each candidate primer against each library sequence and
-rejects those primers for which the local alignment score times a
-specified weight (see below) exceeds PRIMER_MAX_MISPRIMING.
-(The maximum value of the weight is arbitrarily set to 100.0.)
-
-Each sequence entry in the FASTA-format file must begin with an
-"id line" that starts with '>'.  The contents of the id line is
-"slightly restricted" in that Primer3 parses everything after any
-optional asterisk ('*') as a floating point number to use as the
-weight mentioned above.  If the id line contains no asterisk then
-the weight defaults to 1.0.  The alignment scoring system used is
-the same as for calculating complementarity among oligos (e.g.
-PRIMER_SELF_ANY), except for the handling of IUB/IUPAC ambiguity
-codes (discussed below).  The remainder of an entry contains the
-sequence as lines following the id line up until a line starting
-with '>' or the end of the file.  Whitespace and newlines are
-ignored.  Characters 'A', 'T', 'G', 'C', 'a', 't', 'g', 'c' 
-and IUB/IUPAC 'ambiguity' codes ('R, 'Y', 'K', 'M', 'S', 'W', 'N',
-including lower case) are retained. 
-
-WARNING: always set PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
-if any sequence in the library contains strings of 'N's:
-NNNNNNNNNNNNNNNNNNNN.
-NOWWW
-There are no restrictions on line length.
-
-An empty value for this parameter indicates that no repeat
-library should be used and "turns off" the use of a
-previously specified library.
-
-Repbase (J. Jurka, A.F.A. Smit, C. Pethiyagoda, and
-others, 1995-1996, ftp://ncbi.nlm.nih.gov/repository/repbase)
-is an excellent source of repeat sequences and pointers to the
-literature. (The Repbase files need to be converted to Fasta
-format before they can be used by Primer3.)
-
-
-PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS (boolean, default 1)
-
-If set to 1, treat ambiguity codes as if they were consensus
-codes when matching oligos to mispriming or mishyb
-libraries. For example, if this flag is set, then a C in an
-oligo will be scored as a perfect match to an S in a library
-sequence, as will a G in the oligo. More importantly,
-though, any base in an oligo will be scored as a perfect
-match to an N in the library.  This is very bad if the
-library contains strings of Ns, as no oligo will be legal
-(and it will take a long time to find this out). So unless
-you know for sure that your library does not have runs of Ns
-(or Xs), then set this flag to 0.
-
-PRIMER_MAX_MISPRIMING (decimal,9999.99, default 12.00)
-
-The maximum allowed weighted similarity with any sequence in
-PRIMER_MISPRIMING_LIBRARY.  
-
-PRIMER_MAX_TEMPLATE_MISPRIMING (decimal,9999.99, default -1.00)
-
-The maximum allowed similarity to ectopic sites in the
-template.  A negative value means do not check.  The scoring
-system is the same as used for PRIMER_MAX_MISPRIMING, except
-that an ambiguity code in the template is never treated as a
-consensus (see PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS).
-
-PRIMER_PAIR_MAX_MISPRIMING (decimal,9999.99, default 24.00)
-
-The maximum allowed sum of similarities of a primer pair
-(one similarity for each primer) with any single sequence in
-PRIMER_MISPRIMING_LIBRARY.  
-Library sequence weights are not used in computing the sum
-of similarities.
-
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING (decimal,9999.99, default -1.00)
-
-The maximum allowed summed similarity of both primers to
-ectopic sites in the template. A negative value means do not
-check.  The scoring system is the same as used for
-PRIMER_PAIR_MAX_MISPRIMING, except that an ambiguity code in
-the template is never treated as a consensus (see
-PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS).  Primer3 does not
-check the similarity of hybridization oligos (internal
-oligos) to locations outside of the amplicon.
-
-PRIMER_PRODUCT_MAX_TM (float, default 1000000.0)
-
-The maximum allowed melting temperature of the amplicon.  Primer3
-calculates product Tm calculated using the formula from Bolton
-and McCarthy, PNAS 84:1390 (1962) as presented in Sambrook,
-Fritsch and Maniatis, Molecular Cloning, p 11.46 (1989, CSHL
-Press).
-
-   Tm = 81.5 + 16.6(log10([Na+])) + .41*(%GC) - 600/length
-
-Where [Na+] is the molar sodium concentration, (%GC) is the
-percent of Gs and Cs in the sequence, and length is the length of
-the sequence.
-
-A similar formula is used by the prime primer selection program
-in GCG (http://www.gcg.com), which instead uses 675.0 / length in
-the last term (after F. Baldino, Jr, M.-F. Chesselet, and M.E.
-Lewis, Methods in Enzymology 168:766 (1989) eqn (1) on page 766
-without the mismatch and formamide terms).  The formulas here and
-in Baldino et al. assume Na+ rather than K+.  According to
-J.G. Wetmur, Critical Reviews in BioChem. and Mol. Bio. 26:227
-(1991) 50 mM K+ should be equivalent in these formulae to .2 M
-Na+.  Primer3 uses the same salt concentration value for
-calculating both the primer melting temperature and the oligo
-melting temperature.  If you are planning to use the PCR product
-for hybridization later this behavior will not give you the Tm
-under hybridization conditions.
-
-PRIMER_PRODUCT_MIN_TM (float, default -1000000.0)
-
-The minimum allowed melting temperature of the amplicon.  Please
-see the documentation on the maximum melting temperature of the
-product for details.
-
-PRIMER_EXPLAIN_FLAG (boolean, default 0)
-
-If this flag is non-0, produce PRIMER_LEFT_EXPLAIN,
-PRIMER_RIGHT_EXPLAIN, and PRIMER_INTERNAL_OLIGO_EXPLAIN output
-tags, which are intended to provide information on the number of
-oligos and primer pairs that Primer3 examined, and statistics on
-the number discarded for various reasons.  If -format_output is
-set similar information is produced in the user-oriented output.
-
-PRIMER_PRODUCT_SIZE_RANGE (size range list, default 100-300)
-
-The associated values specify the lengths of the product that the
-user wants the primers to create, and is a space separated list
-of elements of the form
-
-<x>-<y>
-
-where an <x>-<y> pair is a legal range of lengths for the
-product.  For example, if one wants PCR products to be between
-100 to 150 bases (inclusive) then one would set this parameter to
-100-150.  If one desires PCR products in either the range from
-100 to 150 bases or in the range from 200 to 250 bases then one
-would set this parameter to 100-150 200-250.
-
-Primer3 favors ranges to the left side of the parameter string.
-Primer3 will return legal primers pairs in the first range
-regardless the value of the objective function for these pairs.
-Only if there are an insufficient number of primers in the first
-range will Primer3 return primers in a subsequent range.
-
-PRIMER_PICK_INTERNAL_OLIGO (boolean, default 0)
-
-If the associated value is non-0, then Primer3 will attempt to
-pick an internal oligo (hybridization probe to detect the PCR
-product).  This tag is maintained for backward compatibility.
-Use PRIMER_TASK.
-
-PRIMER_GC_CLAMP (int, default 0)
-
-Require the specified number of consecutive Gs and Cs at the 3'
-end of both the left and right primer.  (This parameter has no
-effect on the internal oligo if one is requested.)
-
-PRIMER_OPT_SIZE (int, default 20)
-
-Optimum length (in bases) of a primer oligo. Primer3 will attempt
-to pick primers close to this length.
-
-PRIMER_DEFAULT_SIZE (int, default 20)
-
-A deprecated synonym for PRIMER_OPT_SIZE, maintained for v2
-compatibility.
-
-PRIMER_MIN_SIZE (int, default 18)
-
-Minimum acceptable length of a primer.  Must be greater than 0
-and less than or equal to PRIMER_MAX_SIZE.
-
-PRIMER_MAX_SIZE (int, default 27)
-
-Maximum acceptable length (in bases) of a primer.  Currently this
-parameter cannot be larger than 35.  This limit is governed by
-maximum oligo size for which Primer3's melting-temperature is
-valid.
-
-PRIMER_OPT_TM (float, default 60.0C)
-
-Optimum melting temperature(Celsius) for a primer oligo. Primer3
-will try to pick primers with melting temperatures are close to
-this temperature.  The oligo melting temperature formula in
-Primer3 is that given in Rychlik, Spencer and Rhoads, Nucleic
-Acids Research, 18(21): 6409-6412 and Breslauer,
-Frank, Bloeker and Marky, PNAS, 83: 3746-3750.
-Please refer to the former paper for background discussion.
-
-PRIMER_MIN_TM (float, default 57.0C)
-
-Minimum acceptable melting temperature(Celsius) for a primer
-oligo.
-
-PRIMER_MAX_TM (float, default 63.0C)
-
-Maximum acceptable melting temperature(Celsius) for a primer
-oligo.
-
-PRIMER_MAX_DIFF_TM (float, default 100.0C)
-
-Maximum acceptable (unsigned) difference between the melting
-temperatures of the left and right primers.
-
-PRIMER_MIN_GC (float, default 20.0%)
-
-Minimum allowable percentage of Gs and Cs in any primer.
-
-PRIMER_OPT_GC_PERCENT (float, default 50.0%)
-
-Optimum GC percent.  This parameter influences primer selection only if
-PRIMER_WT_GC_PERCENT_GT or PRIMER_WT_GC_PERCENT_LT are non-0.
-
-PRIMER_MAX_GC (float, default 80.0%)
-
-Maximum allowable percentage of Gs and Cs in any primer generated
-by Primer.
-
-PRIMER_SALT_CONC (float, default 50.0 mM)
-
-The millimolar concentration of salt (usually KCl) in the PCR.
-Primer3 uses this argument to calculate oligo melting
-temperatures.
-
-PRIMER_DNA_CONC (float, default 50.0 nM)
-
-The nanomolar concentration of annealing oligos in the PCR.
-Primer3 uses this argument to calculate oligo melting
-temperatures.  The default (50nM) works well with the standard
-protocol used at the Whitehead/MIT Center for Genome
-Research--0.5 microliters of 20 micromolar concentration for each
-primer oligo in a 20 microliter reaction with 10 nanograms
-template, 0.025 units/microliter Taq polymerase in 0.1 mM each
-dNTP, 1.5mM MgCl2, 50mM KCl, 10mM Tris-HCL (pH 9.3) using 35
-cycles with an annealing temperature of 56 degrees Celsius.  This
-parameter corresponds to 'c' in Rychlik, Spencer and Rhoads'
-equation (ii) (Nucleic Acids Research, 18(21): 6409-6412)
-where a suitable value (for a lower initial concentration of template)
-is "empirically determined".  The value of this parameter is less
-than the actual concentration of oligos in the reaction because
-it is the concentration of annealing oligos, which in turn
-depends on the amount of template (including PCR product) in a
-given cycle.  This concentration increases a great deal during a
-PCR; fortunately PCR seems quite robust for a variety of oligo
-melting temperatures.
-
-See ADVICE FOR PICKING PRIMERS.
-
-PRIMER_NUM_NS_ACCEPTED (int, default 0)
-
-Maximum number of unknown bases (N) allowable in any primer.
-
-PRIMER_SELF_ANY (decimal,9999.99, default 8.00)
-
-The maximum allowable local alignment score when testing a single
-primer for (local) self-complementarity and the maximum allowable
-local alignment score when testing for complementarity between
-left and right primers.  Local self-complementarity is taken to
-predict the tendency of primers to anneal to each other without
-necessarily causing self-priming in the PCR.  The scoring system
-gives 1.00 for complementary bases, -0.25 for a match of any base
-(or N) with an N, -1.00 for a mismatch, and -2.00 for a gap.
-Only single-base-pair gaps are allowed.  For example, the
-alignment
-
-5' ATCGNA 3'
-   || | |
-3' TA-CGT 5'
-
-is allowed (and yields a score of 1.75), but the alignment
-
-5' ATCCGNA 3'
-   ||  | |
-3' TA--CGT 5'
-
-is not considered.  Scores are non-negative, and a score of 0.00
-indicates that there is no reasonable local alignment between two
-oligos.
-
-PRIMER_SELF_END (decimal 9999.99, default 3.00)
-
-The maximum allowable 3'-anchored global alignment score when
-testing a single primer for self-complementarity, and the maximum
-allowable 3'-anchored global alignment score when testing for
-complementarity between left and right primers.  The 3'-anchored
-global alignment score is taken to predict the likelihood of
-PCR-priming primer-dimers, for example
-
-5' ATGCCCTAGCTTCCGGATG 3'
-             ||| |||||
-          3' AAGTCCTACATTTAGCCTAGT 5'
-
-or
-
-5` AGGCTATGGGCCTCGCGA 3'
-               ||||||
-            3' AGCGCTCCGGGTATCGGA 5'
-
-The scoring system is as for the Maximum Complementarity
-argument.  In the examples above the scores are 7.00 and 6.00
-respectively.  Scores are non-negative, and a score of 0.00
-indicates that there is no reasonable 3'-anchored global
-alignment between two oligos.  In order to estimate 3'-anchored
-global alignments for candidate primers and primer pairs, Primer
-assumes that the sequence from which to choose primers is
-presented 5'->3'.  It is nonsensical to provide a larger value
-for this parameter than for the Maximum (local) Complementarity
-parameter because the score of a local alignment will always be at
-least as great as the score of a global alignment.
-
-PRIMER_DEFAULT_PRODUCT (size range list, default 100-300)
-
-A deprecated synonym for PRIMER_PRODUCT_SIZE_RANGE, maintained
-for v2 compatibility.
-
-PRIMER_FILE_FLAG (boolean, default 0)
-
-If the associated value is non-0, then Primer3 creates two output
-files for each input SEQUENCE.  File <sequence_id>.for lists all
-acceptable left primers for <sequence_id>, and <sequence_id>.rev
-lists all acceptable right primers for <sequence_id>, where
-<sequence_id> is the value of the PRIMER_SEQUENCE_ID tag (which
-must be supplied).  In addition, if the input tag
-PRIMER_PICK_INTERNAL_OLIGO is non-0, Primer3 produces a file
-<sequence_id>.int, which lists all acceptable internal oligos.
-
-PRIMER_MAX_POLY_X (int, default 5)
-
-The maximum allowable length of a mononucleotide repeat,
-for example AAAAAA.
-
-PRIMER_LIBERAL_BASE (boolean, default 0)
-
-This parameter provides a quick-and-dirty way to get Primer3 to
-accept IUB / IUPAC codes for ambiguous bases (i.e. by changing
-all unrecognized bases to N).  If you wish to include an
-ambiguous
-base in an oligo, you must set PRIMER_NUM_NS_ACCEPTED to a
-non-0 value.
-
-Perhaps '-' and '* ' should be squeezed out rather than changed
-to 'N', but currently they simply get converted to N's.  The authors
-invite user comments.
-
-PRIMER_NUM_RETURN (int, default 5)
-
-The maximum number of primer pairs to return.  Primer pairs
-returned are sorted by their "quality", in other words by the
-value of the objective function (where a lower number indicates a
-better primer pair).  Caution: setting this parameter to a large
-value will increase running time.
-
-PRIMER_FIRST_BASE_INDEX (int, default 0)
-
-This parameter is the index of the first base in the input
-sequence.  For input and output using 1-based indexing (such as
-that used in GenBank and to which many users are accustomed) set
-this parameter to 1.  For input and output using 0-based indexing
-set this parameter to 0.  (This parameter also affects the
-indexes in the contents of the files produced when the primer
-file flag is set.)
-
-PRIMER_MIN_QUALITY (int, default 0)
-
-The minimum sequence quality (as specified by
-PRIMER_SEQUENCE_QUALITY) allowed within a primer.
-
-PRIMER_MIN_END_QUALITY (int, default 0)
-
-The minimum sequence quality (as specified by
-PRIMER_SEQUENCE_QUALITY) allowed within the 5' pentamer of a
-primer.
-
-PRIMER_QUALITY_RANGE_MIN (int, default 0)
-
-The minimum legal sequence quality (used for error checking
-of PRIMER_MIN_QUALITY and PRIMER_MIN_END_QUALITY).
-
-PRIMER_QUALITY_RANGE_MAX (int, default 100)
-
-The maximum legal sequence quality (used for error checking
-of PRIMER_MIN_QUALITY and PRIMER_MIN_END_QUALITY).
-
-PRIMER_INSIDE_PENALTY (float, default -1.0)
-
-This experimental parameter might not be maintained in this form
-in the next release.  Non-default values valid only for sequences
-with 0 or 1 target regions.  If the primer is part of a pair that
-spans a target and overlaps the target, then multiply this value
-times the number of nucleotide positions by which the primer
-overlaps the (unique) target to get the 'position penalty'.  The
-effect of this parameter is to allow Primer3 to include overlap
-with the target as a term in the objective function.
-
-PRIMER_OUTSIDE_PENALTY (float, default 0.0)
-
-This experimental parameter might not be maintained in this form
-in the next release.  Non-default values valid only for sequences
-with 0 or 1 target regions.  If the primer is part of a pair that
-spans a target and does not overlap the target, then multiply
-this value times the number of nucleotide positions from the 3'
-end to the (unique) target to get the 'position penalty'.
-The effect of this parameter is to allow Primer3 to include
-nearness to the target as a term in the objective function.
-
-PRIMER_MAX_END_STABILITY (float 999.9999, default 100.0)
-
-The maximum stability for the five 3' bases of a left or right
-primer.  Bigger numbers mean more stable 3' ends.  The value is
-the maximum delta G for duplex disruption for the five 3' bases
-as calculated using the nearest neighbor parameters published in
-Breslauer, Frank, Bloeker and Marky, Proc. Natl. Acad. Sci. USA,
-vol 83, pp 3746-3750.  Primer3 uses a completely permissive
-default value for backward compatibility (which we may change in
-the next release).  Rychlik recommends a maximum value of 9
-(Wojciech Rychlik, "Selection of Primers for Polymerase Chain
-Reaction" in BA White, Ed., "Methods in Molecular Biology,
-Vol. 15: PCR Protocols: Current Methods and Applications", 1993,
-pp 31-40, Humana Press, Totowa NJ).
-
-PRIMER_PRODUCT_OPT_TM (float, default 0.0)
-
-The optimum melting temperature for the PCR product. 0 indicates
-that there is no optimum temperature.
-
-PRIMER_PRODUCT_OPT_SIZE (int, default 0)
-
-The optimum size for the PCR product.  0 indicates that there is
-no optimum product size.  This parameter influences primer
-pair selection only
-if PRIMER_PAIR_WT_PRODUCT_SIZE_GT or
-PRIMER_PAIR_WT_PRODUCT_SIZE_LT is non-0.
-
-PRIMER_TASK (string, default pick_pcr_primers)
-
-Tell Primer3 what task to perform. Legal values are pick_pcr_primers,
-pick_pcr_primers_and_hyb_probe, pick_left_only, pick_right_only,
-pick_hyb_probe_only.  The tasks should be self explanatory, except
-that we note that pick_pcr_primers_and_hyb_probe is
-equivalent to the setting PRIMER_PICK_INTERNAL_OLIGO to a non-zero
-value and setting PRIMER_TASK to pick_pcr_primers.
-
-PRIMER_WT_TM_GT (float, default 1.0)
-
-Penalty weight for primers with Tm over PRIMER_OPT_TM.
-
-PRIMER_WT_TM_LT (float, default 1.0)
-
-Penalty weight for primers with Tm under PRIMER_OPT_TM.
-
-PRIMER_WT_SIZE_LT (float, default 1.0)
-
-Penalty weight for primers shorter than PRIMER_OPT_SIZE.
-
-PRIMER_WT_SIZE_GT (float, default 1.0)
-
-Penalty weight for primers longer than PRIMER_OPT_SIZE.
-
-PRIMER_WT_GC_PERCENT_LT (float, default 1.0)
-
-Penalty weight for primers with GC percent greater than
-PRIMER_OPT_GC_PERCENT.
-
-PRIMER_WT_GC_PERCENT_GT (float, default 1.0)
-
-Penalty weight for primers with GC percent greater than
-PRIMER_OPT_GC_PERCENT.
-
-PRIMER_WT_COMPL_ANY (float, default 0.0)
-PRIMER_WT_COMPL_END (float, default 0.0)
-PRIMER_WT_NUM_NS (float, default 0.0)
-PRIMER_WT_REP_SIM (float, default 0.0)
-PRIMER_WT_SEQ_QUAL (float, default 0.0)
-PRIMER_WT_END_QUAL (float, default 0.0)
-PRIMER_WT_POS_PENALTY (float, default 0.0)
-PRIMER_WT_END_STABILITY (float, default 0.0)
-PRIMER_WT_TEMPLATE_MISPRIMING (float, default 0.0)
-PRIMER_PAIR_WT_PR_PENALTY (float, default 1.0)
-PRIMER_PAIR_WT_IO_PENALTY (float, default 0.0)
-PRIMER_PAIR_WT_DIFF_TM (float, default 0.0)
-PRIMER_PAIR_WT_COMPL_ANY (float, default 0.0)
-PRIMER_PAIR_WT_COMPL_END (float, default 0.0)
-PRIMER_PAIR_WT_PRODUCT_TM_LT (float, default 0.0)
-PRIMER_PAIR_WT_PRODUCT_TM_GT (float, default 0.0)
-PRIMER_PAIR_WT_PRODUCT_SIZE_GT (float, default 0.0)
-PRIMER_PAIR_WT_PRODUCT_SIZE_LT (float, default 0.0)
-PRIMER_PAIR_WT_REP_SIM (float, default 0.0)
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING (float, default 0.0)
-
-Like the arguments governing PCR primer selection, the input tags
-governing internal oligo selection are divided into sequence
-input tags and global input tags, with for former being
-automatically reset after each input record, and the latter
-persisting until explicitly reset.
-
-Because the laboratory detection step using internal oligos
-is independent of the PCR amplification procedure,
-internal oligo tags have defaults that are independent
-of the parameters that govern the selection of PCR primers.
-For example, the melting temperature of an oligo
-used for hybridization might be considerably lower
-than that used as a PCR primer.
-
-Internal Oligo "Sequence" Input Tags
-------------------------------------
-
-PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION (interval list, default empty)
-
-Middle oligos may not overlap any region specified by this tag.
-The associated value must be a space-separated list of
-
-<start>,<length>
-
-pairs, where <start> is the index of the first base of
-an excluded region, and <length> is its length.  Often one would
-make Target regions excluded regions for internal oligos.
-
-PRIMER_INTERNAL_OLIGO_INPUT (nucleotide sequence, default empty)
-
-The sequence of an internal oligo to check and around which to
-design left and right primers.  Must be a substring of SEQUENCE.
-
-Internal Oligo "Global" Input Tags
-----------------------------------
-
-These tags are analogous to the global input tags (those
-governing primer oligos) discussed above.  The exception is
-PRIMER_INTERNAL_OLIGO_SELF_END which is meaningless when applied
-to internal oligos used for hybridization-based detection, since
-primer-dimer will not occur.  We recommend that
-PRIMER_INTERNAL_OLIGO_SELF_END be set at least as high as
-PRIMER_INTERNAL_OLIGO_SELF_ANY.
-
-PRIMER_INTERNAL_OLIGO_OPT_SIZE (int, default 20)
-PRIMER_INTERNAL_OLIGO_MIN_SIZE (int, default 18)
-PRIMER_INTERNAL_OLIGO_MAX_SIZE (int, default 27)
-PRIMER_INTERNAL_OLIGO_OPT_TM (float, default 60.0 degrees C)
-PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT (float, default 50.0%)
-PRIMER_INTERNAL_OLIGO_MIN_TM (float, default 57.0 degrees C)
-PRIMER_INTERNAL_OLIGO_MAX_TM (float, default 63.0 degrees C)
-PRIMER_INTERNAL_OLIGO_MIN_GC (float, default 20.0%)
-PRIMER_INTERNAL_OLIGO_MAX_GC (float, default 80.0%)
-PRIMER_INTERNAL_OLIGO_SALT_CONC (float, default 50.0 mM)
-PRIMER_INTERNAL_OLIGO_DNA_CONC (float, default 50.0 nM)
-PRIMER_INTERNAL_OLIGO_SELF_ANY (decimal 9999.99, default 12.00)
-PRIMER_INTERNAL_OLIGO_MAX_POLY_X (int, default 5)
-PRIMER_INTERNAL_OLIGO_SELF_END (decimal 9999.99, default 12.00)
-PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY (string, optional)
-
-Similar to PRIMER_MISPRIMING_LIBRARY, except that the event we
-seek to avoid is hybridization of the internal oligo to sequences
-in this library rather than priming from them.
-
-PRIMER_INTERNAL_OLIGO_MAX_MISHYB (decimal,9999.99, default 12.00)
-
-Similar to PRIMER_MAX_MISPRIMING except that this parameter applies
-to the similarity of candidate internal oligos to the library
-specified in PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY.
-
-PRIMER_INTERNAL_OLIGO_MAX_TEMPLATE_MISHYB (decimal,9999.99, default 12.00)
-
-Not implemented.
-
-PRIMER_INTERNAL_OLIGO_MIN_QUALITY (int, default 0)
-
-(Note that there is no PRIMER_INTERNAL_OLIGO_MIN_END_QUALITY.)
-
-PRIMER_IO_WT_TM_GT (float, default 1.0)
-PRIMER_IO_WT_TM_LT (float, default 1.0)
-PRIMER_IO_WT_GC_PERCENT_GT (float, default 1.0)
-PRIMER_IO_WT_GC_PERCENT_LT (float, default 1.0)
-PRIMER_IO_WT_SIZE_LT (float, default 1.0)
-PRIMER_IO_WT_SIZE_GT (float, default 1.0)
-PRIMER_IO_WT_COMPL_ANY (float, default 0.0)
-PRIMER_IO_WT_COMPL_END (float, default 0.0)
-PRIMER_IO_WT_NUM_NS (float, default 0.0)
-PRIMER_IO_WT_REP_SIM (float, default 0.0)
-PRIMER_IO_WT_SEQ_QUAL (float, default 0.0)
-PRIMER_IO_WT_END_QUAL (float, default 0.0)
-
-AN EXAMPLE
-----------
-One might be interested in performing PCR on an STS with a CA
-repeat in the middle of it. Primers need to be chosen based on
-the criteria of the experiment.
-
-We need to come up with a boulder-io record to send to Primer3 via
-stdin. There are lots of ways to accomplish this. We could save
-the record into a text file called 'input', and then type the
-UNIX command 'primer3 < input'. 
-
-Let's look at the input record itself:
-
-PRIMER_SEQUENCE_ID=example
-SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
-TARGET=37,21
-PRIMER_OPT_SIZE=18
-PRIMER_MIN_SIZE=15
-PRIMER_MAX_SIZE=21
-PRIMER_NUM_NS_ACCEPTED=1
-PRIMER_PRODUCT_SIZE_RANGE=75-100
-PRIMER_FILE_FLAG=1
-PRIMER_PICK_INTERNAL_OLIGO=1
-PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=37,21
-PRIMER_EXPLAIN_FLAG=1
-=
-
-A breakdown of the reasoning behind each of the TAG=VALUE pairs
-is below:
-
-PRIMER_SEQUENCE_ID=example
-
-The main intent of this tag is to provide an identifier for the
-sequence that is meaningful to the user, for example when Primer3
-processes multiple records, and by default this tag is optional.
-However, this tag is _required_ when PRIMER_FILE_FLAG is non-0
-Because it provides the names of the files that contain lists
-of oligos that Primer3 considered.
-
-SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
-
-The SEQUENCE tag is of ultimate importance. Without it, Primer3
-has no idea what to do. This sequence is 92 bases long. Note that
-there is no newline until the sequence terminates completely.
-
-TARGET=37,21
-
-There is a simple sequence repeat in our sequence, which starts
-at base 37, and has a length of 21 bases. We want Primer3 to
-choose primers which flank the repeat site, so we let Primer3 know
-that we consider this site to be important.
-
-PRIMER_OPT_SIZE=18
-
-Since our sequence length is rather small (only 92 bases
-long), we lower the PRIMER_OPT_SIZE from 20 to 18. It's
-more likely that Primer3 will succeed if it shoots for smaller
-primers with such a small sequence.
-
-PRIMER_MIN_SIZE=15
-PRIMER_MAX_SIZE=21
-
-With the lowering of optimal primer size, it's good to lower
-the minimum and maximum sizes as well.
-
-PRIMER_NUM_NS_ACCEPTED=1
-
-Again, since we've got such a small sequence with a
-non-negligible amount of unknown bases (N's) in it, let's make
-Primer3's job easier by allowing it to pick primers that have
-at most 1 unknown base.
-
-PRIMER_PRODUCT_SIZE_RANGE=75-100
-
-We reduce the product size range from the default of 100-300
-because our source sequence is only 108 base pairs long.  If we
-insisted on a product size of 100 base pairs Primer3 would have
-few possibilities to choose from.
-
-PRIMER_FILE_FLAG=1
-
-Since we've got such a small sequence, Primer might fail to
-pick primers. We want to get the list of primers it
-considered, then, so that we might manually pick primers
-ourselves if Primer fails to do so. Setting this flag to 1
-will force Primer to output the primers it considered to a
-forward_primer and a reverse_primer output file.
-
-PRIMER_PICK_INTERNAL_OLIGO=1
-
-We want to see if Primer v2.3 can pick an internal oligo for
-the sequence, so we set this flag to 1 (true).
-
-PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=37,21
-
-Normally CA-repeats make poor hybridization probes (because they
-not specific enough).  Therefor we exclude the CA repeat (which
-is the TARGET) from consideration for the middle oligo.
-
-PRIMER_EXPLAIN_FLAG=1
-
-We want to see statistics about the oligos and oligo triples
-(left primer, internal oligo, right primer) that Primer3
-examined.
-
-=
-
-The '=' character terminates the record.
-
-Tere are some boulderio tags that we never even
-specified. (INCLUDED_REGION, EXCLUDED_REGION, et al.), which is
-perfectly legal.  For the tags with default values, those
-defaults will be used in the analysis. For the tags with NO
-default values (like TARGET, for instance), the functionality
-requested by the those tags will simply be absent. It's not the
-case that we need to surround a simple sequence repeat every time
-we want to pick primers!
-
-
-OUTPUT TAGS
------------
-For each boulderio record passed into primer3 via stdin, exactly
-one boulderio record comes out of primer3 on stdout. These output
-records contain everything that the input record contains, plus a
-subset of the following tag/value pairs.  Unless noted by (*),
-each tag appears for each primer pair returned.  The first
-version is PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO,PAIR}_<tag_name>.
-Tags of additional primers chosen are of the form
-PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO,PAIR}_<j>_<tag_name>.  where
-<j> is an integer from 1 to n, where n is at most the value of
-PRIMER_NUM_RETURN.
-
-In the descriptions below, 'i,n' represents a start/length pair,
-'s' represents a string, x represents an arbitrary integer, and f
-represents a float.
-
-PRIMER_ERROR=s (*)
-
-s describes user-correctible errors detected in the input
-(separated by semicolons).  This tag is absent if there are no
-errors.
-
-PRIMER_LEFT=i,n
-(FORWARD_PRIMER if -v2_compat is set)
-
-The selected left primer (the primer to the left in the input
-sequence).  i is the 0-based index of the start base of the
-primer, and n is t its length.
-
-PRIMER_RIGHT=i,n
-(REVERSE_PRIMER if -v2_compat is set)
-
-The selected right primer (the primer to the right in the input
-sequence).  i is the 0-based index of the last base of the
-primer, and n is its length.
-
-PRIMER_INTERNAL_OLIGO=i,n
-(MIDDLE_OLIGO if -v2_compat is set)
-
-The selected internal oligo. Primer3 outputs this tag if
-PRIMER_PICK_INTERNAL_OLIGO was non-0.  If primer3 fails to pick a
-middle oligo upon request, this tag will not be output.  i is the
-0-based index of start base of the internal oligo, and n is its
-length.
-
-PRIMER_PRODUCT_SIZE=x
-(PRODUCT_SIZE if -v2_compat is set)
-
-x is the product size of the PCR product.
-
-PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_EXPLAIN=s (*)
-
-s is a (more or less) self-documenting string containing
-statistics on the possiblities that primer3 considered in
-selecting a single oligo.  For example
-
-PRIMER_LEFT_EXPLAIN=considered 62, too many Ns 53, ok 9
-PRIMER_RIGHT_EXPLAIN=considered 62, too many Ns 53, ok 9
-PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 87, too many Ns 39, overlap excluded region 40, ok 8
-
-All the categories are exclusive, except the 'considered' category.
-
-PRIMER_PAIR_EXPLAIN=s (*)
-
-s is a self-documenting string containing statistics on picking a
-primer pair (plus internal oligo if requested).  For exaple
-
-PRIMER_PAIR_EXPLAIN=considered 81, unacceptable product size 49, no internal oligo 32, ok 0
-
-All the categories are exclusive, except the 'considered' category.
-
-In some cases Primer3 will examine a primer pair before it
-discovers that one of the primers in the pair violates specified
-constraints.  In this case PRIMER_PAIR_EXPLAIN might have a non-0
-number 'considered', even though one or more of
-PRIMER_LEFT_EXPLAIN, PRIMER_RIGHT_EXPLAIN, or
-PRIMER_INTERNAL_OLIGO_EXPLAIN has 'ok 0'.
-
-PRIMER_PAIR_PENALTY=f
-
-The value of the objective function for this pair (lower is better).
-
-PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_PENALTY=f
-
-The contribution of this individual primer or oligo to the
-objective function.
-
-PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_SEQUENCE=s
-
-The actual sequence of the oligo. The sequence of left primer and
-internal oligo is presented 5' -> 3' on the same strand as the
-input SEQUENCE (which must be presented 5' -> 3').  The sequence
-of the right primer is presented 5' -> 3' on the opposite strand
-from the input SEQUENCE.
-
-PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_TM=f
-
-The melting TM for the selected oligo.
-
-PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_GC_PERCENT=f
-
-The percent GC for the selected oligo (denominator is the number
-of non-ambiguous bases).
-
-PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_SELF_ANY=f
-PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_SELF_END=f
-
-The self-complementarity measures for the selected oligo.
-
-PRIMER_PAIR_COMPL_ANY=f
-PRIMER_PAIR_COMPL_END=f
-
-The inter-pair complementarity measures for the selected left and
-right primer
-
-PRIMER_WARNING=s (*)
-
-s lists warnings generated by primer (separated by semicolons);
-this tag is absent if there are no warnings
-
-PRIMER_{LEFT,RIGHT,PAIR}_MISPRIMING_SCORE=f, s
-
-f is the maximum mispriming score for the right primer
-against any sequence in the given PRIMER_MISPRIMING_LIBRARY;
-s is the id of corresponding library sequence.
-PRIMER_PAIR_MISPRIMING_SCORE is the maximum sum of
-mispriming scores in any single library sequence (perhaps a
-more reasonable estimator of the likelihood of mispriming).
-
-PRIMER_{LEFT,RIGHT,PAIR}_TEMPLATE_MISPRIMING=f
-
-Analogous to PRIMER_{LEFT,RIGHT,PAIR}_MISPRIMING_SCORE, except that
-these output tags apply to mispriming within the template sequence.
-This often arises, for example, in genes with repeated exons. For
-backward compatibility, these tags only appear if the corresponding
-input tags have defined values.
-
-PRIMER_PRODUCT_TM=f
-
-f is the melting temperature of the product. Calculated using equation (iii)
-from Rychlik, Spencer and Rhoads, Nucleic Acids Research 18(21) pg. 6410.
-Printed only if a non-default value of PRIMER_MAX_PRODUCT_TM or
-PRIMER_MIN_PRODUCT_TM is specified.
-
-PRIMER_PRODUCT_TM_OLIGO_TM_DIFF=f
-
-f is the difference between the melting temperature of the
-product and the melting temperature of the less stable primer.
-Printed only if PRIMER_MAX_PRODUCT_TM or PRIMER_MIN_PRODUCT_TM is
-specified.
-
-PRIMER_PAIR_T_OPT_A=f
-
-f is T sub a super OPT from equation (i) in Rychlik, Spencer, and
-Rhoads, Nucleic Acids Research 18(21), page 6410.  Printed only if
-PRIMER_MAX_PRODUCT_TM or PRIMER_MIN_PRODUCT_TM is specified.
-
-PRIMER_INTERNAL_OLIGO_MISHYB_SCORE=f, s
-
-f is the maximum mishybridization score for the right primer
-against any sequence in the given
-PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY; s is the id of
-corresponding library sequence.
-
-PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_MIN_SEQ_QUALITY=i
-
-i is the minimum _sequence_ quality within the primer
-or oligo (not to be confused with the PRIMER_PAIR_QUALITY
-output tag, which is really the value of the objective
-function.)
-
-PRIMER_{LEFT,RIGHT}_END_STABILITY=f
-
-f is the delta G of disruption of the five 3' bases of the
-primer.
-
-PRIMER_STOP_CODON_POSITION=i
-
-i is the position of the first base of the stop codon,
-if Primer3 found one, or -1 if Primer3 did not.  Printed
-only if the input tag PRIMER_START_CODON_POSITION with a
-non-default value is supplied.
-
-EXAMPLE OUTPUT
---------------
-You should run it youself.  Use the file 'example' in this
-directory as input.
-
-
-ADVICE FOR PICKING PRIMERS
---------------------------
-We suggest referring to: Wojciech Rychlik, "Selection of Primers
-for Polymerase Chain Reaction" in BA White, Ed., "Methods in
-Molecular Biology, Vol. 15: PCR Protocols: Current Methods and
-Applications", 1993, pp 31-40, Humana Press, Totowa NJ
-
-
-Cautions
---------
-Some of the most important issues in primer picking can be
-addressed only before using Primer3.  These are sequence quality
-(including making sure the sequence is not vector and not
-chimeric) and avoiding repetitive elements.
-
-Techniques for avoiding problems include a thorough understanding
-of possible vector contaminants and cloning artifacts coupled
-with database searches using blast, fasta, or other similarity
-searching program to screen for vector contaminants and possible
-repeats.  Repbase (J. Jurka, A.F.A. Smit, C. Pethiyagoda, and
-others, 1995-1996, ftp://ncbi.nlm.nih.gov/repository/repbase)
-is an excellent source of repeat sequences and pointers to the
-literature.  (The Repbase files need to be converted to Fasta format
-before they can be used by Primer3.) Primer3 now allows you to screen
-candidate oligos against a Mispriming Library (or a Mishyb Library in
-the case of internal oligos).
-
-
-Sequence quality can be controlled by manual trace viewing and
-quality clipping or automatic quality clipping programs.  Low-
-quality bases should be changed to N's or can be made part of
-Excluded Regions. The beginning of a sequencing read is often
-problematic because of primer peaks, and the end of the read
-often contains many low-quality or even meaningless called bases.
-Therefore when picking primers from single-pass sequence it is
-often best to use the INCLUDED_REGION parameter to ensure that
-Primer3 chooses primers in the high quality region of the read.
-
-In addition, Primer3 takes as input a Sequence Quality list for
-use with those base calling programs 
-
-(e.g. Phred, Bass/Grace, Trout) that output this information.
-
-
-
-
-
-What to do if Primer3 cannot find a primers?
---------------------------------------------
-Try relaxing various parameters, including the
-self-complementarity parameters and max and min oligo melting
-temperatures.  For example, for very A-T-rich regions you might
-have to increase maximum primer size or decrease minimum melting
-temperature.  It is usually unwise to reduce the minimum primer
-size if your template is complex (e.g. a mammalian genome), since
-small primers are more likely to be non-specific.  Make sure that
-there are adequate stretches of non-Ns in the regions in which
-you wish to pick primers.  If necessary you can also allow an N
-in your primer and use an oligo mixture containing all four bases
-at that position.
-
-Try setting the PRIMER_EXPLAIN_FLAG input tag.
-
-DIFFERENCES FROM EARLIER VERSIONS
----------------------------------
-
-Also see the file release notes in this directory.
-
-Compared to 0.5
----------------
-Completely different input format.  
-
-It has been reported the 0.5 deleted Ns when they occurred in
-primers.  
-
-More stringent self-complementarity defaults.
-
-Primer3 selects internal oligos on request (and produces .int
-files if requested).
-
-Compared to both 0.5 and v2
----------------------------
-The format of the contents of .for, .rev (and .int) files is
-different.
-
-Primer3 returns a user-specifiable number of primer pairs (or
-triples) sorted by "goodness".
-
-Primer3 will find a primer pair if any acceptable pair exists.
-
-Optional n-based indexing into source sequence.
-
-Use of sequence quality and 3' stability as constraints in primer
-picking.  Optional positional component to objective function.
-
-Compared to v2
--------------
-Tag name changes.  However, Primer3 should understand most or
-all Primer v2 input tags, and should produce v2-compatible output
-tag names when the -v2_compat command-line switch is used.
-
-The one exception is that the PRIMER_RECOMMEND tag is no longer
-produced. Instead Primer3 produces the PRIMER_x_EXPLAIN output
-tags.  The format of the data in this tags is different from the
-data in v2's PRIMER_RECOMMEND output tag.
-
-Numerous fixes.
-
-Uses the PRIMER_SELF_ANY and PRIMER_SELF_END parameters to govern
-maximum allowable complementarity between left and right primers,
-as well as complementarity between copies of a single oligo or
-within a single oligo.  This behaviour is very close to that of
-primer 0.5; self complementarity calculations in v2 were
-unreliable.
-
-Primer3 produces much more output information, including the TMs
-and self complementarity measures of selected primers.
-
-
-EXIT STATUS CODES
------------------
-
- 0 on normal operation
--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).
--2 on out-of-memory
--3 empty input
--4 error in a "Global" input tag (message in PRIMER_ERROR).
-
-Primer3 calls abort() and dumps core (if possible) if a
-programming error is detected by an assertion violation.
-
-SIGINT and SIGTERM are handled essentially as empty input, except
-the signal received is returned as the exit status and printed to
-stderr.
-
-In all of the error cases above Primer3 prints a message to stderr.
-
-THE NEW PRIMER3 WWW INTERFACE
------------------------------
-This distribution does not contain the Primer3 WWW interface.  A
-snapshot of the interface used at Whitehead Institute may be available
-strictly 'AS-IS' and without support by e-mail request to
-primer3(at)wi.mit.edu, replacing (at) with @.
-
-The remainder of this section is out-of-date.
-
-The web interface consists of:
-
-primer3_www.cgi              (the user input screen)
-primer3_www_help.html        (user help for the input screen)
-primer3_www_results.cgi      (the results screen)
-primer3_www_results_help.cgi (user help for the results screen)
-
-To use this interface you will need perl5 and the perl5
-module CGI.pm.  Refer to your perl book to locate the perl5
-distribution.  CGI.pm was written by Lincoln D. Stein and is
-available from CPAN (www.cpan.org). You will also need to
-know enough about your operating system and web server to
-install a new CGI script, and enough about perl5 to read the
-script and figure out how it does what it does.
-
-You will have to make some modifications to primer3_www.cgi and
-to primer_www_results.cgi:
-
-1. Correct the path to perl5 on the first line of each .cgi file,
-since this path varies from system to system.
-
-2. Change the value of the $MAINTAINER variable near the top of
-both .cgi files so that they address the person maintaining your
-installation of the primer WWW interface.
-
-3. Specify available mispriming libraries.  In primer3_www.cgi
-modify the variable $SELECT_SEQ_LIBRARY as necessary and in
-primer3_www_results modify the value of %SEQ_LIBRARY in a
-corresponding way.
-
-4. Depending on your primer picking application you might want to
-change defaults; many of these are set in primer3_www.cgi, but
-there are some subtleties dealing with in the interpretation of
-empty input fields.  You have to read the code to really
-understand what is going on.
-
-5. If primer3_www_help.html is not in the same directory as
-primer3_www.cgi fix $DOC_URL in primer3_www.cgi.
-
-6. If primer3_www_results.cgi is not in the same directory as
-primer3_www.cgi fix $PROCESS_INPUT_URL in primer3_www.cgi.
-
-7. If primer3_core is not in same directory as
-primer3_www_results.cgi, fix $PRIMER_BIN in
-primer3_www_results.cgi.
- 
-8. If primer3_www_results_help.html is not in the same directory
-as primer3_www_results.cgi fix $ODOC_URL in
-primer3_www_results.cgi.
-
-
-ACKNOWLEDGMENTS
----------------
-
-The development of Primer3 was funded by Howard Hughes Medical
-Institute and by the National Institutes of Health, National
-Human Genome Research Institute under grants R01-HG00257 (to
-David C. Page) and P50-HG00098 (to Eric S. Lander).
-
-We gratefully acknowledge the support of Digital Equipment
-Corporation, which provided the Alphas which were used for most
-of the development of Primer3, and of Centerline Software, Inc.,
-whose TestCenter memory-error, -leak, and test-coverage checker
-helped us discover and correct a number of otherwise latent
-errors in Primer3.
-
-Primer3 was written by Helen J. Skaletsky (Howard Hughes Medical
-Institute, Whitehead Institute) and Steve Rozen (Whitehead
-Institute/MIT Center for Genome Research), based on the design of
-earlier versions: Primer 0.5 (Steve Lincoln, Mark Daly, and Eric
-S. Lander) and Primer v2 (Richard Resnick).  This documentation
-was written by Richard Resnick and Steve Rozen.  The original web
-interface was designed by Richard Resnick.  Lincoln Stein 
-championed the use of the Boulder-IO format and the idea of
-making Primer3 a software component.
-
-In addition, following is a partial list of people who kindly
-contributed to the design of Primer3
-
-Ernst Molitor
-Carl Foeller
-
-The authors of the current version would be pleased to receive
-error reports or requests for enhancements.  Please send e-mail
-to primer3(at)wi.mit.edu after replacing (at) with @.

Added: trunk/packages/primer3/branches/upstream/current/README.primer3_1.0b.txt
===================================================================
--- trunk/packages/primer3/branches/upstream/current/README.primer3_1.0b.txt	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/README.primer3_1.0b.txt	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1,1463 @@
+primer3 release 1.0b
+
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+INTRODUCTION
+------------
+Primer3 picks primers for PCR reactions, considering as criteria:
+
+o oligonucleotide melting temperature, size, GC content,
+  and primer-dimer possibilities,
+
+o PCR product size,
+
+o positional constraints within the source sequence, and
+
+o miscellaneous other constraints.
+
+All of these criteria are user-specifiable as constraints, and
+some are specifiable as terms in an objective function that
+characterizes an optimal primer pair.  
+
+Whitehead Institute for Biomedical Research provides a web-based
+front end to Primer3 at
+http://fokker.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi
+
+CITING PRIMER3
+--------------
+We request but do not require that use of this software be cited in
+publications as
+
+Steve Rozen and Helen J. Skaletsky (2000)
+Primer3 on the WWW for general users and for biologist programmers.
+In: Krawetz S, Misener S (eds)
+Bioinformatics Methods and Protocols: Methods in Molecular Biology.
+Humana Press, Totowa, NJ, pp 365-386
+
+Source code available at http://fokker.wi.mit.edu/primer3/.
+The paper above is available at
+http://jura.wi.mit.edu/rozen/papers/rozen-and-skaletsky-2000-primer3.pdf
+
+INSTALLATION INSTRUCTIONS
+-------------------------
+Unzip and untar the distribution.
+
+DO NOT do this on a PC -- primer3_core will not compile if pc
+newlines get inserted into the source files.  Instead, move the
+distribution (primer3_<release>.tar.gz) to Unix, and then
+
+$ unzip primer3_1.0b.tar.gz
+$ tar xvf primer3_1.0b.tar
+$ cd primer3_1.0b/src
+
+If you do not use gcc, modify the makefile to
+  use your (ANSI) C compiler and appropriate 
+  compile and link flags.
+
+$ make all
+# Warnings about pr_release being unused are harmless.
+# You should have created executables primer3_core, ntdpal,
+#  olgotm, and long_seq_tm_test
+
+$ cd ../test
+$ perl -w p3test.pl
+$ perl -w dpal_test.pl
+# You should not see 'FAILED' during the tests.
+
+If your perl command is not called perl (for example, if it is
+called perl5) you will have to modify the internals of the test
+scripts).
+
+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").  It is provided
+strictly as is; for further documentation please see the code.
+
+SYSTEM REQUIREMENTS
+-------------------
+Primer3 has been successfully installed and tested on the
+following systems
+
+     o Sparc running SunOS 4.1 (gcc 2.7.0)
+     o Alpha running DEC Unix 3.2 (gcc 2.7.0 and DEC cc)
+     o Pentium running Linux 1.2 (Red Hat) (gcc 2.7.0)
+
+Primer3 will likely compile and run on other POSIX architectures with
+ANSI C compilers.
+
+
+INPUT AND OUTPUT CONVENTIONS
+----------------------------
+
+By default, Primer3 accepts input and produces output in
+Boulder-io format, a pre-XML text-based input/output format
+for program-to-program data interchange format.  When run
+with the -format_output command-line flag, Primer3 prints a
+more user-oriented report for each sequence.  Additional
+command-line flags include -2x_compat (which causes Primer3
+to print its output using Primer v2 compatible tag names),
+and -strict_tags (both discussed below).  Primer3 exits with
+0 status if it operates correctly.  See EXIT STATUS CODES
+below for additional information.
+
+The syntax of the version of Boulder-io recognized by Primer3 is
+as follows:
+
+  o Input consists of a sequence of RECORDs.
+
+  o A RECORD consists of a sequence of (TAG,VALUE) pairs, each terminated
+    by a newline character (\n). A RECORD is terminated by  '='
+    appearing by itself on a line.
+
+  o A (TAG,VALUE) pair has the following requirements:
+
+        o the TAG must be immediately (without spaces) 
+          followed by '='.
+	o the pair must be terminated by a newline character.
+
+An example of a legal (TAG,VALUE) pair is
+
+PRIMER_SEQUENCE_ID=my_marker
+
+and an example of a BOULDER-IO record is
+
+PRIMER_SEQUENCE_ID=test1
+SEQUENCE=GACTGATCGATGCTAGCTACGATCGATCGATGCATGCTAGCTAGCTAGCTGCTAGC
+=
+
+Many records can be sent, one after another. Below is an example
+of three different records which might be passed through a
+boulder-io stream:
+
+PRIMER_SEQUENCE_ID=test1
+SEQUENCE=GACTGATCGATGCTAGCTACGATCGATCGATGCATGCTAGCTAGCTAGCTGCTAGC
+=
+PRIMER_SEQUENCE_ID=test2
+SEQUENCE=CATCATCATCATCGATGCTAGCATCNNACGTACGANCANATGCATCGATCGT
+=
+PRIMER_SEQUENCE_ID=test3
+SEQUENCE=NACGTAGCTAGCATGCACNACTCGACNACGATGCACNACAGCTGCATCGATGC
+=
+
+Primer3 reads boulder-io on stdin and echos its input and returns
+results in boulder-io format on stdout.  Primer3 indicates many
+user-correctable errors by a value in the PRIMER_ERROR tag (see
+below) and indicates other errors, including system configuration
+errors, resource errors (such out-of-memory errors), and detected
+programming errors by a message on stderr and a non-zero exit
+status.
+
+Below is the list of input tags that Primer3 recognizes.
+Primer3 echos and ignores any tags it does not recognize, unless
+the -strict_tags flag is set on the command line, in which case
+Primer3 prints an error in the PRIMER_ERROR output tag (see
+below), and prints additional information on stdout; this option
+can be useful for debugging systems that incorporate primer.
+
+Except for tags with the type "interval list" each tag is allowed
+only ONCE in any given input record.  This restriction is not
+systematically checked in this beta release: use care.
+
+There are 2 major classes of input tags.  "Sequence" input tags
+describe a particular input sequence to Primer3, and are reset
+after every boulder record.  "Global" input tags describe the
+general parameters that Primer3 should use in its searches, and
+the values of these tags persist between input boulder records
+until or unless they are explicitly reset.  Errors in "Sequence"
+input tags invalidate the current record, but Primer3 will
+continue to process additional records.  Errors in "Global" input
+tags are fatal because they invalidate the basic conditions under
+which primers are being picked.
+
+"Sequence" Input Tags
+---------------------
+
+PRIMER_SEQUENCE_ID (string, optional)
+
+(MARKER_NAME is a deprecated synonym maintained for v2
+compatibility.)
+
+An identifier that is reproduced in the output to enable users to
+identify the source of the chosen primers.
+
+This tag must be present if PRIMER_FILE_FLAG is non-zero.
+
+SEQUENCE (nucleotide sequence, REQUIRED)
+
+The sequence from which to choose primers.  The sequence
+must be presented 5' -> 3' (see the discussion of the
+PRIMER_SELF_END argument).  The bases may be upper or lower case.
+No newlines should be inserted into the sequence, because the
+Boulder-IO parser will assume that a line ends at a newline.
+
+INCLUDED_REGION (interval, optional)
+
+A sub-region of the given sequence in which to pick primers.  For
+example, often the first dozen or so bases of a sequence are
+vector, and should be excluded from consideration. The value for
+this parameter has the form
+
+<start>,<length>
+
+where <start> is the index of the first base to consider,
+and <length> is the number of subsequent bases in the
+primer-picking region.
+
+TARGET (interval list, default empty)
+
+If one or more Targets is specified then a legal primer pair must
+flank at least one of them.  A Target might be a simple sequence
+repeat site (for example a CA repeat) or a single-base-pair
+polymorphism.  The value should be a space-separated list of
+
+<start>,<length>
+
+pairs where <start> is the index of the first base of a
+Target, and <length> is its length.
+
+For backward compatibility Primer3 accepts (but ignores)
+a trailing ,<description> for each element of this argument.
+
+EXCLUDED_REGION (interval list, default empty)
+
+Primer oligos may not overlap any region specified in this tag.
+The associated value must be a space-separated list of
+
+<start>,<length>
+
+pairs where <start> is the index of the first base of
+the excluded region, and <length> is its length.  This tag is
+useful for tasks such as excluding regions of low sequence
+quality or for excluding regions containing repetitive elements
+such as ALUs or LINEs.
+
+PRIMER_COMMENT (string, optional)
+
+The value of this tag is ignored.
+
+COMMENT (string, optional)
+
+Deprecated synonym for PRIMER_COMMENT.
+
+PRIMER_SEQUENCE_QUALITY (quality list, default empty)
+
+A list of space separated integers. There must be exactly
+one integer for each base in SEQUENCE if this argument is
+non-empty.  For example, for the sequence ANNTTCA...
+PRIMER_SEQUENCE_QUALITY might be 45 10 0 50 30 34 50 67 ....
+High numbers indicate high confidence in the base called at
+that position and low numbers indicate low confidence in the
+base call at that position.  This parameter is only relevant
+if you are using a base calling program that provides
+quality information (for example phred).
+
+PRIMER_LEFT_INPUT (nucleotide sequence, default empty)
+
+The sequence of a left primer to check and around which to design
+right primers and optional internal oligos.  Must be a substring
+of SEQUENCE.
+
+PRIMER_RIGHT_INPUT (nucleotide sequence, default empty)
+
+The sequence of a right primer to check and around which to
+design left primers and optional internal oligos.  Must be a
+substring of the reverse strand of SEQUENCE.
+
+PRIMER_START_CODON_POSITION (int, default -1000000)
+
+This parameter should be considered EXPERIMENTAL at this point.
+Please check the output carefully; some erroneous inputs might
+cause an error in Primer3.
+
+Index of the first base of a start codon.  This parameter allows
+Primer3 to select primer pairs to create in-frame amplicons
+e.g. to create a template for a fusion protein.  Primer3 will
+attempt to select an in-frame left primer, ideally starting at or
+to the left of the start codon, or to the right if necessary.
+Negative values of this parameter are legal if the actual start
+codon is to the left of available sequence. If this parameter is
+non-negative Primer3 signals an error if the codon at the
+position specified by this parameter is not an ATG.  A value less
+than or equal to -10^6 indicates that Primer3 should ignore this
+parameter.
+
+Primer3 selects the position of the right primer by scanning
+right from the left primer for a stop codon.  Ideally the right
+primer will end at or after the stop codon.
+
+"Global" Input Tags
+-------------------
+
+PRIMER_PICK_ANYWAY (boolean, default 0)
+
+If true pick a primer pair even if PRIMER_LEFT_INPUT,
+PRIMER_RIGHT_INPUT, or PRIMER_INTERNAL_OLIGO_INPUT violates
+specific constraints.
+
+PRIMER_MISPRIMING_LIBRARY (string, optional)
+
+The name of a file containing a nucleotide sequence library of
+sequences to avoid amplifying (for example repetitive sequences, or
+possibly the sequences of genes in a gene family that should
+not be amplified.)  The file must be in (a slightly restricted)
+FASTA format (W. B. Pearson and D.J. Lipman, PNAS 85:8 pp
+2444-2448 [1988]); we briefly discuss the organization of this
+file below.  If this parameter is specified then Primer3 locally
+aligns each candidate primer against each library sequence and
+rejects those primers for which the local alignment score times a
+specified weight (see below) exceeds PRIMER_MAX_MISPRIMING.
+(The maximum value of the weight is arbitrarily set to 100.0.)
+
+Each sequence entry in the FASTA-format file must begin with an
+"id line" that starts with '>'.  The contents of the id line is
+"slightly restricted" in that Primer3 parses everything after any
+optional asterisk ('*') as a floating point number to use as the
+weight mentioned above.  If the id line contains no asterisk then
+the weight defaults to 1.0.  The alignment scoring system used is
+the same as for calculating complementarity among oligos (e.g.
+PRIMER_SELF_ANY), except for the handling of IUB/IUPAC ambiguity
+codes (discussed below).  The remainder of an entry contains the
+sequence as lines following the id line up until a line starting
+with '>' or the end of the file.  Whitespace and newlines are
+ignored.  Characters 'A', 'T', 'G', 'C', 'a', 't', 'g', 'c' 
+and IUB/IUPAC 'ambiguity' codes ('R, 'Y', 'K', 'M', 'S', 'W', 'N',
+including lower case) are retained. 
+
+WARNING: always set PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
+if any sequence in the library contains strings of 'N's:
+NNNNNNNNNNNNNNNNNNNN.
+NOWWW
+There are no restrictions on line length.
+
+An empty value for this parameter indicates that no repeat
+library should be used and "turns off" the use of a
+previously specified library.
+
+Repbase (J. Jurka, A.F.A. Smit, C. Pethiyagoda, and
+others, 1995-1996, ftp://ncbi.nlm.nih.gov/repository/repbase)
+is an excellent source of repeat sequences and pointers to the
+literature. (The Repbase files need to be converted to Fasta
+format before they can be used by Primer3.)
+
+
+PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS (boolean, default 1)
+
+If set to 1, treat ambiguity codes as if they were consensus
+codes when matching oligos to mispriming or mishyb
+libraries. For example, if this flag is set, then a C in an
+oligo will be scored as a perfect match to an S in a library
+sequence, as will a G in the oligo. More importantly,
+though, any base in an oligo will be scored as a perfect
+match to an N in the library.  This is very bad if the
+library contains strings of Ns, as no oligo will be legal
+(and it will take a long time to find this out). So unless
+you know for sure that your library does not have runs of Ns
+(or Xs), then set this flag to 0.
+
+PRIMER_MAX_MISPRIMING (decimal,9999.99, default 12.00)
+
+The maximum allowed weighted similarity with any sequence in
+PRIMER_MISPRIMING_LIBRARY.  
+
+PRIMER_MAX_TEMPLATE_MISPRIMING (decimal,9999.99, default -1.00)
+
+The maximum allowed similarity to ectopic sites in the
+template.  A negative value means do not check.  The scoring
+system is the same as used for PRIMER_MAX_MISPRIMING, except
+that an ambiguity code in the template is never treated as a
+consensus (see PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS).
+
+PRIMER_PAIR_MAX_MISPRIMING (decimal,9999.99, default 24.00)
+
+The maximum allowed sum of similarities of a primer pair
+(one similarity for each primer) with any single sequence in
+PRIMER_MISPRIMING_LIBRARY.  
+Library sequence weights are not used in computing the sum
+of similarities.
+
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING (decimal,9999.99, default -1.00)
+
+The maximum allowed summed similarity of both primers to
+ectopic sites in the template. A negative value means do not
+check.  The scoring system is the same as used for
+PRIMER_PAIR_MAX_MISPRIMING, except that an ambiguity code in
+the template is never treated as a consensus (see
+PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS).  Primer3 does not
+check the similarity of hybridization oligos (internal
+oligos) to locations outside of the amplicon.
+
+PRIMER_PRODUCT_MAX_TM (float, default 1000000.0)
+
+The maximum allowed melting temperature of the amplicon.  Primer3
+calculates product Tm calculated using the formula from Bolton
+and McCarthy, PNAS 84:1390 (1962) as presented in Sambrook,
+Fritsch and Maniatis, Molecular Cloning, p 11.46 (1989, CSHL
+Press).
+
+   Tm = 81.5 + 16.6(log10([Na+])) + .41*(%GC) - 600/length
+
+Where [Na+] is the molar sodium concentration, (%GC) is the
+percent of Gs and Cs in the sequence, and length is the length of
+the sequence.
+
+A similar formula is used by the prime primer selection program
+in GCG (http://www.gcg.com), which instead uses 675.0 / length in
+the last term (after F. Baldino, Jr, M.-F. Chesselet, and M.E.
+Lewis, Methods in Enzymology 168:766 (1989) eqn (1) on page 766
+without the mismatch and formamide terms).  The formulas here and
+in Baldino et al. assume Na+ rather than K+.  According to
+J.G. Wetmur, Critical Reviews in BioChem. and Mol. Bio. 26:227
+(1991) 50 mM K+ should be equivalent in these formulae to .2 M
+Na+.  Primer3 uses the same salt concentration value for
+calculating both the primer melting temperature and the oligo
+melting temperature.  If you are planning to use the PCR product
+for hybridization later this behavior will not give you the Tm
+under hybridization conditions.
+
+PRIMER_PRODUCT_MIN_TM (float, default -1000000.0)
+
+The minimum allowed melting temperature of the amplicon.  Please
+see the documentation on the maximum melting temperature of the
+product for details.
+
+PRIMER_EXPLAIN_FLAG (boolean, default 0)
+
+If this flag is non-0, produce PRIMER_LEFT_EXPLAIN,
+PRIMER_RIGHT_EXPLAIN, and PRIMER_INTERNAL_OLIGO_EXPLAIN output
+tags, which are intended to provide information on the number of
+oligos and primer pairs that Primer3 examined, and statistics on
+the number discarded for various reasons.  If -format_output is
+set similar information is produced in the user-oriented output.
+
+PRIMER_PRODUCT_SIZE_RANGE (size range list, default 100-300)
+
+The associated values specify the lengths of the product that the
+user wants the primers to create, and is a space separated list
+of elements of the form
+
+<x>-<y>
+
+where an <x>-<y> pair is a legal range of lengths for the
+product.  For example, if one wants PCR products to be between
+100 to 150 bases (inclusive) then one would set this parameter to
+100-150.  If one desires PCR products in either the range from
+100 to 150 bases or in the range from 200 to 250 bases then one
+would set this parameter to 100-150 200-250.
+
+Primer3 favors ranges to the left side of the parameter string.
+Primer3 will return legal primers pairs in the first range
+regardless the value of the objective function for these pairs.
+Only if there are an insufficient number of primers in the first
+range will Primer3 return primers in a subsequent range.
+
+PRIMER_PICK_INTERNAL_OLIGO (boolean, default 0)
+
+If the associated value is non-0, then Primer3 will attempt to
+pick an internal oligo (hybridization probe to detect the PCR
+product).  This tag is maintained for backward compatibility.
+Use PRIMER_TASK.
+
+PRIMER_GC_CLAMP (int, default 0)
+
+Require the specified number of consecutive Gs and Cs at the 3'
+end of both the left and right primer.  (This parameter has no
+effect on the internal oligo if one is requested.)
+
+PRIMER_OPT_SIZE (int, default 20)
+
+Optimum length (in bases) of a primer oligo. Primer3 will attempt
+to pick primers close to this length.
+
+PRIMER_DEFAULT_SIZE (int, default 20)
+
+A deprecated synonym for PRIMER_OPT_SIZE, maintained for v2
+compatibility.
+
+PRIMER_MIN_SIZE (int, default 18)
+
+Minimum acceptable length of a primer.  Must be greater than 0
+and less than or equal to PRIMER_MAX_SIZE.
+
+PRIMER_MAX_SIZE (int, default 27)
+
+Maximum acceptable length (in bases) of a primer.  Currently this
+parameter cannot be larger than 35.  This limit is governed by
+maximum oligo size for which Primer3's melting-temperature is
+valid.
+
+PRIMER_OPT_TM (float, default 60.0C)
+
+Optimum melting temperature(Celsius) for a primer oligo. Primer3
+will try to pick primers with melting temperatures are close to
+this temperature.  The oligo melting temperature formula in
+Primer3 is that given in Rychlik, Spencer and Rhoads, Nucleic
+Acids Research, 18(21): 6409-6412 and Breslauer,
+Frank, Bloeker and Marky, PNAS, 83: 3746-3750.
+Please refer to the former paper for background discussion.
+
+PRIMER_MIN_TM (float, default 57.0C)
+
+Minimum acceptable melting temperature(Celsius) for a primer
+oligo.
+
+PRIMER_MAX_TM (float, default 63.0C)
+
+Maximum acceptable melting temperature(Celsius) for a primer
+oligo.
+
+PRIMER_MAX_DIFF_TM (float, default 100.0C)
+
+Maximum acceptable (unsigned) difference between the melting
+temperatures of the left and right primers.
+
+PRIMER_MIN_GC (float, default 20.0%)
+
+Minimum allowable percentage of Gs and Cs in any primer.
+
+PRIMER_OPT_GC_PERCENT (float, default 50.0%)
+
+Optimum GC percent.  This parameter influences primer selection only if
+PRIMER_WT_GC_PERCENT_GT or PRIMER_WT_GC_PERCENT_LT are non-0.
+
+PRIMER_MAX_GC (float, default 80.0%)
+
+Maximum allowable percentage of Gs and Cs in any primer generated
+by Primer.
+
+PRIMER_SALT_CONC (float, default 50.0 mM)
+
+The millimolar concentration of salt (usually KCl) in the PCR.
+Primer3 uses this argument to calculate oligo melting
+temperatures.
+
+PRIMER_DNA_CONC (float, default 50.0 nM)
+
+The nanomolar concentration of annealing oligos in the PCR.
+Primer3 uses this argument to calculate oligo melting
+temperatures.  The default (50nM) works well with the standard
+protocol used at the Whitehead/MIT Center for Genome
+Research--0.5 microliters of 20 micromolar concentration for each
+primer oligo in a 20 microliter reaction with 10 nanograms
+template, 0.025 units/microliter Taq polymerase in 0.1 mM each
+dNTP, 1.5mM MgCl2, 50mM KCl, 10mM Tris-HCL (pH 9.3) using 35
+cycles with an annealing temperature of 56 degrees Celsius.  This
+parameter corresponds to 'c' in Rychlik, Spencer and Rhoads'
+equation (ii) (Nucleic Acids Research, 18(21): 6409-6412)
+where a suitable value (for a lower initial concentration of template)
+is "empirically determined".  The value of this parameter is less
+than the actual concentration of oligos in the reaction because
+it is the concentration of annealing oligos, which in turn
+depends on the amount of template (including PCR product) in a
+given cycle.  This concentration increases a great deal during a
+PCR; fortunately PCR seems quite robust for a variety of oligo
+melting temperatures.
+
+See ADVICE FOR PICKING PRIMERS.
+
+PRIMER_NUM_NS_ACCEPTED (int, default 0)
+
+Maximum number of unknown bases (N) allowable in any primer.
+
+PRIMER_SELF_ANY (decimal,9999.99, default 8.00)
+
+The maximum allowable local alignment score when testing a single
+primer for (local) self-complementarity and the maximum allowable
+local alignment score when testing for complementarity between
+left and right primers.  Local self-complementarity is taken to
+predict the tendency of primers to anneal to each other without
+necessarily causing self-priming in the PCR.  The scoring system
+gives 1.00 for complementary bases, -0.25 for a match of any base
+(or N) with an N, -1.00 for a mismatch, and -2.00 for a gap.
+Only single-base-pair gaps are allowed.  For example, the
+alignment
+
+5' ATCGNA 3'
+   || | |
+3' TA-CGT 5'
+
+is allowed (and yields a score of 1.75), but the alignment
+
+5' ATCCGNA 3'
+   ||  | |
+3' TA--CGT 5'
+
+is not considered.  Scores are non-negative, and a score of 0.00
+indicates that there is no reasonable local alignment between two
+oligos.
+
+PRIMER_SELF_END (decimal 9999.99, default 3.00)
+
+The maximum allowable 3'-anchored global alignment score when
+testing a single primer for self-complementarity, and the maximum
+allowable 3'-anchored global alignment score when testing for
+complementarity between left and right primers.  The 3'-anchored
+global alignment score is taken to predict the likelihood of
+PCR-priming primer-dimers, for example
+
+5' ATGCCCTAGCTTCCGGATG 3'
+             ||| |||||
+          3' AAGTCCTACATTTAGCCTAGT 5'
+
+or
+
+5` AGGCTATGGGCCTCGCGA 3'
+               ||||||
+            3' AGCGCTCCGGGTATCGGA 5'
+
+The scoring system is as for the Maximum Complementarity
+argument.  In the examples above the scores are 7.00 and 6.00
+respectively.  Scores are non-negative, and a score of 0.00
+indicates that there is no reasonable 3'-anchored global
+alignment between two oligos.  In order to estimate 3'-anchored
+global alignments for candidate primers and primer pairs, Primer
+assumes that the sequence from which to choose primers is
+presented 5'->3'.  It is nonsensical to provide a larger value
+for this parameter than for the Maximum (local) Complementarity
+parameter because the score of a local alignment will always be at
+least as great as the score of a global alignment.
+
+PRIMER_DEFAULT_PRODUCT (size range list, default 100-300)
+
+A deprecated synonym for PRIMER_PRODUCT_SIZE_RANGE, maintained
+for v2 compatibility.
+
+PRIMER_FILE_FLAG (boolean, default 0)
+
+If the associated value is non-0, then Primer3 creates two output
+files for each input SEQUENCE.  File <sequence_id>.for lists all
+acceptable left primers for <sequence_id>, and <sequence_id>.rev
+lists all acceptable right primers for <sequence_id>, where
+<sequence_id> is the value of the PRIMER_SEQUENCE_ID tag (which
+must be supplied).  In addition, if the input tag
+PRIMER_PICK_INTERNAL_OLIGO is non-0, Primer3 produces a file
+<sequence_id>.int, which lists all acceptable internal oligos.
+
+PRIMER_MAX_POLY_X (int, default 5)
+
+The maximum allowable length of a mononucleotide repeat,
+for example AAAAAA.
+
+PRIMER_LIBERAL_BASE (boolean, default 0)
+
+This parameter provides a quick-and-dirty way to get Primer3 to
+accept IUB / IUPAC codes for ambiguous bases (i.e. by changing
+all unrecognized bases to N).  If you wish to include an
+ambiguous
+base in an oligo, you must set PRIMER_NUM_NS_ACCEPTED to a
+non-0 value.
+
+Perhaps '-' and '* ' should be squeezed out rather than changed
+to 'N', but currently they simply get converted to N's.  The authors
+invite user comments.
+
+PRIMER_NUM_RETURN (int, default 5)
+
+The maximum number of primer pairs to return.  Primer pairs
+returned are sorted by their "quality", in other words by the
+value of the objective function (where a lower number indicates a
+better primer pair).  Caution: setting this parameter to a large
+value will increase running time.
+
+PRIMER_FIRST_BASE_INDEX (int, default 0)
+
+This parameter is the index of the first base in the input
+sequence.  For input and output using 1-based indexing (such as
+that used in GenBank and to which many users are accustomed) set
+this parameter to 1.  For input and output using 0-based indexing
+set this parameter to 0.  (This parameter also affects the
+indexes in the contents of the files produced when the primer
+file flag is set.)
+
+PRIMER_MIN_QUALITY (int, default 0)
+
+The minimum sequence quality (as specified by
+PRIMER_SEQUENCE_QUALITY) allowed within a primer.
+
+PRIMER_MIN_END_QUALITY (int, default 0)
+
+The minimum sequence quality (as specified by
+PRIMER_SEQUENCE_QUALITY) allowed within the 5' pentamer of a
+primer.
+
+PRIMER_QUALITY_RANGE_MIN (int, default 0)
+
+The minimum legal sequence quality (used for error checking
+of PRIMER_MIN_QUALITY and PRIMER_MIN_END_QUALITY).
+
+PRIMER_QUALITY_RANGE_MAX (int, default 100)
+
+The maximum legal sequence quality (used for error checking
+of PRIMER_MIN_QUALITY and PRIMER_MIN_END_QUALITY).
+
+PRIMER_INSIDE_PENALTY (float, default -1.0)
+
+This experimental parameter might not be maintained in this form
+in the next release.  Non-default values valid only for sequences
+with 0 or 1 target regions.  If the primer is part of a pair that
+spans a target and overlaps the target, then multiply this value
+times the number of nucleotide positions by which the primer
+overlaps the (unique) target to get the 'position penalty'.  The
+effect of this parameter is to allow Primer3 to include overlap
+with the target as a term in the objective function.
+
+PRIMER_OUTSIDE_PENALTY (float, default 0.0)
+
+This experimental parameter might not be maintained in this form
+in the next release.  Non-default values valid only for sequences
+with 0 or 1 target regions.  If the primer is part of a pair that
+spans a target and does not overlap the target, then multiply
+this value times the number of nucleotide positions from the 3'
+end to the (unique) target to get the 'position penalty'.
+The effect of this parameter is to allow Primer3 to include
+nearness to the target as a term in the objective function.
+
+PRIMER_MAX_END_STABILITY (float 999.9999, default 100.0)
+
+The maximum stability for the five 3' bases of a left or right
+primer.  Bigger numbers mean more stable 3' ends.  The value is
+the maximum delta G for duplex disruption for the five 3' bases
+as calculated using the nearest neighbor parameters published in
+Breslauer, Frank, Bloeker and Marky, Proc. Natl. Acad. Sci. USA,
+vol 83, pp 3746-3750.  Primer3 uses a completely permissive
+default value for backward compatibility (which we may change in
+the next release).  Rychlik recommends a maximum value of 9
+(Wojciech Rychlik, "Selection of Primers for Polymerase Chain
+Reaction" in BA White, Ed., "Methods in Molecular Biology,
+Vol. 15: PCR Protocols: Current Methods and Applications", 1993,
+pp 31-40, Humana Press, Totowa NJ).
+
+PRIMER_PRODUCT_OPT_TM (float, default 0.0)
+
+The optimum melting temperature for the PCR product. 0 indicates
+that there is no optimum temperature.
+
+PRIMER_PRODUCT_OPT_SIZE (int, default 0)
+
+The optimum size for the PCR product.  0 indicates that there is
+no optimum product size.  This parameter influences primer
+pair selection only
+if PRIMER_PAIR_WT_PRODUCT_SIZE_GT or
+PRIMER_PAIR_WT_PRODUCT_SIZE_LT is non-0.
+
+PRIMER_TASK (string, default pick_pcr_primers)
+
+Tell Primer3 what task to perform. Legal values are pick_pcr_primers,
+pick_pcr_primers_and_hyb_probe, pick_left_only, pick_right_only,
+pick_hyb_probe_only.  The tasks should be self explanatory, except
+that we note that pick_pcr_primers_and_hyb_probe is
+equivalent to the setting PRIMER_PICK_INTERNAL_OLIGO to a non-zero
+value and setting PRIMER_TASK to pick_pcr_primers.
+
+PRIMER_WT_TM_GT (float, default 1.0)
+
+Penalty weight for primers with Tm over PRIMER_OPT_TM.
+
+PRIMER_WT_TM_LT (float, default 1.0)
+
+Penalty weight for primers with Tm under PRIMER_OPT_TM.
+
+PRIMER_WT_SIZE_LT (float, default 1.0)
+
+Penalty weight for primers shorter than PRIMER_OPT_SIZE.
+
+PRIMER_WT_SIZE_GT (float, default 1.0)
+
+Penalty weight for primers longer than PRIMER_OPT_SIZE.
+
+PRIMER_WT_GC_PERCENT_LT (float, default 1.0)
+
+Penalty weight for primers with GC percent greater than
+PRIMER_OPT_GC_PERCENT.
+
+PRIMER_WT_GC_PERCENT_GT (float, default 1.0)
+
+Penalty weight for primers with GC percent greater than
+PRIMER_OPT_GC_PERCENT.
+
+PRIMER_WT_COMPL_ANY (float, default 0.0)
+PRIMER_WT_COMPL_END (float, default 0.0)
+PRIMER_WT_NUM_NS (float, default 0.0)
+PRIMER_WT_REP_SIM (float, default 0.0)
+PRIMER_WT_SEQ_QUAL (float, default 0.0)
+PRIMER_WT_END_QUAL (float, default 0.0)
+PRIMER_WT_POS_PENALTY (float, default 0.0)
+PRIMER_WT_END_STABILITY (float, default 0.0)
+PRIMER_WT_TEMPLATE_MISPRIMING (float, default 0.0)
+PRIMER_PAIR_WT_PR_PENALTY (float, default 1.0)
+PRIMER_PAIR_WT_IO_PENALTY (float, default 0.0)
+PRIMER_PAIR_WT_DIFF_TM (float, default 0.0)
+PRIMER_PAIR_WT_COMPL_ANY (float, default 0.0)
+PRIMER_PAIR_WT_COMPL_END (float, default 0.0)
+PRIMER_PAIR_WT_PRODUCT_TM_LT (float, default 0.0)
+PRIMER_PAIR_WT_PRODUCT_TM_GT (float, default 0.0)
+PRIMER_PAIR_WT_PRODUCT_SIZE_GT (float, default 0.0)
+PRIMER_PAIR_WT_PRODUCT_SIZE_LT (float, default 0.0)
+PRIMER_PAIR_WT_REP_SIM (float, default 0.0)
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING (float, default 0.0)
+
+Like the arguments governing PCR primer selection, the input tags
+governing internal oligo selection are divided into sequence
+input tags and global input tags, with for former being
+automatically reset after each input record, and the latter
+persisting until explicitly reset.
+
+Because the laboratory detection step using internal oligos
+is independent of the PCR amplification procedure,
+internal oligo tags have defaults that are independent
+of the parameters that govern the selection of PCR primers.
+For example, the melting temperature of an oligo
+used for hybridization might be considerably lower
+than that used as a PCR primer.
+
+Internal Oligo "Sequence" Input Tags
+------------------------------------
+
+PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION (interval list, default empty)
+
+Middle oligos may not overlap any region specified by this tag.
+The associated value must be a space-separated list of
+
+<start>,<length>
+
+pairs, where <start> is the index of the first base of
+an excluded region, and <length> is its length.  Often one would
+make Target regions excluded regions for internal oligos.
+
+PRIMER_INTERNAL_OLIGO_INPUT (nucleotide sequence, default empty)
+
+The sequence of an internal oligo to check and around which to
+design left and right primers.  Must be a substring of SEQUENCE.
+
+Internal Oligo "Global" Input Tags
+----------------------------------
+
+These tags are analogous to the global input tags (those
+governing primer oligos) discussed above.  The exception is
+PRIMER_INTERNAL_OLIGO_SELF_END which is meaningless when applied
+to internal oligos used for hybridization-based detection, since
+primer-dimer will not occur.  We recommend that
+PRIMER_INTERNAL_OLIGO_SELF_END be set at least as high as
+PRIMER_INTERNAL_OLIGO_SELF_ANY.
+
+PRIMER_INTERNAL_OLIGO_OPT_SIZE (int, default 20)
+PRIMER_INTERNAL_OLIGO_MIN_SIZE (int, default 18)
+PRIMER_INTERNAL_OLIGO_MAX_SIZE (int, default 27)
+PRIMER_INTERNAL_OLIGO_OPT_TM (float, default 60.0 degrees C)
+PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT (float, default 50.0%)
+PRIMER_INTERNAL_OLIGO_MIN_TM (float, default 57.0 degrees C)
+PRIMER_INTERNAL_OLIGO_MAX_TM (float, default 63.0 degrees C)
+PRIMER_INTERNAL_OLIGO_MIN_GC (float, default 20.0%)
+PRIMER_INTERNAL_OLIGO_MAX_GC (float, default 80.0%)
+PRIMER_INTERNAL_OLIGO_SALT_CONC (float, default 50.0 mM)
+PRIMER_INTERNAL_OLIGO_DNA_CONC (float, default 50.0 nM)
+PRIMER_INTERNAL_OLIGO_SELF_ANY (decimal 9999.99, default 12.00)
+PRIMER_INTERNAL_OLIGO_MAX_POLY_X (int, default 5)
+PRIMER_INTERNAL_OLIGO_SELF_END (decimal 9999.99, default 12.00)
+PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY (string, optional)
+
+Similar to PRIMER_MISPRIMING_LIBRARY, except that the event we
+seek to avoid is hybridization of the internal oligo to sequences
+in this library rather than priming from them.
+
+PRIMER_INTERNAL_OLIGO_MAX_MISHYB (decimal,9999.99, default 12.00)
+
+Similar to PRIMER_MAX_MISPRIMING except that this parameter applies
+to the similarity of candidate internal oligos to the library
+specified in PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY.
+
+PRIMER_INTERNAL_OLIGO_MAX_TEMPLATE_MISHYB (decimal,9999.99, default 12.00)
+
+Not implemented.
+
+PRIMER_INTERNAL_OLIGO_MIN_QUALITY (int, default 0)
+
+(Note that there is no PRIMER_INTERNAL_OLIGO_MIN_END_QUALITY.)
+
+PRIMER_IO_WT_TM_GT (float, default 1.0)
+PRIMER_IO_WT_TM_LT (float, default 1.0)
+PRIMER_IO_WT_GC_PERCENT_GT (float, default 1.0)
+PRIMER_IO_WT_GC_PERCENT_LT (float, default 1.0)
+PRIMER_IO_WT_SIZE_LT (float, default 1.0)
+PRIMER_IO_WT_SIZE_GT (float, default 1.0)
+PRIMER_IO_WT_COMPL_ANY (float, default 0.0)
+PRIMER_IO_WT_COMPL_END (float, default 0.0)
+PRIMER_IO_WT_NUM_NS (float, default 0.0)
+PRIMER_IO_WT_REP_SIM (float, default 0.0)
+PRIMER_IO_WT_SEQ_QUAL (float, default 0.0)
+PRIMER_IO_WT_END_QUAL (float, default 0.0)
+
+AN EXAMPLE
+----------
+One might be interested in performing PCR on an STS with a CA
+repeat in the middle of it. Primers need to be chosen based on
+the criteria of the experiment.
+
+We need to come up with a boulder-io record to send to Primer3 via
+stdin. There are lots of ways to accomplish this. We could save
+the record into a text file called 'input', and then type the
+UNIX command 'primer3 < input'. 
+
+Let's look at the input record itself:
+
+PRIMER_SEQUENCE_ID=example
+SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
+TARGET=37,21
+PRIMER_OPT_SIZE=18
+PRIMER_MIN_SIZE=15
+PRIMER_MAX_SIZE=21
+PRIMER_NUM_NS_ACCEPTED=1
+PRIMER_PRODUCT_SIZE_RANGE=75-100
+PRIMER_FILE_FLAG=1
+PRIMER_PICK_INTERNAL_OLIGO=1
+PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=37,21
+PRIMER_EXPLAIN_FLAG=1
+=
+
+A breakdown of the reasoning behind each of the TAG=VALUE pairs
+is below:
+
+PRIMER_SEQUENCE_ID=example
+
+The main intent of this tag is to provide an identifier for the
+sequence that is meaningful to the user, for example when Primer3
+processes multiple records, and by default this tag is optional.
+However, this tag is _required_ when PRIMER_FILE_FLAG is non-0
+Because it provides the names of the files that contain lists
+of oligos that Primer3 considered.
+
+SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
+
+The SEQUENCE tag is of ultimate importance. Without it, Primer3
+has no idea what to do. This sequence is 92 bases long. Note that
+there is no newline until the sequence terminates completely.
+
+TARGET=37,21
+
+There is a simple sequence repeat in our sequence, which starts
+at base 37, and has a length of 21 bases. We want Primer3 to
+choose primers which flank the repeat site, so we let Primer3 know
+that we consider this site to be important.
+
+PRIMER_OPT_SIZE=18
+
+Since our sequence length is rather small (only 92 bases
+long), we lower the PRIMER_OPT_SIZE from 20 to 18. It's
+more likely that Primer3 will succeed if it shoots for smaller
+primers with such a small sequence.
+
+PRIMER_MIN_SIZE=15
+PRIMER_MAX_SIZE=21
+
+With the lowering of optimal primer size, it's good to lower
+the minimum and maximum sizes as well.
+
+PRIMER_NUM_NS_ACCEPTED=1
+
+Again, since we've got such a small sequence with a
+non-negligible amount of unknown bases (N's) in it, let's make
+Primer3's job easier by allowing it to pick primers that have
+at most 1 unknown base.
+
+PRIMER_PRODUCT_SIZE_RANGE=75-100
+
+We reduce the product size range from the default of 100-300
+because our source sequence is only 108 base pairs long.  If we
+insisted on a product size of 100 base pairs Primer3 would have
+few possibilities to choose from.
+
+PRIMER_FILE_FLAG=1
+
+Since we've got such a small sequence, Primer might fail to
+pick primers. We want to get the list of primers it
+considered, then, so that we might manually pick primers
+ourselves if Primer fails to do so. Setting this flag to 1
+will force Primer to output the primers it considered to a
+forward_primer and a reverse_primer output file.
+
+PRIMER_PICK_INTERNAL_OLIGO=1
+
+We want to see if Primer v2.3 can pick an internal oligo for
+the sequence, so we set this flag to 1 (true).
+
+PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=37,21
+
+Normally CA-repeats make poor hybridization probes (because they
+not specific enough).  Therefor we exclude the CA repeat (which
+is the TARGET) from consideration for the middle oligo.
+
+PRIMER_EXPLAIN_FLAG=1
+
+We want to see statistics about the oligos and oligo triples
+(left primer, internal oligo, right primer) that Primer3
+examined.
+
+=
+
+The '=' character terminates the record.
+
+Tere are some boulderio tags that we never even
+specified. (INCLUDED_REGION, EXCLUDED_REGION, et al.), which is
+perfectly legal.  For the tags with default values, those
+defaults will be used in the analysis. For the tags with NO
+default values (like TARGET, for instance), the functionality
+requested by the those tags will simply be absent. It's not the
+case that we need to surround a simple sequence repeat every time
+we want to pick primers!
+
+
+OUTPUT TAGS
+-----------
+For each boulderio record passed into primer3 via stdin, exactly
+one boulderio record comes out of primer3 on stdout. These output
+records contain everything that the input record contains, plus a
+subset of the following tag/value pairs.  Unless noted by (*),
+each tag appears for each primer pair returned.  The first
+version is PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO,PAIR}_<tag_name>.
+Tags of additional primers chosen are of the form
+PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO,PAIR}_<j>_<tag_name>.  where
+<j> is an integer from 1 to n, where n is at most the value of
+PRIMER_NUM_RETURN.
+
+In the descriptions below, 'i,n' represents a start/length pair,
+'s' represents a string, x represents an arbitrary integer, and f
+represents a float.
+
+PRIMER_ERROR=s (*)
+
+s describes user-correctible errors detected in the input
+(separated by semicolons).  This tag is absent if there are no
+errors.
+
+PRIMER_LEFT=i,n
+(FORWARD_PRIMER if -v2_compat is set)
+
+The selected left primer (the primer to the left in the input
+sequence).  i is the 0-based index of the start base of the
+primer, and n is t its length.
+
+PRIMER_RIGHT=i,n
+(REVERSE_PRIMER if -v2_compat is set)
+
+The selected right primer (the primer to the right in the input
+sequence).  i is the 0-based index of the last base of the
+primer, and n is its length.
+
+PRIMER_INTERNAL_OLIGO=i,n
+(MIDDLE_OLIGO if -v2_compat is set)
+
+The selected internal oligo. Primer3 outputs this tag if
+PRIMER_PICK_INTERNAL_OLIGO was non-0.  If primer3 fails to pick a
+middle oligo upon request, this tag will not be output.  i is the
+0-based index of start base of the internal oligo, and n is its
+length.
+
+PRIMER_PRODUCT_SIZE=x
+(PRODUCT_SIZE if -v2_compat is set)
+
+x is the product size of the PCR product.
+
+PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_EXPLAIN=s (*)
+
+s is a (more or less) self-documenting string containing
+statistics on the possiblities that primer3 considered in
+selecting a single oligo.  For example
+
+PRIMER_LEFT_EXPLAIN=considered 62, too many Ns 53, ok 9
+PRIMER_RIGHT_EXPLAIN=considered 62, too many Ns 53, ok 9
+PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 87, too many Ns 39, overlap excluded region 40, ok 8
+
+All the categories are exclusive, except the 'considered' category.
+
+PRIMER_PAIR_EXPLAIN=s (*)
+
+s is a self-documenting string containing statistics on picking a
+primer pair (plus internal oligo if requested).  For exaple
+
+PRIMER_PAIR_EXPLAIN=considered 81, unacceptable product size 49, no internal oligo 32, ok 0
+
+All the categories are exclusive, except the 'considered' category.
+
+In some cases Primer3 will examine a primer pair before it
+discovers that one of the primers in the pair violates specified
+constraints.  In this case PRIMER_PAIR_EXPLAIN might have a non-0
+number 'considered', even though one or more of
+PRIMER_LEFT_EXPLAIN, PRIMER_RIGHT_EXPLAIN, or
+PRIMER_INTERNAL_OLIGO_EXPLAIN has 'ok 0'.
+
+PRIMER_PAIR_PENALTY=f
+
+The value of the objective function for this pair (lower is better).
+
+PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_PENALTY=f
+
+The contribution of this individual primer or oligo to the
+objective function.
+
+PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_SEQUENCE=s
+
+The actual sequence of the oligo. The sequence of left primer and
+internal oligo is presented 5' -> 3' on the same strand as the
+input SEQUENCE (which must be presented 5' -> 3').  The sequence
+of the right primer is presented 5' -> 3' on the opposite strand
+from the input SEQUENCE.
+
+PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_TM=f
+
+The melting TM for the selected oligo.
+
+PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_GC_PERCENT=f
+
+The percent GC for the selected oligo (denominator is the number
+of non-ambiguous bases).
+
+PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_SELF_ANY=f
+PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_SELF_END=f
+
+The self-complementarity measures for the selected oligo.
+
+PRIMER_PAIR_COMPL_ANY=f
+PRIMER_PAIR_COMPL_END=f
+
+The inter-pair complementarity measures for the selected left and
+right primer
+
+PRIMER_WARNING=s (*)
+
+s lists warnings generated by primer (separated by semicolons);
+this tag is absent if there are no warnings
+
+PRIMER_{LEFT,RIGHT,PAIR}_MISPRIMING_SCORE=f, s
+
+f is the maximum mispriming score for the right primer
+against any sequence in the given PRIMER_MISPRIMING_LIBRARY;
+s is the id of corresponding library sequence.
+PRIMER_PAIR_MISPRIMING_SCORE is the maximum sum of
+mispriming scores in any single library sequence (perhaps a
+more reasonable estimator of the likelihood of mispriming).
+
+PRIMER_{LEFT,RIGHT,PAIR}_TEMPLATE_MISPRIMING=f
+
+Analogous to PRIMER_{LEFT,RIGHT,PAIR}_MISPRIMING_SCORE, except that
+these output tags apply to mispriming within the template sequence.
+This often arises, for example, in genes with repeated exons. For
+backward compatibility, these tags only appear if the corresponding
+input tags have defined values.
+
+PRIMER_PRODUCT_TM=f
+
+f is the melting temperature of the product. Calculated using equation (iii)
+from Rychlik, Spencer and Rhoads, Nucleic Acids Research 18(21) pg. 6410.
+Printed only if a non-default value of PRIMER_MAX_PRODUCT_TM or
+PRIMER_MIN_PRODUCT_TM is specified.
+
+PRIMER_PRODUCT_TM_OLIGO_TM_DIFF=f
+
+f is the difference between the melting temperature of the
+product and the melting temperature of the less stable primer.
+Printed only if PRIMER_MAX_PRODUCT_TM or PRIMER_MIN_PRODUCT_TM is
+specified.
+
+PRIMER_PAIR_T_OPT_A=f
+
+f is T sub a super OPT from equation (i) in Rychlik, Spencer, and
+Rhoads, Nucleic Acids Research 18(21), page 6410.  Printed only if
+PRIMER_MAX_PRODUCT_TM or PRIMER_MIN_PRODUCT_TM is specified.
+
+PRIMER_INTERNAL_OLIGO_MISHYB_SCORE=f, s
+
+f is the maximum mishybridization score for the right primer
+against any sequence in the given
+PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY; s is the id of
+corresponding library sequence.
+
+PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_MIN_SEQ_QUALITY=i
+
+i is the minimum _sequence_ quality within the primer
+or oligo (not to be confused with the PRIMER_PAIR_QUALITY
+output tag, which is really the value of the objective
+function.)
+
+PRIMER_{LEFT,RIGHT}_END_STABILITY=f
+
+f is the delta G of disruption of the five 3' bases of the
+primer.
+
+PRIMER_STOP_CODON_POSITION=i
+
+i is the position of the first base of the stop codon,
+if Primer3 found one, or -1 if Primer3 did not.  Printed
+only if the input tag PRIMER_START_CODON_POSITION with a
+non-default value is supplied.
+
+EXAMPLE OUTPUT
+--------------
+You should run it youself.  Use the file 'example' in this
+directory as input.
+
+
+ADVICE FOR PICKING PRIMERS
+--------------------------
+We suggest referring to: Wojciech Rychlik, "Selection of Primers
+for Polymerase Chain Reaction" in BA White, Ed., "Methods in
+Molecular Biology, Vol. 15: PCR Protocols: Current Methods and
+Applications", 1993, pp 31-40, Humana Press, Totowa NJ
+
+
+Cautions
+--------
+Some of the most important issues in primer picking can be
+addressed only before using Primer3.  These are sequence quality
+(including making sure the sequence is not vector and not
+chimeric) and avoiding repetitive elements.
+
+Techniques for avoiding problems include a thorough understanding
+of possible vector contaminants and cloning artifacts coupled
+with database searches using blast, fasta, or other similarity
+searching program to screen for vector contaminants and possible
+repeats.  Repbase (J. Jurka, A.F.A. Smit, C. Pethiyagoda, and
+others, 1995-1996, ftp://ncbi.nlm.nih.gov/repository/repbase)
+is an excellent source of repeat sequences and pointers to the
+literature.  (The Repbase files need to be converted to Fasta format
+before they can be used by Primer3.) Primer3 now allows you to screen
+candidate oligos against a Mispriming Library (or a Mishyb Library in
+the case of internal oligos).
+
+
+Sequence quality can be controlled by manual trace viewing and
+quality clipping or automatic quality clipping programs.  Low-
+quality bases should be changed to N's or can be made part of
+Excluded Regions. The beginning of a sequencing read is often
+problematic because of primer peaks, and the end of the read
+often contains many low-quality or even meaningless called bases.
+Therefore when picking primers from single-pass sequence it is
+often best to use the INCLUDED_REGION parameter to ensure that
+Primer3 chooses primers in the high quality region of the read.
+
+In addition, Primer3 takes as input a Sequence Quality list for
+use with those base calling programs 
+
+(e.g. Phred, Bass/Grace, Trout) that output this information.
+
+
+
+
+
+What to do if Primer3 cannot find a primers?
+--------------------------------------------
+Try relaxing various parameters, including the
+self-complementarity parameters and max and min oligo melting
+temperatures.  For example, for very A-T-rich regions you might
+have to increase maximum primer size or decrease minimum melting
+temperature.  It is usually unwise to reduce the minimum primer
+size if your template is complex (e.g. a mammalian genome), since
+small primers are more likely to be non-specific.  Make sure that
+there are adequate stretches of non-Ns in the regions in which
+you wish to pick primers.  If necessary you can also allow an N
+in your primer and use an oligo mixture containing all four bases
+at that position.
+
+Try setting the PRIMER_EXPLAIN_FLAG input tag.
+
+DIFFERENCES FROM EARLIER VERSIONS
+---------------------------------
+
+See the file release_notes.txt in this directory.
+
+Compared to 0.5
+---------------
+Completely different input format.  
+
+It has been reported the 0.5 deleted Ns when they occurred in
+primers.  
+
+More stringent self-complementarity defaults.
+
+Primer3 selects internal oligos on request (and produces .int
+files if requested).
+
+Compared to both 0.5 and v2
+---------------------------
+The format of the contents of .for, .rev (and .int) files is
+different.
+
+Primer3 returns a user-specifiable number of primer pairs (or
+triples) sorted by "goodness".
+
+Primer3 will find a primer pair if any acceptable pair exists.
+
+Optional n-based indexing into source sequence.
+
+Use of sequence quality and 3' stability as constraints in primer
+picking.  Optional positional component to objective function.
+
+Compared to v2
+-------------
+Tag name changes.  However, Primer3 should understand most or
+all Primer v2 input tags, and should produce v2-compatible output
+tag names when the -v2_compat command-line switch is used.
+
+The one exception is that the PRIMER_RECOMMEND tag is no longer
+produced. Instead Primer3 produces the PRIMER_x_EXPLAIN output
+tags.  The format of the data in this tags is different from the
+data in v2's PRIMER_RECOMMEND output tag.
+
+Numerous fixes.
+
+Uses the PRIMER_SELF_ANY and PRIMER_SELF_END parameters to govern
+maximum allowable complementarity between left and right primers,
+as well as complementarity between copies of a single oligo or
+within a single oligo.  This behaviour is very close to that of
+primer 0.5; self complementarity calculations in v2 were
+unreliable.
+
+Primer3 produces much more output information, including the TMs
+and self complementarity measures of selected primers.
+
+
+EXIT STATUS CODES
+-----------------
+
+ 0 on normal operation
+-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).
+-2 on out-of-memory
+-3 empty input
+-4 error in a "Global" input tag (message in PRIMER_ERROR).
+
+Primer3 calls abort() and dumps core (if possible) if a
+programming error is detected by an assertion violation.
+
+SIGINT and SIGTERM are handled essentially as empty input, except
+the signal received is returned as the exit status and printed to
+stderr.
+
+In all of the error cases above Primer3 prints a message to stderr.
+
+THE NEW PRIMER3 WWW INTERFACE
+-----------------------------
+This distribution does not contain the Primer3 WWW interface.  A
+snapshot of the interface used at Whitehead Institute may be available
+strictly 'AS-IS' and without support by e-mail request to
+primer3(at)wi.mit.edu, replacing (at) with @.
+
+The remainder of this section is out-of-date.
+
+The web interface consists of:
+
+primer3_www.cgi              (the user input screen)
+primer3_www_help.html        (user help for the input screen)
+primer3_www_results.cgi      (the results screen)
+primer3_www_results_help.cgi (user help for the results screen)
+
+To use this interface you will need perl5 and the perl5
+module CGI.pm.  Refer to your perl book to locate the perl5
+distribution.  CGI.pm was written by Lincoln D. Stein and is
+available from CPAN (www.cpan.org). You will also need to
+know enough about your operating system and web server to
+install a new CGI script, and enough about perl5 to read the
+script and figure out how it does what it does.
+
+You will have to make some modifications to primer3_www.cgi and
+to primer_www_results.cgi:
+
+1. Correct the path to perl5 on the first line of each .cgi file,
+since this path varies from system to system.
+
+2. Change the value of the $MAINTAINER variable near the top of
+both .cgi files so that they address the person maintaining your
+installation of the primer WWW interface.
+
+3. Specify available mispriming libraries.  In primer3_www.cgi
+modify the variable $SELECT_SEQ_LIBRARY as necessary and in
+primer3_www_results modify the value of %SEQ_LIBRARY in a
+corresponding way.
+
+4. Depending on your primer picking application you might want to
+change defaults; many of these are set in primer3_www.cgi, but
+there are some subtleties dealing with the interpretation of
+empty input fields.  You have to read the code to really
+understand what is going on.
+
+5. If primer3_www_help.html is not in the same directory as
+primer3_www.cgi fix $DOC_URL in primer3_www.cgi.
+
+6. If primer3_www_results.cgi is not in the same directory as
+primer3_www.cgi fix $PROCESS_INPUT_URL in primer3_www.cgi.
+
+7. If primer3_core is not in same directory as
+primer3_www_results.cgi, fix $PRIMER_BIN in
+primer3_www_results.cgi.
+ 
+8. If primer3_www_results_help.html is not in the same directory
+as primer3_www_results.cgi fix $DOC_URL in
+primer3_www_results.cgi.
+
+
+ACKNOWLEDGMENTS
+---------------
+
+The development of Primer3 was funded by Howard Hughes Medical
+Institute and by the National Institutes of Health, National
+Human Genome Research Institute under grants R01-HG00257 (to
+David C. Page) and P50-HG00098 (to Eric S. Lander).
+
+We gratefully acknowledge the support of Digital Equipment
+Corporation, which provided the Alphas which were used for most
+of the development of Primer3, and of Centerline Software, Inc.,
+whose TestCenter memory-error, -leak, and test-coverage checker
+helped us discover and correct a number of otherwise latent
+errors in Primer3.
+
+Primer3 was written by Helen J. Skaletsky (Howard Hughes Medical
+Institute, Whitehead Institute) and Steve Rozen (Whitehead
+Institute/MIT Center for Genome Research), based on the design of
+earlier versions: Primer 0.5 (Steve Lincoln, Mark Daly, and Eric
+S. Lander) and Primer v2 (Richard Resnick).  This documentation
+was written by Richard Resnick and Steve Rozen.  The original web
+interface was designed by Richard Resnick.  Lincoln Stein 
+championed the use of the Boulder-IO format and the idea of
+making Primer3 a software component.
+
+In addition, following is a partial list of people who kindly
+contributed to the design of Primer3
+
+Ernst Molitor
+Carl Foeller
+
+The authors of the current version would be pleased to receive
+error reports or requests for enhancements.  Please send e-mail
+to primer3(at)wi.mit.edu after replacing (at) with @.

Added: trunk/packages/primer3/branches/upstream/current/how-to-cite.txt
===================================================================
--- trunk/packages/primer3/branches/upstream/current/how-to-cite.txt	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/how-to-cite.txt	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1,12 @@
+We request but do not require that use of this software be cited in
+publications as
+
+Steve Rozen and Helen J. Skaletsky (2000)
+Primer3 on the WWW for general users and for biologist programmers.
+In: Krawetz S, Misener S (eds)
+Bioinformatics Methods and Protocols: Methods in Molecular Biology.
+Humana Press, Totowa, NJ, pp 365-386
+
+Source code available at http://fokker.wi.mit.edu/primer3/.
+The paper above is available at
+http://jura.wi.mit.edu/rozen/papers/rozen-and-skaletsky-2000-primer3.pdf

Modified: trunk/packages/primer3/branches/upstream/current/src/Makefile
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/Makefile	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/Makefile	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,47 +1,44 @@
-#  Copyright (c) 1996,1997,1998,1999,2000,2001,2004
-#         Whitehead Institute for Biomedical Research. All rights reserved.
+# ======================================================================
+# (c) Copyright 1996,1997,1998,1999,2000,2001,2004,2006 Whitehead
+# Institute for Biomedical Research, Steve Rozen, and Helen Skaletsky
+# All rights reserved.
 # 
 # Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
+# modification, are permitted provided that the following conditions are
+# met:
 # 
-# 1.      Redistributions must reproduce the above copyright notice, this
-# list of conditions and the following disclaimer in the  documentation
-# and/or other materials provided with the distribution.  Redistributions of
-# source code must also reproduce this information in the source code itself.
+#    * Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#    * Redistributions in binary form must reproduce the above
+# copyright notice, this list of conditions and the following disclaimer
+# in the documentation and/or other materials provided with the
+# distribution.
+#    * Neither the names of the copyright holders nor contributors may
+# be used to endorse or promote products derived from this software
+# without specific prior written permission.
 # 
-# 2.      If the program is modified, redistributions must include a notice
-# (in the same places as above) indicating that the redistributed program is
-# not identical to the version distributed by Whitehead Institute.
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# ======================================================================
+
+# ======================================================================
+# CITING PRIMER3
 # 
-# 3.      All advertising materials mentioning features or use of this
-# software  must display the following acknowledgment:
-#         This product includes software developed by the
-#         Whitehead Institute for Biomedical Research.
-# 
-# 4.      The name of the Whitehead Institute may not be used to endorse or
-# promote products derived from this software  without specific prior written
-# permission.
-# 
-# We also request that use of this software be cited in publications as 
-# 
-#   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. Code available at
-#   http://www-genome.wi.mit.edu/genome_software/other/primer3.html
-# 
-# THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS'' AND  ANY
-# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE  IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE  ARE
-# DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE  FOR ANY
-# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL  DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS  OR
-# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)  HOWEVER
-# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-# OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
-# SUCH DAMAGE.
+# Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for
+# general users and for biologist programmers. In: Krawetz S, Misener S
+# (eds) Bioinformatics Methods and Protocols: Methods in Molecular
+# Biology. Humana Press, Totowa, NJ, pp 365-386.  Source code available
+# at http://fokker.wi.mit.edu/primer3/.
+# ======================================================================
 
 MAX_PRIMER_LENGTH = 36
 
@@ -54,7 +51,13 @@
 
 CFLAGS  = $(CC_OPTS) $(O_OPTS)
 LDFLAGS = -g
+
+# ======================================================================
+# IMPORTANT: on MacOS X and some other Unix/Linux systems where
+# static libraries are not routinely available, -static has to
+# be removed.
 LIBOPTS ='-static'
+
 PRIMER_EXE = primer3_core
 
 PRIMER_OBJECTS=primer3_main.o\
@@ -66,7 +69,7 @@
 
 EXES=$(PRIMER_EXE) ntdpal oligotm long_seq_tm_test
 
-all: $(PRIMER_EXE)
+all: $(EXES)
 
 clean:
 	-rm *.o $(EXES) *~
@@ -82,8 +85,8 @@
 ntdpal: ntdpal_main.o dpal.o
 	$(CC) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
 
-oligotm: oligotm_main.o oligotm.o
-	$(CC) $(CFLAGS) -o $@ oligotm_main.o oligotm.o $(LIBOPTS) $(LDLIBS)
+oligotm: oligotm_main.c oligotm.o
+	$(CC) $(CFLAGS) -o $@ oligotm_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
 
 long_seq_tm_test: long_seq_tm_test_main.c oligotm.o
 	$(CC) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
@@ -105,11 +108,11 @@
 # We use CC_OPTS above rather than CFLAGS because
 # gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2
 
+oligotm_main.o: oligotm_main.c oligotm.h
+	$(CC) -c $(CFLAGS) -o $@ ntdpal_main.c
 
 oligotm.o: oligotm.c oligotm.h primer3_release.h
 
-oligotm_main.o: oligotm_main.c oligotm.h
-
 primer3.o: primer3.c primer3.h primer3_release.h
 	$(CC) -c $(CFLAGS) $(P_DEFINES) primer3.c
 

Modified: trunk/packages/primer3/branches/upstream/current/src/boulder_input.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/boulder_input.c	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/boulder_input.c	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,9 +1,36 @@
 /*
- * Copyright (c) 1996, Whitehead Institute for Biomedical Research. All rights
- * reserved.  Please see full software use agreement in primer3_main.c or by
- * executing primer3 with -h.
- */
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
 
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
 #include <limits.h>
 #include <stdlib.h>  /* strtod, strtol,... */
 #include <ctype.h> /* toupper */
@@ -921,16 +948,16 @@
 	case 'T' : s[i-j] = 'T'; break;
 	case 'N' : s[i-j] = 'N'; break;
 
-        case 'b': case 'B': 
-        case 'd': case 'D':
-        case 'h': case 'H':
-        case 'v': case 'V':
-        case 'r': case 'R':
-        case 'y': case 'Y':
-        case 'k': case 'K':
-        case 'm': case 'M':
-	case 's': case 'S':
-	case 'w': case 'W':
+        case 'b' : case 'B': 
+        case 'd' : case 'D':
+        case 'h' : case 'H':
+        case 'v' : case 'V':
+        case 'r' : case 'R':
+        case 'y' : case 'Y':
+        case 'k' : case 'K':
+        case 'm' : case 'M':
+	case 's' : case 'S':
+	case 'w' : case 'W':
 	  s[i-j] = toupper(s[i]); break;
 
 	case '\n': j++;          break;

Modified: trunk/packages/primer3/branches/upstream/current/src/boulder_input.h
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/boulder_input.h	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/boulder_input.h	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,3 +1,36 @@
+/*
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
 #ifndef BOULDER_INPUT_H
 #define BOULDER_INPUT_H 1
 #include "primer3.h"

Modified: trunk/packages/primer3/branches/upstream/current/src/dpal.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/dpal.c	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/dpal.c	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,9 +1,36 @@
 /*
- * Copyright (c) 1996, 2000, Whitehead Institute for
- * Biomedical Research. All rights reserved.  Please see
- * full software use agreement in primer3_main.c or by
- * executing primer3 with -h.  */
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
 
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
 #include <limits.h>
 #include <stdio.h>
 #include <stdlib.h>

Modified: trunk/packages/primer3/branches/upstream/current/src/dpal.h
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/dpal.h	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/dpal.h	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,3 +1,36 @@
+/*
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
 #ifndef _DPAL_H
 #define _DPAL_H
 #include <limits.h>

Modified: trunk/packages/primer3/branches/upstream/current/src/format_output.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/format_output.c	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/format_output.c	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,9 +1,36 @@
 /*
- * Copyright (c) 1997 Whitehead Institute for Biomedical Research. All rights
- * reserved.  Please see full software use agreement in primer3_main.c or by
- * executing primer3 with -h.
- */
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
 
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
 #include <stdio.h>
 #include <string.h>
 #include "format_output.h"

Modified: trunk/packages/primer3/branches/upstream/current/src/format_output.h
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/format_output.h	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/format_output.h	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,3 +1,36 @@
+/*
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
 #ifndef PR_FORMAT_OUTPUT_H
 #define PR_FORMAT_OUTPUT_H 1
 

Added: trunk/packages/primer3/branches/upstream/current/src/long_seq_tm_test_main.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/long_seq_tm_test_main.c	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/src/long_seq_tm_test_main.c	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1,83 @@
+/*
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/* 
+
+Test main for function long_seq_tm() in oligotm.c
+
+Usage is e.g 
+
+long_seq_tm_test AAAAGGGCCCCCCCCTTTTTTTTTTT 3 20
+
+In this example 3 is the 0-based start of the
+substring to use and 30 is the length of the
+substring to use, so Tm is calculated on
+GGGCCCCCCCCTTTTTTTTT (= 52.452902).
+
+For testing compare to independent implementation
+in ../test/long_seq_tm_test.pl.
+
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+
+double long_seq_tm(const char* s, int start, int len, double salt_conc);
+
+int
+main(argc, argv)
+  int argc;
+  const char**argv;
+{
+  const char *s;
+  double salt_conc = 50;
+  double tm;
+  int start, len;
+  char *endptr;
+
+  s = argv[1]; 
+  if (0 == s) {
+    fprintf(stderr, "\n%s: incorrect arguments.\n", argv[0]);
+    fprintf(stderr, "See file long_seq_tm_test_main.c for usage.\n\n");
+    exit(-1);
+  }
+  start = strtol(argv[2], &endptr, 10); 
+  len = strtol(argv[3], &endptr, 10);
+  printf("s=%s, start=%d, length=%d\n", s, start, len);
+  
+  tm = long_seq_tm(s, start, len, salt_conc);
+  printf("tm = %f\n", tm);
+  return 0;
+}

Modified: trunk/packages/primer3/branches/upstream/current/src/ntdpal_main.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/ntdpal_main.c	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/ntdpal_main.c	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,11 +1,36 @@
 /*
- * Copyright (c) 1996, 2002, Steve Rozen, Helen
- * Skaletsky, and Whitehead Institute for
- * Biomedical Research. All rights reserved.
- * Please see full software use agreement in
- * primer3_main.c or by executing primer3 with -h.
- */
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
 
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
 #include "dpal.h"
 #include <string.h>
 #include <stdio.h>

Modified: trunk/packages/primer3/branches/upstream/current/src/oligotm.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/oligotm.c	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/oligotm.c	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,9 +1,36 @@
 /*
- * Copyright (c) 1996,2004 Whitehead Institute for Biomedical Research. All rights
- * reserved.  Please see full software use agreement in primer3_main.c or by
- * executing primer3 with -h.
- */
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
 
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
 #include <limits.h>
 #include <math.h>
 #include <string.h>
@@ -11,9 +38,13 @@
 #include "primer3_release.h"
 
 /* 
- * Tables of nearest-neighbor thermodynamics for DNA bases.  See Breslauer,
- * Frank, Bloecker, and Markey, Proc. Natl. Acad. Sci. USA, vol 83, page 3748,
- * table 2.
+ * Tables of nearest-neighbor thermodynamics for DNA bases.
+ * See Breslauer, Frank, Blocker, and Markey, 
+ * "Predicting DNA duplex stability from the base sequence."
+ * Proc. Natl. Acad. Sci. USA, vol 83, page 3746 (1986).
+ * Article free at
+ * http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=323600&blobtype=pdf
+ * See table 2.
  */
 #define S_A_A 240
 #define S_A_C 173
@@ -169,8 +200,13 @@
 			      */
 
     /* 
-     * See Rychlik, Spencer, Roads, Nucleic Acids Research, vol 18, no 21,
-     * page 6410, eqn (ii).
+     * See Rychlik, Spencer, Rhoads,
+     * "Optimization of the annealing temperature for
+     * DNA amplification in vitro."
+     * Nucleic Acids Research, vol 18, no 21, page 6409 (1990).
+     * Article free at 
+     * http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2243783
+     * See eqn (ii).
      */
     return delta_H / (delta_S + 1.987 * log(DNA_nM/4000000000.0))
 	- 273.15 + 16.6 * log10(K_mM/1000.0);

Modified: trunk/packages/primer3/branches/upstream/current/src/oligotm.h
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/oligotm.h	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/oligotm.h	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,3 +1,36 @@
+/*
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
 #ifndef _OLIGO_TM
 #define _OLIGO_TM 1
 #define OLIGOTM_ERROR -999999.9999

Added: trunk/packages/primer3/branches/upstream/current/src/oligotm_main.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/oligotm_main.c	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/src/oligotm_main.c	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1,97 @@
+/*
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "oligotm.h"
+
+/* Print the melting tm of an oligo on stdout. */
+int
+main(argc, argv)
+    int argc;
+    const char **argv;
+{
+    double tm;
+    char *msg = "Usage: %s [-k salt-conc] [-d template-conc] oligo\n\n"
+                "where oligo is an oligonucleotide sequence of between 2 and 36 bases.\n"
+		"(Bases in oligo must be uppercase.)\n"
+                "salt-conc is mM salt (usually K) concentration; defaults to 50mM\n"
+                "template-conc is nM template concentration\n; defaults to 50nM\n"
+		"Prints oligo's melting temperature on stdout.\n";
+    char *endptr;
+    long k = 50, d = 50;
+    int i;
+
+    if (argc < 2 || argc > 6) {
+	fprintf(stderr, msg, argv[0]);
+        return -1;
+    }
+
+    for (i=1; i < argc; ++i) {
+	if (!strncmp("-k", argv[i], 2)) {
+	    k = strtol(argv[i+1], &endptr, 10);
+	    if ('\0' != *endptr) {
+		fprintf(stderr, msg, argv[0]);
+		exit(-1);
+	    }
+	    i++;
+	} else if (!strncmp("-d", argv[i], 2)) {
+	    d = strtol(argv[i+1], &endptr, 10);
+	    if ('\0' != *endptr) {
+		fprintf(stderr, msg, argv[0]);
+		exit(-1);
+	    }
+	    i++;
+	} else if (!strncmp("-", argv[i], 1)) {
+	    /* Unknown option. */
+	    fprintf(stderr, msg, argv[0]);
+	    exit(-1);
+	} else
+	    break;		/* all args processed. go on to sequences. */
+    }
+
+    tm = oligotm(argv[i], d, k);
+    if (OLIGOTM_ERROR == tm) {
+	fprintf(stderr,
+		"%s: length of %s is less than 2 or it contains an illegal character\n",
+		argv[0], argv[i]);
+        return -1;
+    }
+    fprintf(stdout, "%f\n", tm);
+    return 0;
+}
+
+
+
+

Modified: trunk/packages/primer3/branches/upstream/current/src/primer3.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/primer3.c	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/primer3.c	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,3 +1,36 @@
+/*
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
 #include <string.h>
 #include <float.h>
 #include "primer3.h"

Modified: trunk/packages/primer3/branches/upstream/current/src/primer3.h
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/primer3.h	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/primer3.h	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,3 +1,36 @@
+/*
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
 #ifndef PR_PRIMER_H
 #define PR_PRIMER_H
 
@@ -90,23 +123,32 @@
 } rep_sim;
 
 typedef struct primrec {
-  rep_sim repeat_sim; /* Name of the sequence from given file in fasta
-		       * format with maximum similarity to the oligo
-		       * and corresponding alignment score.
-		       */
+
+  rep_sim repeat_sim;
+                   /* Name of the sequence from given file in fasta
+		    * format with maximum similarity to the oligo
+		    * and corresponding alignment score.
+		    */
+
   double temp;     /* 
 		    * The oligo melting temperature calculated for the
 		    * primer.
 		    */
+
   double gc_content;
+
   double position_penalty; 
                   /*
                    * Penalty for distance from "ideal" position as specified
 	           * by inside_penalty and outside_penalty.
                    */
+
   double quality;  /* Part of objective function due to this primer. */
-  double end_stability; /* Delta G of disription of 5 3' bases. */
-  int    start;    /* The 0-based index of the leftmost base of the primer. */
+
+  double end_stability;
+                   /* Delta G of disription of 5 3' bases. */
+  int    start;    /* The 0-based index of the leftmost base of the primer
+                      WITH RESPECT TO THE seq_args FIELD trimmed_seq. */
   int    seq_quality; /* Minimum quality score of bases included. */   
   short  self_any; /* Self complementarity as local alignment * 100. */
   short  self_end; /* Self complementarity at 3' end * 100. */
@@ -373,9 +415,6 @@
 
     int    pick_anyway;    /* Pick even if input primer or oligos
                               violate constraints. */
-                                
-  /*  not used
-      int    short_match;   */ /* Length of 3' suffix for library mispriming. */
 
     int    lib_ambiguity_codes_consensus;
        /* If non-0, treat ambiguity codes in a mispriming/mishyb

Modified: trunk/packages/primer3/branches/upstream/current/src/primer3_main.c
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/primer3_main.c	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/primer3_main.c	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,9 +1,36 @@
-/* 
- * Copyright (c) 1996,1997,1998,2004 Whitehead Institute for Biomedical Research. All
- * rights reserved.  Please see full software use agreement in primer3_main.c or
- * by executing primer3 with -h.
- */
+/*
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
 
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
 #include <stdio.h>
 #include <math.h>
 #include <signal.h>
@@ -132,50 +159,36 @@
 /* Global static variables. */
 static const char * copyright[] = {
 "",
-"Copyright (c) 1996,1997,1998,1999,2000,2001,2004",
-"        Whitehead Institute for Biomedical Research. All rights reserved.",
+"Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006",
+"Whitehead Institute for Biomedical Research, Steve Rozen",
+"(http://jura.wi.mit.edu/rozen), and Helen Skaletsky",
+"All rights reserved.",
 "",
 "Redistribution and use in source and binary forms, with or without",
-"modification, are permitted provided that the following conditions are met:",
+"modification, are permitted provided that the following conditions are",
+"met:",
 "",
-"1.      Redistributions must reproduce the above copyright notice, this",
-"list of conditions and the following disclaimer in the  documentation",
-"and/or other materials provided with the distribution.  Redistributions of",
-"source code must also reproduce this information in the source code itself.",
+"   * Redistributions of source code must retain the above copyright",
+"notice, this list of conditions and the following disclaimer.",
+"   * Redistributions in binary form must reproduce the above",
+"copyright notice, this list of conditions and the following disclaimer",
+"in the documentation and/or other materials provided with the",
+"distribution.",
+"   * Neither the names of the copyright holders nor contributors may",
+"be used to endorse or promote products derived from this software",
+"without specific prior written permission.",
 "",
-"2.      If the program is modified, redistributions must include a notice",
-"(in the same places as above) indicating that the redistributed program is",
-"not identical to the version distributed by Whitehead Institute.",
-"",
-"3.      All advertising materials mentioning features or use of this",
-"software  must display the following acknowledgment:",
-"        This product includes software developed by the",
-"        Whitehead Institute for Biomedical Research.",
-"",
-"4.      The name of the Whitehead Institute may not be used to endorse or",
-"promote products derived from this software without specific prior written",
-"permission.",
-"",
-"We also request that use of this software be cited in publications as ",
-"",
-"  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.",
-"  Code available at",
-"  http://fokker.wi.mit.edu/primer3/.",
-"",
-"THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS'' AND  ANY",
-"EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE  IMPLIED",
-"WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE  ARE",
-"DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE  FOR ANY",
-"DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL  DAMAGES",
-"(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS  OR",
-"SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)  HOWEVER",
-"CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT",
-"LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY",
-"OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF",
-"SUCH DAMAGE.",
+"THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS",
+"\"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT",
+"LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR",
+"A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT",
+"OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,",
+"SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT",
+"LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,",
+"DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY",
+"THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT",
+"(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE",
+"OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.",
 NULL
 };
 
@@ -1004,18 +1017,30 @@
 	    (pa->primer_weights.compl_any || pa->primer_weights.compl_end))
 	|| (OT_INTL == l 
 	    && (pa->io_weights.compl_any || pa->io_weights.compl_end))) {
+
       oligo_compl(h, pa, sa, l, local_args, end_args, local_end_args);
-      if (h->ok != OV_UNINITIALIZED && !must_use) return;
-    } else h->self_any = h->self_end  = ALIGN_SCORE_UNDEF;
 
+      if (h->ok != OV_UNINITIALIZED && !must_use) {
+	PR_ASSERT(h->ok != OV_OK);
+	return; 
+      }
+
+    } else
+      h->self_any = h->self_end  = ALIGN_SCORE_UNDEF;
+
     if (must_use
 	|| pa->file_flag
 	||(pa->primer_task != pick_pcr_primers && 
 	   pa->primer_task != pick_pcr_primers_and_hyb_probe)
 	|| ((OT_RIGHT == l || OT_LEFT == l) && pa->primer_weights.repeat_sim)
+	|| ((OT_RIGHT == l || OT_LEFT == l) 
+	    && pa->primer_weights.template_mispriming)
 	|| (OT_INTL == l && pa->io_weights.repeat_sim)) {
+
       oligo_mispriming(h, pa, sa, l, local_end_args);
+
     }
+
     if (OV_UNINITIALIZED == h->ok) h->ok = OV_OK;
 }
 #undef OUTSIDE_START_WT
@@ -2519,7 +2544,13 @@
   char *oseq, *target, *target_r;
   double w;
   const seq_lib *lib;
-  int i, first, last, min, max, tmp;
+  int i;
+  int first, last; /* Indexes of first and last bases of the oligo in sa->trimmed_seq,
+		     that is, WITHIN THE INCLUDED REGION. */
+  int first_untrimmed, last_untrimmed;  
+                  /* Indexes of first and last bases of the oligo in sa->seq,
+		     that is, WITHIN THE TOTAL SEQUENCE INPUT. */
+  int min, max, tmp;
   int seqlen;
   int debug = 0;
   int match_length;
@@ -2536,9 +2567,11 @@
   }
 
   first =  (OT_LEFT == l || OT_INTL == l)
-    ? h->start : h->start - h->length + 1;
+    ? h->start 
+    : h->start - h->length + 1;
   last  =  (OT_LEFT == l || OT_INTL == l)
-    ? h->start + h->length - 1 : h->start;
+    ? h->start + h->length - 1
+    : h->start;
 
   /* NOT USED
   if (pa->short_match && pa->short_match < h->length) {
@@ -2552,7 +2585,7 @@
 
   _pr_substr(sa->trimmed_seq, first, h->length, s_tmp);
   _pr_substr(s_tmp, 0, match_length, s);
-  _pr_reverse_complement(s, s_tmp);
+  _pr_reverse_complement(s, s_tmp);  /* FIX ME -- is s_tmp needed? */
   _pr_substr(s_tmp, 0, match_length, s_r);
 
   /*
@@ -2600,56 +2633,60 @@
 	if (!h->must_use) return;
       }
     }
-  } 
+  }
 
   if (_pr_need_template_mispriming(pa) && (l == OT_RIGHT || l == OT_LEFT)) {
     /* Calculate maximum similarity to ectopic sites in the template. */
 
     seqlen = strlen(sa->upcased_seq);
+    first_untrimmed = sa->incl_s + first;
+    last_untrimmed = sa->incl_s + last;
 
     if (l == OT_LEFT) {
       oseq = &s[0];
       target = &sa->upcased_seq[0];
       target_r = &sa->upcased_seq_r[0];
-    } else {
-      if (debug) fprintf(stderr, "first = %d, last = %d\n", first, last);
+    } else {  /* l == OT_RIGHT */
+      if (debug) 
+	fprintf(stderr, "first_untrimmed = %d, last_untrimmed = %d\n",
+		first_untrimmed, last_untrimmed);
       oseq = &s_r[0];
       target = &sa->upcased_seq_r[0];
       target_r = &sa->upcased_seq[0];
-      /* We need to adjust first and last to that
+      /* We need to adjust first_untrimmed and last_untrimmed so that
 	 they are correct in the reverse-complemented
-	 sequence. It would be better to introduce new
-	 variables, e.g. first_templ_mis, last_templ_mis.
+	 sequence.
       */
-      tmp = (seqlen - last) - 1;
-      last  = (seqlen - first) - 1;
-      first = tmp;
+      tmp = (seqlen - last_untrimmed) - 1;
+      last_untrimmed  = (seqlen - first_untrimmed) - 1;
+      first_untrimmed = tmp;
     }
 
     /* 1. Align to the template 5' of the oligo. */
-    tmp_char = target[first];
-    target[first] = '\0';
+    tmp_char = target[first_untrimmed];
+    target[first_untrimmed] = '\0';
 
-    tmp_score = align(oseq, target, align_args); /* lib_local_end_dpal_args); */
+    tmp_score = align(oseq, target, align_args);
 
     if (debug) {
       if (l == OT_LEFT) fprintf(stderr, "\n************ OLIGO = LEFT\n");
       else fprintf(stderr,              "\n************ OLIGO = RIGHT\n");
-      fprintf(stderr, "first = %d, last = %d\n", first, last);
+      fprintf(stderr, "first_untrimmed = %d, last_untrimmed = %d\n",
+	      first_untrimmed, last_untrimmed);
 			
       fprintf(stderr, "5' of oligo: Score %d aligning %s against %s\n\n", tmp_score,
 	      oseq, target);
     }
 
-    target[first] = tmp_char;
+    target[first_untrimmed] = tmp_char;
 
     /* 2. Align to the template 3' of the oligo. */
     h->template_mispriming
-      = align(oseq, &target[0] + last, align_args); /* lib_local_end_dpal_args); */
+      = align(oseq, &target[0] + last_untrimmed + 1, align_args);
 
     if (debug)
       fprintf(stderr, "3' of oligo Score %d aligning %s against %s\n\n",
-	      h->template_mispriming, oseq, &target[0] + last);
+	      h->template_mispriming, oseq, &target[0] + last_untrimmed + 1);
 
     /* 3. Take the max of 1. and 2. */
     if (tmp_score > h->template_mispriming)
@@ -2677,7 +2714,6 @@
       if (!h->must_use) return;
     }
   }
-
 }
 
 static int

Modified: trunk/packages/primer3/branches/upstream/current/src/primer3_release.h
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/primer3_release.h	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/primer3_release.h	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,4 +1,38 @@
+/*
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
 #ifndef RELEASE_H
 #define RELEASE_H 1
-static const char * pr_release = "primer3 release 1.0";
+static const char * pr_release = "primer3 release 1.0b";
+/* This is a beta release. */
 #endif

Deleted: trunk/packages/primer3/branches/upstream/current/src/release_notes
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/release_notes	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/src/release_notes	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,186 +0,0 @@
-release 1.0 6/04
-
-  Added ability to search source sequence (template) for
-  mispriming or mishybing sites.
-
-  Added _experimental_ facility to calculate Tm on long
-  oligos using a GC% based formula.  This can only be
-  modified at compile time, by altering the #defines
-  for MAX_PRIMER_LENGTH (defined in Makefile), and
-  MAX_NN_TM_LENGTH (defined in primer3_main.c).  Use at your
-  own risk.
-
-  Avoided closing NULL file handles when a mispriming or mishyb
-  library is missing
-
-  Correction to long_seq_tm() in oligotm.c plus addition of
-  related tests.  (The error only arose in the calculation
-  of the Tm of the PCR product.)
-
-  Gave user the ability to _not_ treat IUB/IUPAC ambiguity
-  codes as a consensus while matching against mispriming
-  or mishyb libraries.  Inability to turn off this "feature"
-  caused severe problems when libraries contained strings
-  of N's:  NNNNNNNNN, since if N is treated as a consensus,
-  any base matches.
-
-
-PREVIOUS RELEASES:
-
-release 0.2:
-  Made 0-length excluded region legal, and adjusted tests.
-  Tweaked error reporting of negative-length excluded regions,
-  internal oligo excluded regions, and target.
-
-release 0.2a:
-  Tweaks to formated output to make it more complete
-  (included complementarity measures);  adjusted tests.
-
-release 0.2b (10/11/96)
-  Added PRIMER_WARNING tag.
-
-  Made it legal for excluded regions and targets to lie outside
-  of included region.  Documentation fixes (especially to
-  PRIMER_DNA_CONC).
-
-release 0.3
-
-  Changes to dpal to make it substantially faster on the maxgap=1
-  case for local and end-anchored complementarity measures.
-
-  Removed restriction on maximum sequence length (by removing
-  ftar, fexcl, fexcl_int, fnn, fn, fgc arrays, which necessitated
-  internal changes to methods for calculating overlap with
-  excluded regions and targets and to calculate spanning of
-  targets.
-
-  Modified 'primer list' format (clean up and hopefully got rid
-  of spurious regression test discrepancy on some systems due to
-  differences in rounding).
-
-  Exit codes for some errors changed.
-
-  Text of error messages for PRIMER_PRODUCT_SIZE -> PRIMER_PRODUCT_SIZE_RANGE.
-
-  Some errors that should have been global (fatal) were not.
-  These were fixed and error handling rationalized somewhat.
-  
-  An error in the display of the start position of targets, and
-  excluded regions in formated output was corrected.
-
-  An error in which overlapping product size ranges caused
-  primer3 to return duplicate primer pairs was corrected.
-
-  Made regression tests more complete.
-  
-  Made the maximum number of primer pairs to return a 
-  parameter (PRIMER_NUM_RETURN).
-
-  Added optional n-based indexing in input and output
-  (PRIMER_FIRST_BASE_INDEX=n).  Has not been tested
-  for n < 0.
-
-release 0.4
-
-  Added optional check of oligos against "mispriming" or
-  "mishyb" libraries  with related changes to formated output
-  and to the contents of primer list files.
-
-  Modified search algorithm to compute complementarity/
-  similarity measures as late as possible.
-
-  Got rid of quotes (") around error and warning strings.
-
-  Fixed numerical overflow on input sequences longer than
-  MAX_SHRT.  (Thanks to Pete Young for finding this one.)
-
-release 0.4b
-
-  Corrected bug in parsing of INCLUDED_REGION tag.
-
-release 0.5
-
-  ** Non-Backward compatible change:
-  Fixed inconsistency in output format;
-  PRIMER_INTERNAL_n_OLIGO_SEQUENCE
-  -> PRIMER_INTERNAL_OLIGO_n_SEQUENCE.
-  The old format can be preserved by
-  compiling with the precompiler
-  symbol USE_OLD_FORMAT_MISTAKE defined.
-
-  Added end-anchored local alignment option to dpal.
-
-  Removed some un-needed dpal implementations.
-
-  Added end-anchored local alignments for checking
-  mispriming libraries.
-
-  Added mispriming estimates for primer _pairs_
-  (see PRIMER_PAIR_MISPRIMING_LIBRARY),
-  with related new output tags.  Trivial change
-  in maximum allowable library sequence weight.
-
-  Added an experimental primer position component to
-  the objective function (PRIMER_{IN,OUT}SIDE_PENALTY),
-  with related new output tags.
-
-  Added sequence quality scores as constraints
-  in primer picking (PRIMER_MIN_{,END_}_QUALITY,
-  PRIMER_QUALITY_RANGE_{MIN,MAX}) with related
-  new output tags.
-
-  Added more error reporting to primer3.cgi when primer3
-  exits with a non-0 termination status.
-
-  Fixed bug when non-0, non-1 value was supplied
-  for pick internal oligos.
-
-  Added PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_INPUT
-  for checking or for designing around existing primers or
-  internal oligos.
-
-  Added error checking for duplicates of certain
-  tags, such as SEQUENCE.
-
-  Added PRIMER_MAX_END_STABILITY and related changes
-  to output.
-
-release 0.6
-
-  Bug fixes (most introduced as part of 0.5 enhancements).
-
-release 0.7  5/98
-
-  Fixed the 'case problem' for
-  PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_INPUT (and at the
-  same time a related bug).
-
-  Added experimental PRIMER_START_CODON_POSITION tag
-  and related outputs.  This feature should still be
-  considered experimental and the user should scrutinize
-  the output.
-
-  Added PRIMER_PRODUCT_{MAX,MIN}_TM and related outputs.
-
-release 0.8  6/98
-
-  Added flexible objective function.  Various tags governing
-  the penalty weights are not fully documented in this
-  release.
-  
-  Added much changed web interface.
-
-  Added ability to select only a single
-  left or right primer or hyb probe.
-
-  Made it possible to continue even if 
-  PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_INPUT is
-  not legal.
-
-  Added PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_GC_PERCENT
-  output tags.
-
-release 0.9  9/98
-
-  Corrected errors in calculation of amplicon Tm.
-

Added: trunk/packages/primer3/branches/upstream/current/src/release_notes.txt
===================================================================
--- trunk/packages/primer3/branches/upstream/current/src/release_notes.txt	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/src/release_notes.txt	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1,197 @@
+release 1.0a  9/06 ==================================================
+
+  No new functionality (bug fixes and minor code cleanup only)
+
+  Bug fixes:
+
+    * Corrected calculation of ..._TEMPLATE_MISPRIMING when
+      INCLUDED_REGION was set (thanks to Tomoaki Nishiyama, Advanced
+      Sciences Research Center, Kanazawa University, Japan).
+
+    * Corrected error that caused crash when
+      PRIMER_WT_TEMPLATE_MISPRIMING was set (thanks to Peng Yu,
+      Functional Genomics Group II, Chinese National Human Genome
+      Center, Beijing).
+
+    * Added olgiotm_main.c (for executable oligotm)
+
+release 1.0   6/04 ==================================================
+
+  Added ability to search source sequence (template) for
+  mispriming or mishybing sites.
+
+  Added _experimental_ facility to calculate Tm on long
+  oligos using a GC% based formula.
+
+  Miscellaneous fixes and cleanup, including:
+
+    * Avoiding closing NULL file handles when a mispriming or mishyb
+      library is missing
+
+    * Correction to long_seq_tm() in oligotm.c plus addition of
+      related tests.
+
+    * Gave user the ability to _not_ treat IUB/IUPAC ambiguity
+      codes as a consensus while matching against mispriming
+      or mishyb libraries.  Inability to turn off this "feature"
+      caused severe problems when libraries contained strings
+      of N's:  NNNNNNNNN, since if N is treated as a consensus,
+      any base matches.
+
+release 0.9  9/98 ==================================================
+
+  Corrected errors in calculation of amplicon Tm.
+
+release 0.8  6/98 ==================================================
+
+  Added flexible objective function.  Various tags governing
+  the penalty weights are not fully documented in this
+  release.
+  
+  Added much changed web interface.
+
+  Added ability to select only a single
+  left or right primer or hyb probe.
+
+  Made it possible to continue even if 
+  PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_INPUT is
+  not legal.
+
+  Added PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_GC_PERCENT
+  output tags.
+
+release 0.7  5/98   ==================================================
+
+  Fixed the 'case problem' for
+  PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_INPUT (and at the
+  same time a related bug).
+
+  Added experimental PRIMER_START_CODON_POSITION tag
+  and related outputs.  This feature should still be
+  considered experimental and the user should scrutinize
+  the output.
+
+  Added PRIMER_PRODUCT_{MAX,MIN}_TM and related outputs.
+
+release 0.6   ==================================================
+
+  Bug fixes (most introduced as part of 0.5 enhancements).
+
+release 0.5   ==================================================
+
+  ** Non-Backward compatible change:
+  Fixed inconsistency in output format;
+  PRIMER_INTERNAL_n_OLIGO_SEQUENCE
+  -> PRIMER_INTERNAL_OLIGO_n_SEQUENCE.
+  The old format can be preserved by
+  compiling with the precompiler
+  symbol USE_OLD_FORMAT_MISTAKE defined.
+
+  Added end-anchored local alignment option to dpal.
+
+  Removed some un-needed dpal implementations.
+
+  Added end-anchored local alignments for checking
+  mispriming libraries.
+
+  Added mispriming estimates for primer _pairs_
+  (see PRIMER_PAIR_MISPRIMING_LIBRARY),
+  with related new output tags.  Trivial change
+  in maximum allowable library sequence weight.
+
+  Added an experimental primer position component to
+  the objective function (PRIMER_{IN,OUT}SIDE_PENALTY),
+  with related new output tags.
+
+  Added sequence quality scores as constraints
+  in primer picking (PRIMER_MIN_{,END_}_QUALITY,
+  PRIMER_QUALITY_RANGE_{MIN,MAX}) with related
+  new output tags.
+
+  Added more error reporting to primer3.cgi when primer3
+  exits with a non-0 termination status.
+
+  Fixed bug when non-0, non-1 value was supplied
+  for pick internal oligos.
+
+  Added PRIMER_{LEFT,RIGHT,INTERNAL_OLIGO}_INPUT
+  for checking or for designing around existing primers or
+  internal oligos.
+
+  Added error checking for duplicates of certain
+  tags, such as SEQUENCE.
+
+  Added PRIMER_MAX_END_STABILITY and related changes
+  to output.
+
+release 0.4b   ==================================================
+
+  Corrected bug in parsing of INCLUDED_REGION tag.
+
+release 0.4   ==================================================
+
+  Added optional check of oligos against "mispriming" or
+  "mishyb" libraries  with related changes to formated output
+  and to the contents of primer list files.
+
+  Modified search algorithm to compute complementarity/
+  similarity measures as late as possible.
+
+  Got rid of quotes (") around error and warning strings.
+
+  Fixed numerical overflow on input sequences longer than
+  MAX_SHRT.  (Thanks to Pete Young for finding this one.)
+
+release 0.3   ==================================================
+
+  Changes to dpal to make it substantially faster on the maxgap=1
+  case for local and end-anchored complementarity measures.
+
+  Removed restriction on maximum sequence length (by removing
+  ftar, fexcl, fexcl_int, fnn, fn, fgc arrays, which necessitated
+  internal changes to methods for calculating overlap with
+  excluded regions and targets and to calculate spanning of
+  targets.
+
+  Modified 'primer list' format (clean up and hopefully got rid
+  of spurious regression test discrepancy on some systems due to
+  differences in rounding).
+
+  Exit codes for some errors changed.
+
+  Text of error messages for PRIMER_PRODUCT_SIZE -> PRIMER_PRODUCT_SIZE_RANGE.
+
+  Some errors that should have been global (fatal) were not.
+  These were fixed and error handling rationalized somewhat.
+  
+  An error in the display of the start position of targets, and
+  excluded regions in formated output was corrected.
+
+  An error in which overlapping product size ranges caused
+  primer3 to return duplicate primer pairs was corrected.
+
+  Made regression tests more complete.
+  
+  Made the maximum number of primer pairs to return a 
+  parameter (PRIMER_NUM_RETURN).
+
+  Added optional n-based indexing in input and output
+  (PRIMER_FIRST_BASE_INDEX=n).  Has not been tested
+  for n < 0.
+
+release 0.2b (10/11/96)  ==================================================
+  Added PRIMER_WARNING tag.
+
+  Made it legal for excluded regions and targets to lie outside
+  of included region.  Documentation fixes (especially to
+  PRIMER_DNA_CONC).
+
+release 0.2a ==================================================
+  Tweaks to formated output to make it more complete
+  (included complementarity measures);  adjusted tests.
+
+release 0.2 ==================================================
+  Made 0-length excluded region legal, and adjusted tests.
+  Tweaked error reporting of negative-length excluded regions,
+  internal oligo excluded regions, and target.
+


Property changes on: trunk/packages/primer3/branches/upstream/current/test/dpal_gen.pl
___________________________________________________________________
Name: svn:executable
   - 
   + *


Property changes on: trunk/packages/primer3/branches/upstream/current/test/dpal_test.pl
___________________________________________________________________
Name: svn:executable
   - 
   + *


Property changes on: trunk/packages/primer3/branches/upstream/current/test/long_seq_tm_test.pl
___________________________________________________________________
Name: svn:executable
   - 
   + *

Added: trunk/packages/primer3/branches/upstream/current/test/p3-tmpl-mispriming_input
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/p3-tmpl-mispriming_input	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/test/p3-tmpl-mispriming_input	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1,268 @@
+PRIMER_SEQUENCE_ID=template_mis_1
+PRIMER_NUM_RETURN=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
+=
+PRIMER_SEQUENCE_ID=template_mis_2
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTG
+=
+PRIMER_SEQUENCE_ID=template_mis_3
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCC
+=
+PRIMER_SEQUENCE_ID=template_mis_4
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCCACSCCCCCCCCCCCCCCCCA
+=
+PRIMER_SEQUENCE_ID=template_mis_5
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCCACTCCCCCCCCCCCCCCCCA
+=
+PRIMER_SEQUENCE_ID=template_mis_6
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+PRIMER_PRODUCT_SIZE_RANGE=36-300
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCACCCCCCCCACCCCCCCCCCCCCCCCCC
+=
+PRIMER_SEQUENCE_ID=template_mis_7
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+PRIMER_PRODUCT_SIZE_RANGE=36-300
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
+=
+PRIMER_SEQUENCE_ID=template_mis_8
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=11
+PRIMER_MAX_POLY_X=40
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+PRIMER_PRODUCT_SIZE_RANGE=36-300
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
+COMMENT=Should succeed
+=
+PRIMER_SEQUENCE_ID=template_mis_9
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=9
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+PRIMER_PRODUCT_SIZE_RANGE=36-300
+PRIMER_MAX_GC=100
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
+COMMENT=Should succeed
+=
+PRIMER_SEQUENCE_ID=template_mis_10
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=6.7
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+PRIMER_PRODUCT_SIZE_RANGE=36-300
+PRIMER_MAX_GC=100
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
+COMMENT=Should fail
+=
+PRIMER_SEQUENCE_ID=template_mis_11
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_TASK=pick_left_only
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
+SEQUENCE=aTTGATGGAGAATTGCGCAGAGGGGcTTGATGGAGAATTGCGCAGAGGGGc
+COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo
+=
+PRIMER_SEQUENCE_ID=template_mis_12
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_TASK=pick_left_only
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
+INCLUDED_REGION=25,26
+SEQUENCE=aTTGATGGAGAATTGCGCAGAGGGGcTTGATGGAGAATTGCGCAGAGGGGc
+COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo plus former error in ignoring included_region offset
+=
+PRIMER_SEQUENCE_ID=template_mis_13
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_TASK=pick_left_only
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
+SEQUENCE=cTTGATGGAGAATTGCGCAGAGGGGcTTGATGGAGAATTGCGCAGAGGGc
+COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo
+=
+PRIMER_SEQUENCE_ID=template_mis_14
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_TASK=pick_right_only
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_RIGHT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
+SEQUENCE=GCCCCTCTGCGCAATTCTCCATCAAGCCCCTCTGCGCAATTCTCCATCAAT
+COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo; SEQUENCE is complements of template_mis_11
+=
+PRIMER_SEQUENCE_ID=template_mis_15
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_TASK=pick_right_only
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_RIGHT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
+SEQUENCE=GCCCTCTGCGCAATTCTCCATCAAGCCCCTCTGCGCAATTCTCCATCAAG
+COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo; SEQUENCE is complements of template_mis_13
+=
+PRIMER_SEQUENCE_ID=template_mis_16
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_TASK=pick_right_only
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_RIGHT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
+INCLUDED_REGION=24,26
+SEQUENCE=GCCCTCTGCGCAATTCTCCATCAAGCCCCTCTGCGCAATTCTCCATCAAG
+COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo; SEQUENCE is complements of template_mis_13
+=

Added: trunk/packages/primer3/branches/upstream/current/test/p3-tmpl-mispriming_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/p3-tmpl-mispriming_output	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/test/p3-tmpl-mispriming_output	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1,550 @@
+PRIMER_SEQUENCE_ID=template_mis_1
+PRIMER_NUM_RETURN=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
+PRIMER_PAIR_PENALTY=0.9341
+PRIMER_LEFT_PENALTY=0.323851
+PRIMER_RIGHT_PENALTY=0.610234
+PRIMER_LEFT_SEQUENCE=Gatgcgtacgatccatgcta
+PRIMER_RIGHT_SEQUENCE=tagcggcctagtgtgtgtgt
+PRIMER_LEFT=20,20
+PRIMER_RIGHT=131,20
+PRIMER_LEFT_TM=59.676
+PRIMER_RIGHT_TM=59.390
+PRIMER_LEFT_GC_PERCENT=50.000
+PRIMER_RIGHT_GC_PERCENT=55.000
+PRIMER_LEFT_SELF_ANY=8.00
+PRIMER_RIGHT_SELF_ANY=4.00
+PRIMER_LEFT_SELF_END=2.00
+PRIMER_RIGHT_SELF_END=0.00
+PRIMER_LEFT_END_STABILITY=7.5000
+PRIMER_RIGHT_END_STABILITY=6.4000
+PRIMER_LEFT_TEMPLATE_MISPRIMING=6.0000
+PRIMER_RIGHT_TEMPLATE_MISPRIMING=6.0000
+PRIMER_PAIR_COMPL_ANY=4.00
+PRIMER_PAIR_COMPL_END=2.00
+PRIMER_PRODUCT_SIZE=112
+PRIMER_PAIR_TEMPLATE_MISPRIMING=12.00
+=
+PRIMER_SEQUENCE_ID=template_mis_2
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTG
+PRIMER_WARNING=Left primer is unacceptable: High self complementarity
+PRIMER_RIGHT_EXPLAIN=considered 1240, low tm 698, high tm 374, high any compl 13, high end compl 34, ok 121
+PRIMER_PAIR_EXPLAIN=considered 242, ok 242
+PRIMER_PAIR_PENALTY=2600.1166
+PRIMER_LEFT_PENALTY=0.102704
+PRIMER_RIGHT_PENALTY=0.013916
+PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_SEQUENCE=gatatCAGTGTGTACATGGCGG
+PRIMER_LEFT=32,23
+PRIMER_RIGHT=197,22
+PRIMER_LEFT_TM=62.054
+PRIMER_RIGHT_TM=60.278
+PRIMER_LEFT_GC_PERCENT=43.478
+PRIMER_RIGHT_GC_PERCENT=50.000
+PRIMER_LEFT_SELF_ANY=12.00
+PRIMER_RIGHT_SELF_ANY=6.00
+PRIMER_LEFT_SELF_END=3.00
+PRIMER_RIGHT_SELF_END=1.00
+PRIMER_LEFT_END_STABILITY=6.5000
+PRIMER_RIGHT_END_STABILITY=12.9000
+PRIMER_LEFT_TEMPLATE_MISPRIMING=23.0000
+PRIMER_RIGHT_TEMPLATE_MISPRIMING=17.0000
+PRIMER_PAIR_COMPL_ANY=4.00
+PRIMER_PAIR_COMPL_END=2.00
+PRIMER_PRODUCT_SIZE=166
+PRIMER_PAIR_TEMPLATE_MISPRIMING=26.00
+=
+PRIMER_SEQUENCE_ID=template_mis_3
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCC
+PRIMER_WARNING=Left primer is unacceptable: High self complementarity; Right primer is unacceptable: Unacceptable GC content/Tm too high/Long poly-X
+PRIMER_PAIR_EXPLAIN=considered 2, ok 2
+PRIMER_PAIR_PENALTY=2601.0969
+PRIMER_LEFT_PENALTY=0.102704
+PRIMER_RIGHT_PENALTY=0.994170
+PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGG
+PRIMER_LEFT=32,23
+PRIMER_RIGHT=240,18
+PRIMER_LEFT_TM=62.054
+PRIMER_RIGHT_TM=79.883
+PRIMER_LEFT_GC_PERCENT=43.478
+PRIMER_RIGHT_GC_PERCENT=100.000
+PRIMER_LEFT_SELF_ANY=12.00
+PRIMER_RIGHT_SELF_ANY=0.00
+PRIMER_LEFT_SELF_END=3.00
+PRIMER_RIGHT_SELF_END=0.00
+PRIMER_LEFT_END_STABILITY=6.5000
+PRIMER_RIGHT_END_STABILITY=12.4000
+PRIMER_LEFT_TEMPLATE_MISPRIMING=23.0000
+PRIMER_RIGHT_TEMPLATE_MISPRIMING=3.0000
+PRIMER_PAIR_COMPL_ANY=2.00
+PRIMER_PAIR_COMPL_END=0.00
+PRIMER_PRODUCT_SIZE=209
+PRIMER_PAIR_TEMPLATE_MISPRIMING=26.00
+=
+PRIMER_SEQUENCE_ID=template_mis_4
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCCACSCCCCCCCCCCCCCCCCA
+PRIMER_WARNING=Unrecognized base in input sequence; Left primer is unacceptable: High self complementarity; Right primer is unacceptable: Unacceptable GC content/Tm too high/Long poly-X
+PRIMER_PAIR_EXPLAIN=considered 2, ok 2
+PRIMER_PAIR_PENALTY=2701.0969
+PRIMER_LEFT_PENALTY=0.102704
+PRIMER_RIGHT_PENALTY=0.994170
+PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGG
+PRIMER_LEFT=23,23
+PRIMER_RIGHT=231,18
+PRIMER_LEFT_TM=62.054
+PRIMER_RIGHT_TM=79.883
+PRIMER_LEFT_GC_PERCENT=43.478
+PRIMER_RIGHT_GC_PERCENT=100.000
+PRIMER_LEFT_SELF_ANY=12.00
+PRIMER_RIGHT_SELF_ANY=0.00
+PRIMER_LEFT_SELF_END=3.00
+PRIMER_RIGHT_SELF_END=0.00
+PRIMER_LEFT_END_STABILITY=6.5000
+PRIMER_RIGHT_END_STABILITY=12.4000
+PRIMER_LEFT_TEMPLATE_MISPRIMING=23.0000
+PRIMER_RIGHT_TEMPLATE_MISPRIMING=16.0000
+PRIMER_PAIR_COMPL_ANY=2.00
+PRIMER_PAIR_COMPL_END=0.00
+PRIMER_PRODUCT_SIZE=209
+PRIMER_PAIR_TEMPLATE_MISPRIMING=27.00
+=
+PRIMER_SEQUENCE_ID=template_mis_5
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCCACTCCCCCCCCCCCCCCCCA
+PRIMER_WARNING=Left primer is unacceptable: High self complementarity; Right primer is unacceptable: Unacceptable GC content/Tm too high/Long poly-X
+PRIMER_PAIR_EXPLAIN=considered 2, ok 2
+PRIMER_PAIR_PENALTY=2701.0969
+PRIMER_LEFT_PENALTY=0.102704
+PRIMER_RIGHT_PENALTY=0.994170
+PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGG
+PRIMER_LEFT=23,23
+PRIMER_RIGHT=231,18
+PRIMER_LEFT_TM=62.054
+PRIMER_RIGHT_TM=79.883
+PRIMER_LEFT_GC_PERCENT=43.478
+PRIMER_RIGHT_GC_PERCENT=100.000
+PRIMER_LEFT_SELF_ANY=12.00
+PRIMER_RIGHT_SELF_ANY=0.00
+PRIMER_LEFT_SELF_END=3.00
+PRIMER_RIGHT_SELF_END=0.00
+PRIMER_LEFT_END_STABILITY=6.5000
+PRIMER_RIGHT_END_STABILITY=12.4000
+PRIMER_LEFT_TEMPLATE_MISPRIMING=23.0000
+PRIMER_RIGHT_TEMPLATE_MISPRIMING=16.0000
+PRIMER_PAIR_COMPL_ANY=2.00
+PRIMER_PAIR_COMPL_END=0.00
+PRIMER_PRODUCT_SIZE=209
+PRIMER_PAIR_TEMPLATE_MISPRIMING=27.00
+=
+PRIMER_SEQUENCE_ID=template_mis_6
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+PRIMER_PRODUCT_SIZE_RANGE=36-300
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCACCCCCCCCACCCCCCCCCCCCCCCCCC
+PRIMER_WARNING=Left primer is unacceptable: High self complementarity; Right primer is unacceptable: Unacceptable GC content/Tm too high/Long poly-X
+PRIMER_PAIR_EXPLAIN=considered 1, ok 1
+PRIMER_PAIR_PENALTY=1901.0969
+PRIMER_LEFT_PENALTY=0.102704
+PRIMER_RIGHT_PENALTY=0.994170
+PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGG
+PRIMER_LEFT=0,23
+PRIMER_RIGHT=67,18
+PRIMER_LEFT_TM=62.054
+PRIMER_RIGHT_TM=79.883
+PRIMER_LEFT_GC_PERCENT=43.478
+PRIMER_RIGHT_GC_PERCENT=100.000
+PRIMER_LEFT_SELF_ANY=12.00
+PRIMER_RIGHT_SELF_ANY=0.00
+PRIMER_LEFT_SELF_END=3.00
+PRIMER_RIGHT_SELF_END=0.00
+PRIMER_LEFT_END_STABILITY=6.5000
+PRIMER_RIGHT_END_STABILITY=12.4000
+PRIMER_LEFT_TEMPLATE_MISPRIMING=3.0000
+PRIMER_RIGHT_TEMPLATE_MISPRIMING=16.0000
+PRIMER_PAIR_COMPL_ANY=2.00
+PRIMER_PAIR_COMPL_END=0.00
+PRIMER_PRODUCT_SIZE=68
+PRIMER_PAIR_TEMPLATE_MISPRIMING=19.00
+=
+PRIMER_SEQUENCE_ID=template_mis_7
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+PRIMER_PRODUCT_SIZE_RANGE=36-300
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
+PRIMER_WARNING=Left primer is unacceptable: High self complementarity; Right primer is unacceptable: Unacceptable GC content/Tm too high/Long poly-X
+PRIMER_PAIR_EXPLAIN=considered 1, ok 1
+PRIMER_PAIR_PENALTY=1276.0969
+PRIMER_LEFT_PENALTY=0.102704
+PRIMER_RIGHT_PENALTY=0.994170
+PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATGat
+PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGG
+PRIMER_LEFT=0,23
+PRIMER_RIGHT=67,18
+PRIMER_LEFT_TM=62.054
+PRIMER_RIGHT_TM=79.883
+PRIMER_LEFT_GC_PERCENT=43.478
+PRIMER_RIGHT_GC_PERCENT=100.000
+PRIMER_LEFT_SELF_ANY=12.00
+PRIMER_RIGHT_SELF_ANY=0.00
+PRIMER_LEFT_SELF_END=3.00
+PRIMER_RIGHT_SELF_END=0.00
+PRIMER_LEFT_END_STABILITY=6.5000
+PRIMER_RIGHT_END_STABILITY=12.4000
+PRIMER_LEFT_TEMPLATE_MISPRIMING=3.0000
+PRIMER_RIGHT_TEMPLATE_MISPRIMING=9.7500
+PRIMER_PAIR_COMPL_ANY=2.00
+PRIMER_PAIR_COMPL_END=0.00
+PRIMER_PRODUCT_SIZE=68
+PRIMER_PAIR_TEMPLATE_MISPRIMING=12.75
+=
+PRIMER_SEQUENCE_ID=template_mis_8
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=11
+PRIMER_MAX_POLY_X=40
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+PRIMER_PRODUCT_SIZE_RANGE=36-300
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
+COMMENT=Should succeed
+PRIMER_LEFT_EXPLAIN=considered 75, too many Ns 34, low tm 14, high any compl 7, ok 20
+PRIMER_PAIR_EXPLAIN=considered 20, high any compl 11, high end compl 5, ok 4
+PRIMER_PAIR_PENALTY=1076.0792
+PRIMER_LEFT_PENALTY=0.085063
+PRIMER_RIGHT_PENALTY=0.994170
+PRIMER_LEFT_SEQUENCE=CCCCCCCCAAAAAAAAAA
+PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGG
+PRIMER_LEFT=32,18
+PRIMER_RIGHT=67,18
+PRIMER_LEFT_TM=61.701
+PRIMER_RIGHT_TM=79.883
+PRIMER_LEFT_GC_PERCENT=44.444
+PRIMER_RIGHT_GC_PERCENT=100.000
+PRIMER_LEFT_SELF_ANY=0.00
+PRIMER_RIGHT_SELF_ANY=0.00
+PRIMER_LEFT_SELF_END=0.00
+PRIMER_RIGHT_SELF_END=0.00
+PRIMER_LEFT_END_STABILITY=7.6000
+PRIMER_RIGHT_END_STABILITY=12.4000
+PRIMER_LEFT_TEMPLATE_MISPRIMING=4.0000
+PRIMER_RIGHT_TEMPLATE_MISPRIMING=9.7500
+PRIMER_PAIR_COMPL_ANY=8.00
+PRIMER_PAIR_COMPL_END=0.00
+PRIMER_PRODUCT_SIZE=36
+PRIMER_PAIR_TEMPLATE_MISPRIMING=10.75
+=
+PRIMER_SEQUENCE_ID=template_mis_9
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=9
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+PRIMER_PRODUCT_SIZE_RANGE=36-300
+PRIMER_MAX_GC=100
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
+COMMENT=Should succeed
+PRIMER_LEFT_EXPLAIN=considered 75, too many Ns 34, low tm 14, high any compl 7, ok 20
+PRIMER_RIGHT_EXPLAIN=considered 177, too many Ns 22,high template mispriming score 5, ok 150
+PRIMER_PAIR_EXPLAIN=considered 3004, unacceptable product size 2784, high any compl 199, ok 21
+PRIMER_PAIR_PENALTY=776.1163
+PRIMER_LEFT_PENALTY=0.085063
+PRIMER_RIGHT_PENALTY=1.031264
+PRIMER_LEFT_SEQUENCE=CCCCCCCCAAAAAAAAAA
+PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGGTTTTT
+PRIMER_LEFT=32,18
+PRIMER_RIGHT=67,23
+PRIMER_LEFT_TM=61.701
+PRIMER_RIGHT_TM=80.625
+PRIMER_LEFT_GC_PERCENT=44.444
+PRIMER_RIGHT_GC_PERCENT=78.261
+PRIMER_LEFT_SELF_ANY=0.00
+PRIMER_RIGHT_SELF_ANY=0.00
+PRIMER_LEFT_SELF_END=0.00
+PRIMER_RIGHT_SELF_END=0.00
+PRIMER_LEFT_END_STABILITY=7.6000
+PRIMER_RIGHT_END_STABILITY=7.6000
+PRIMER_LEFT_TEMPLATE_MISPRIMING=4.0000
+PRIMER_RIGHT_TEMPLATE_MISPRIMING=6.7500
+PRIMER_PAIR_COMPL_ANY=8.00
+PRIMER_PAIR_COMPL_END=5.00
+PRIMER_PRODUCT_SIZE=36
+PRIMER_PAIR_TEMPLATE_MISPRIMING=7.75
+=
+PRIMER_SEQUENCE_ID=template_mis_10
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_TEMPLATE_MISPRIMING=6.7
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_LIBERAL_BASE=1
+PRIMER_PRODUCT_SIZE_RANGE=36-300
+PRIMER_MAX_GC=100
+SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
+COMMENT=Should fail
+PRIMER_LEFT_EXPLAIN=considered 75, too many Ns 34, low tm 14, high any compl 7,high template mispriming score 2, ok 18
+PRIMER_RIGHT_EXPLAIN=considered 177, too many Ns 22,high template mispriming score 19, ok 136
+PRIMER_PAIR_EXPLAIN=considered 2718, unacceptable product size 2710, high any compl 8, ok 0
+=
+PRIMER_SEQUENCE_ID=template_mis_11
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_TASK=pick_left_only
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
+SEQUENCE=aTTGATGGAGAATTGCGCAGAGGGGcTTGATGGAGAATTGCGCAGAGGGGc
+COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo
+PRIMER_LEFT_PENALTY=0.7321
+PRIMER_LEFT_SEQUENCE=cTTGATGGAGAATTGCGCAGAGGGGc
+PRIMER_LEFT=25,26
+PRIMER_LEFT_TM=74.643
+PRIMER_LEFT_GC_PERCENT=57.692
+PRIMER_LEFT_SELF_ANY=6.00
+PRIMER_LEFT_SELF_END=2.00
+PRIMER_LEFT_END_STABILITY=12.4000
+PRIMER_LEFT_TEMPLATE_MISPRIMING=20.00
+=
+PRIMER_SEQUENCE_ID=template_mis_12
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_TASK=pick_left_only
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
+INCLUDED_REGION=25,26
+SEQUENCE=aTTGATGGAGAATTGCGCAGAGGGGcTTGATGGAGAATTGCGCAGAGGGGc
+COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo plus former error in ignoring included_region offset
+PRIMER_LEFT_PENALTY=0.7321
+PRIMER_LEFT_SEQUENCE=cTTGATGGAGAATTGCGCAGAGGGGc
+PRIMER_LEFT=25,26
+PRIMER_LEFT_TM=74.643
+PRIMER_LEFT_GC_PERCENT=57.692
+PRIMER_LEFT_SELF_ANY=6.00
+PRIMER_LEFT_SELF_END=2.00
+PRIMER_LEFT_END_STABILITY=12.4000
+PRIMER_LEFT_TEMPLATE_MISPRIMING=20.00
+=
+PRIMER_SEQUENCE_ID=template_mis_13
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_TASK=pick_left_only
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_LEFT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
+SEQUENCE=cTTGATGGAGAATTGCGCAGAGGGGcTTGATGGAGAATTGCGCAGAGGGc
+COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo
+PRIMER_LEFT_PENALTY=0.7321
+PRIMER_LEFT_SEQUENCE=cTTGATGGAGAATTGCGCAGAGGGGc
+PRIMER_LEFT=0,26
+PRIMER_LEFT_TM=74.643
+PRIMER_LEFT_GC_PERCENT=57.692
+PRIMER_LEFT_SELF_ANY=6.00
+PRIMER_LEFT_SELF_END=2.00
+PRIMER_LEFT_END_STABILITY=12.4000
+PRIMER_LEFT_TEMPLATE_MISPRIMING=22.00
+=
+PRIMER_SEQUENCE_ID=template_mis_14
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_TASK=pick_right_only
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_RIGHT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
+SEQUENCE=GCCCCTCTGCGCAATTCTCCATCAAGCCCCTCTGCGCAATTCTCCATCAAT
+COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo; SEQUENCE is complements of template_mis_11
+PRIMER_RIGHT_PENALTY=0.7321
+PRIMER_RIGHT_SEQUENCE=CTTGATGGAGAATTGCGCAGAGGGGC
+PRIMER_RIGHT=25,26
+PRIMER_RIGHT_TM=74.643
+PRIMER_RIGHT_GC_PERCENT=57.692
+PRIMER_RIGHT_SELF_ANY=6.00
+PRIMER_RIGHT_SELF_END=2.00
+PRIMER_RIGHT_END_STABILITY=12.4000
+PRIMER_RIGHT_TEMPLATE_MISPRIMING=20.00
+=
+PRIMER_SEQUENCE_ID=template_mis_15
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_TASK=pick_right_only
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_RIGHT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
+SEQUENCE=GCCCTCTGCGCAATTCTCCATCAAGCCCCTCTGCGCAATTCTCCATCAAG
+COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo; SEQUENCE is complements of template_mis_13
+PRIMER_RIGHT_PENALTY=0.7321
+PRIMER_RIGHT_SEQUENCE=CTTGATGGAGAATTGCGCAGAGGGGC
+PRIMER_RIGHT=49,26
+PRIMER_RIGHT_TM=74.643
+PRIMER_RIGHT_GC_PERCENT=57.692
+PRIMER_RIGHT_SELF_ANY=6.00
+PRIMER_RIGHT_SELF_END=2.00
+PRIMER_RIGHT_END_STABILITY=12.4000
+PRIMER_RIGHT_TEMPLATE_MISPRIMING=22.00
+=
+PRIMER_SEQUENCE_ID=template_mis_16
+PRIMER_NUM_RETURN=1
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_PICK_ANYWAY=1
+PRIMER_MAX_POLY_X=40
+PRIMER_SELF_END=100
+PRIMER_WT_SIZE_GT=0
+PRIMER_WT_SIZE_LT=0
+PRIMER_WT_TM_GT=.05
+PRIMER_WT_TM_LT=.05
+PRIMER_MAX_GC=100
+PRIMER_MAX_TM=100
+PRIMER_TASK=pick_right_only
+PRIMER_MAX_TEMPLATE_MISPRIMING=100
+PRIMER_RIGHT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
+INCLUDED_REGION=24,26
+SEQUENCE=GCCCTCTGCGCAATTCTCCATCAAGCCCCTCTGCGCAATTCTCCATCAAG
+COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo; SEQUENCE is complements of template_mis_13
+PRIMER_RIGHT_PENALTY=0.7321
+PRIMER_RIGHT_SEQUENCE=CTTGATGGAGAATTGCGCAGAGGGGC
+PRIMER_RIGHT=49,26
+PRIMER_RIGHT_TM=74.643
+PRIMER_RIGHT_GC_PERCENT=57.692
+PRIMER_RIGHT_SELF_ANY=6.00
+PRIMER_RIGHT_SELF_END=2.00
+PRIMER_RIGHT_END_STABILITY=12.4000
+PRIMER_RIGHT_TEMPLATE_MISPRIMING=22.00
+=

Added: trunk/packages/primer3/branches/upstream/current/test/p3test.pl
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/p3test.pl	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/test/p3test.pl	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1,197 @@
+# Regression test driver for primer3 executable.
+#
+# Usage: perl primer_test.pl [<primer3>]
+#
+# <primer3> defaults to primer3_core, in which case the executable
+# run is ../src/primer3_core.
+#
+# If <primer3> is specified, the executable run is 
+# ../src/<primer3>.
+#
+# Stderr difference tests for fatal errors are performed only
+# if <primer3> is 'primer3_core' (because the executable name
+# is part of the text written to stderr).
+
+$ENV{TC_SILENT} = '1';	# TestCenter proofed executables will not 
+                        # write extra stuff to std{err,out}, and
+                        # consequently will not cause spurious diff's.
+
+$ENV{TC_RESULTDIR} = './tc_results'; # Directory for testcenter results.
+    
+
+$exe = 'primer3_core';
+$exe = $ARGV[0] if defined $ARGV[0];
+$p1 =  "../src/$exe";
+$EXIT_STAT = 0;
+
+die "Cannot execute $p1" unless -x $p1;
+
+print STDERR "\n\n$0: testing $p1\n\nSTART, ", scalar(localtime), "\n";
+
+test_fatal_errors($p1);
+
+my $cmd;
+for $test (
+           'primer_boundary',   # Put the quickest tests first.
+           'primer_internal',
+           'primer_boundary_formatted',
+           'primer_internal_formatted',
+	   'primer_start_codon',
+           'primer_boundary1',
+           'primer_internal1',
+	   'primer_task',
+	   'primer_task_formatted',
+           'primer_boundary1_formatted',
+           'primer_internal1_formatted',
+	   'primer_check',
+	   'primer_must_use',
+	   'primer_must_use_formatted',
+           'primer_syntax',
+           'primer_end_pathology',
+           'primer_num_best',
+	   'primer_quality_boundary',
+	   'primer_obj_fn',
+           'primer',
+           'primer1',
+           'primer_mispriming',
+           'primer_mispriming_formatted',
+           'primer_mispriming_boundary1',
+           'primer_mispriming_boundary1_formatted',
+           'primer_mispriming_boundary2',
+           'primer_mispriming_boundary2_formatted',
+           'primer_mispriming_long_lib',
+           'primer_rat',
+           'primer_human',
+           'primer_ch',
+           'long_seq',
+           'primer_position_penalty',
+           'primer_position_penalty_formatted',
+	   'p3-tmpl-mispriming',
+	   'primer_lib_amb_codes',
+	   ) {
+    print STDERR "$test...";
+    if ($test eq 'primer_lib_amb_codes') {
+	print STDERR "\nNOTE: this test takes _much_ longer than the others ";
+	print STDERR "(10 to 20 minutes or more).\n";
+	print STDERR "starting $test at ", scalar(localtime), "...";
+    }
+    $testx = $test;
+    $testx =~ s/_formatted$//;
+    $input = $testx . '_input';
+    $output = $test . '_output';
+    $tmp = $test . '_tmp';
+    if ($test ne 'primer_ch') {
+	die "Cannot read $input"  unless -r $input;
+	die "Cannot read $output"  unless -r $output;
+    }
+
+    if ($test eq 'primer' || $test eq 'primer1') {
+	$list_tmp = $test.'_list_tmp';
+	# We need to chdir below because primer3 puts the 'list' files
+        # in the current working directory.  Therefore we adjust
+	# the TestCenter result directory.
+	$cmd = "rm -f $list_tmp/*.*; "
+	    . "cd $list_tmp; ../$p1 -strict_tags <../$input >../$tmp";
+	$ENV{TC_COMMENT} = $cmd;
+	# Reset the TestCenter result directory.
+	$save_results = $ENV{TC_RESULTDIR};
+	$ENV{TC_RESULTDIR} = "../$save_results";
+	$r = system $cmd;
+	$ENV{TC_RESULTDIR} = $save_results;
+	$ENV{TC_COMMENT} = '';
+    } elsif ($test =~ /formatted$/) {
+	$cmd = "$p1 -strict_tags -format_output <$input >$tmp";
+	$ENV{TC_COMMENT} = $cmd;
+	$r = system $cmd;
+	$ENV{TC_COMMENT} = '';
+    } else {
+	# We do not distribute primer_ch_input.
+	unless ($test eq 'primer_ch' && !-e 'primer_ch_input') {
+	    $cmd = "$p1 -strict_tags <$input >$tmp";
+	    $ENV{TC_COMMENT} = $cmd;
+	    $r = system $cmd;
+	    $ENV{TC_COMMENT} = '';
+	}
+    }
+
+    unless ($r == 0) {
+	print STDERR "NON-0 EXIT: $r\n";
+	$EXIT_STAT = -1;
+	next;
+    }
+
+    $r = system "diff $output $tmp"
+	unless ($test eq 'primer_ch' && !-e 'primer_ch_input');
+
+    if ($r == 0) {
+	print STDERR "OK\n";
+    } else {
+	print STDERR "FAILED\n";
+	$EXIT_STAT = -1;
+    }
+    if ($test eq 'primer' || $test eq 'primer1') {
+	$list_tmp = $test.'_list_tmp';
+	$list_last = $test.'_list_last';
+	if  (-e "$list_tmp/.cvsignore") {
+	    $r = system "mv $list_tmp/.cvsignore ./saved.cvsignore; "
+		. "diff $list_last $list_tmp";
+	    system "mv ./saved.cvsignore $list_tmp/.cvsignore";
+	} else {
+	    $r = system "diff $list_tmp $list_last";
+	}
+	print STDERR "$test list files ";
+	if ($r == 0) {
+	    print STDERR "OK\n";
+	} else { 
+	    print STDERR "FAILED\n";
+	    $EXIT_STAT = -1;
+	}
+    }
+}
+
+unlink("./core") if -e "./core";
+print STDERR "DONE ", scalar(localtime), "\n";
+exit ($EXIT_STAT);
+
+sub test_fatal_errors {
+    my $exe = $_[0];
+    my $skip_stderr = 0;
+    if ($exe ne '../src/primer3_core') {
+	print STDERR "Skipping comparisons of stderr because ",
+	"executable is not ../src/primer3_core";
+	$skip_stderr = 1;
+    }
+    my $inputs = `ls primer_global_err/*.in`;
+    my @inputs = split /\s/, $inputs;
+    my ($root, $cmd, $r);
+    my $problem = 0;
+    print STDERR "\ntesting fatal errors...";
+    for (@inputs) {
+	($root) = /(.*)\.in$/;
+	$cmd = "$exe <$_ > $root.tmp 2> $root.tmp2";
+	$ENV{TC_COMMENT} = $cmd;
+	system $cmd;
+	$ENV{TC_COMMENT} = '';
+	if ($? == 0) {
+	    $r = $? >> 8;
+	    print STDERR "\nErroneous 0 exit status ($?) from command $cmd\n";
+	    $problem = 1;
+	}
+	$r = system "diff $root.out $root.tmp";
+	if ($r != 0) {
+	    print STDERR
+		"Difference found between $root.out and $root.tmp\n\n";
+	    $problem = 1;
+	}
+	unless ($skip_stderr) {
+	    $r = system "diff $root.out2 $root.tmp2";
+	    if ($r != 0) {
+		print STDERR
+		    "\nDifference found between $root.out2 and $root.tmp2\n\n";
+		$problem = 1;
+	    }
+	}
+    }
+    print STDERR $problem ? "FAILED" : "OK" ,"\n";
+}
+


Property changes on: trunk/packages/primer3/branches/upstream/current/test/p3test.pl
___________________________________________________________________
Name: svn:executable
   + *

Modified: trunk/packages/primer3/branches/upstream/current/test/primer_boundary1_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_boundary1_formatted_output	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_boundary1_formatted_output	2006-09-22 14:39:44 UTC (rev 122)
@@ -26,7 +26,7 @@
 Right     10     9     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_01
@@ -57,7 +57,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_02
@@ -88,7 +88,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_03
@@ -112,7 +112,7 @@
 Right      4     3     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, unacceptable product size 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_04
@@ -136,7 +136,7 @@
 Right     10     9     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, unacceptable product size 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_05
@@ -167,7 +167,7 @@
 Right      5     3     0     0     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 4, unacceptable product size 3, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_06
@@ -191,7 +191,7 @@
 Right      5     5     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_07
@@ -223,7 +223,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_08
@@ -251,7 +251,7 @@
 Right      6     5     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_09
@@ -279,7 +279,7 @@
 Right      5     5     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_10
@@ -303,7 +303,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_11
@@ -334,7 +334,7 @@
 Right      5     2     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 3, unacceptable product size 2, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_11
@@ -358,7 +358,7 @@
 Right      5     2     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_12
@@ -389,7 +389,7 @@
 Right      5     0     0     0     0     0     0     0     0     0     0     0     5
 Pair Stats:
 considered 5, unacceptable product size 4, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_13
@@ -420,7 +420,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_14
@@ -444,7 +444,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_15
@@ -475,7 +475,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_16
@@ -499,7 +499,7 @@
 Right      5     4     0     0     1     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_17
@@ -531,7 +531,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_18
@@ -559,7 +559,7 @@
 Right      1     1     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_19
@@ -591,7 +591,7 @@
 Right      1     1     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_21
@@ -624,7 +624,7 @@
 Right      3     2     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_22
@@ -653,7 +653,7 @@
 Right      3     2     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_23
@@ -682,7 +682,7 @@
 Right      2     2     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_24
@@ -711,7 +711,7 @@
 Right      2     2     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_25
@@ -744,7 +744,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_26
@@ -773,7 +773,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_27
@@ -802,7 +802,7 @@
 Right      5     4     1     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_28
@@ -831,7 +831,7 @@
 Right      5     4     1     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_29
@@ -864,7 +864,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_30
@@ -897,7 +897,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_31
@@ -926,7 +926,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, no target 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_32
@@ -959,7 +959,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_33
@@ -988,7 +988,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_34
@@ -1017,7 +1017,7 @@
 Right      5     4     0     1     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_35
@@ -1046,7 +1046,7 @@
 Right      5     4     0     1     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_36
@@ -1079,7 +1079,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_37
@@ -1108,7 +1108,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_37
@@ -1137,7 +1137,7 @@
 Right      5     4     0     1     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_38
@@ -1166,7 +1166,7 @@
 Right      5     4     0     1     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_39
@@ -1199,7 +1199,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_40
@@ -1232,7 +1232,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_41
@@ -1258,7 +1258,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_42
@@ -1291,7 +1291,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_43
@@ -1320,7 +1320,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_44
@@ -1353,7 +1353,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_45
@@ -1386,7 +1386,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_46
@@ -1415,7 +1415,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_47
@@ -1448,7 +1448,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_48
@@ -1477,7 +1477,7 @@
 Right      5     4     0     0     0     1     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_49
@@ -1510,7 +1510,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_50
@@ -1539,7 +1539,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_51
@@ -1572,7 +1572,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_52
@@ -1605,7 +1605,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_53
@@ -1634,7 +1634,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, tm diff too large 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_54
@@ -1669,7 +1669,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_55
@@ -1702,7 +1702,7 @@
 Intl       0     0     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR poly_x_2
@@ -1765,7 +1765,7 @@
 Intl    1585     0     0     0     0     0     0     0     0     0     0     0  1585
 Pair Stats:
 considered 72, unacceptable product size 52, ok 20
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR poly_x_3
@@ -1794,7 +1794,7 @@
 Intl     187     0     0     0     0     0     0     0     0     0   187     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_59
@@ -1827,7 +1827,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_60
@@ -1853,7 +1853,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_61
@@ -1893,7 +1893,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_63
@@ -1923,7 +1923,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_64
@@ -1963,7 +1963,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_66
@@ -1993,7 +1993,7 @@
 Right      1     0     0     1     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_67
@@ -2025,7 +2025,7 @@
 Right      6     5     0     1     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_68
@@ -2058,7 +2058,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_69
@@ -2084,7 +2084,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_70
@@ -2120,7 +2120,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, no target 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_72
@@ -2150,7 +2150,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_73
@@ -2186,7 +2186,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, no target 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_75
@@ -2216,7 +2216,7 @@
 Right      0     0     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_76
@@ -2248,7 +2248,7 @@
 Right      6     5     1     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_77
@@ -2282,7 +2282,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_78
@@ -2316,7 +2316,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_79
@@ -2350,7 +2350,7 @@
 Right      6     5     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_80
@@ -2384,7 +2384,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_81
@@ -2418,7 +2418,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_82
@@ -2451,7 +2451,7 @@
 Right     10     9     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_83
@@ -2480,7 +2480,7 @@
 Right     10     9     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, no target 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_84
@@ -2513,7 +2513,7 @@
 Right     10     9     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_85
@@ -2546,7 +2546,7 @@
 Right      3     2     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_86
@@ -2580,7 +2580,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_71
@@ -2616,7 +2616,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_72
@@ -2648,7 +2648,7 @@
 Right      3     2     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 3, unacceptable product size 2, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_73
@@ -2676,7 +2676,7 @@
 Right      3     2     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 2, unacceptable product size 2, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_74
@@ -2708,7 +2708,7 @@
 Right      3     2     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 2, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_75
@@ -2740,7 +2740,7 @@
 Right      2     1     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 2, unacceptable product size 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_76
@@ -2772,7 +2772,7 @@
 Right      2     1     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 2, unacceptable product size 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_77
@@ -2813,7 +2813,7 @@
 Right     28    26     0     0     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 4, unacceptable product size 2, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_78
@@ -2854,7 +2854,7 @@
 Right     28    26     0     0     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 4, unacceptable product size 2, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_79
@@ -2895,7 +2895,7 @@
 Right     28    26     0     0     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 4, unacceptable product size 1, ok 3
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_80
@@ -2936,7 +2936,7 @@
 Right     28    26     0     0     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 4, unacceptable product size 1, ok 3
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_81
@@ -2968,7 +2968,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_82
@@ -2996,7 +2996,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, high any compl 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_83
@@ -3028,7 +3028,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_84
@@ -3056,7 +3056,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, high end compl 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_85
@@ -3088,7 +3088,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 200, ok 200
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_86
@@ -3122,7 +3122,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_87
@@ -3160,7 +3160,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_89

Modified: trunk/packages/primer3/branches/upstream/current/test/primer_boundary_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_boundary_formatted_output	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_boundary_formatted_output	2006-09-22 14:39:44 UTC (rev 122)
@@ -26,7 +26,7 @@
 Right     10     9     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_01
@@ -57,7 +57,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_02
@@ -88,7 +88,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_03
@@ -112,7 +112,7 @@
 Right      4     3     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, unacceptable product size 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_04
@@ -136,7 +136,7 @@
 Right     10     9     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, unacceptable product size 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_05
@@ -167,7 +167,7 @@
 Right      5     3     0     0     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 4, unacceptable product size 3, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_06
@@ -191,7 +191,7 @@
 Right      5     5     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_07
@@ -223,7 +223,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_08
@@ -251,7 +251,7 @@
 Right      6     5     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_09
@@ -279,7 +279,7 @@
 Right      5     5     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_10
@@ -303,7 +303,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_11
@@ -334,7 +334,7 @@
 Right      5     2     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 3, unacceptable product size 2, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_11
@@ -358,7 +358,7 @@
 Right      5     2     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_12
@@ -389,7 +389,7 @@
 Right      5     0     0     0     0     0     0     0     0     0     0     0     5
 Pair Stats:
 considered 5, unacceptable product size 4, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_13
@@ -420,7 +420,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_14
@@ -444,7 +444,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_15
@@ -475,7 +475,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_16
@@ -499,7 +499,7 @@
 Right      5     4     0     0     1     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_17
@@ -531,7 +531,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_18
@@ -559,7 +559,7 @@
 Right      1     1     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_19
@@ -591,7 +591,7 @@
 Right      1     1     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_21
@@ -624,7 +624,7 @@
 Right      3     2     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_22
@@ -653,7 +653,7 @@
 Right      3     2     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_23
@@ -682,7 +682,7 @@
 Right      2     2     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_24
@@ -711,7 +711,7 @@
 Right      2     2     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_25
@@ -744,7 +744,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_26
@@ -773,7 +773,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_27
@@ -802,7 +802,7 @@
 Right      5     4     1     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_28
@@ -831,7 +831,7 @@
 Right      5     4     1     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_29
@@ -864,7 +864,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_30
@@ -897,7 +897,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_31
@@ -926,7 +926,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, no target 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_32
@@ -959,7 +959,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_33
@@ -988,7 +988,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_34
@@ -1017,7 +1017,7 @@
 Right      5     4     0     1     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_35
@@ -1046,7 +1046,7 @@
 Right      5     4     0     1     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_36
@@ -1079,7 +1079,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_37
@@ -1108,7 +1108,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_37
@@ -1137,7 +1137,7 @@
 Right      5     4     0     1     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_38
@@ -1166,7 +1166,7 @@
 Right      5     4     0     1     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_39
@@ -1199,7 +1199,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_40
@@ -1232,7 +1232,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_41
@@ -1258,7 +1258,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_42
@@ -1291,7 +1291,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_43
@@ -1320,7 +1320,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_44
@@ -1353,7 +1353,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_45
@@ -1386,7 +1386,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_46
@@ -1415,7 +1415,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_47
@@ -1448,7 +1448,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_48
@@ -1477,7 +1477,7 @@
 Right      5     4     0     0     0     1     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_49
@@ -1510,7 +1510,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_50
@@ -1539,7 +1539,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_51
@@ -1572,7 +1572,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_52
@@ -1605,7 +1605,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_53
@@ -1634,7 +1634,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, tm diff too large 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_54
@@ -1669,7 +1669,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_55
@@ -1702,7 +1702,7 @@
 Intl       0     0     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR poly_x_2
@@ -1765,7 +1765,7 @@
 Intl    1585     0     0     0     0     0     0     0     0     0     0     0  1585
 Pair Stats:
 considered 72, unacceptable product size 52, ok 20
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR poly_x_3
@@ -1794,7 +1794,7 @@
 Intl     187     0     0     0     0     0     0     0     0     0   187     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_59
@@ -1827,7 +1827,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_60
@@ -1853,7 +1853,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_61
@@ -1893,7 +1893,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_63
@@ -1923,7 +1923,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_64
@@ -1963,7 +1963,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_66
@@ -1993,7 +1993,7 @@
 Right      1     0     0     1     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_67
@@ -2025,7 +2025,7 @@
 Right      6     5     0     1     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_68
@@ -2058,7 +2058,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_69
@@ -2084,7 +2084,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_70
@@ -2120,7 +2120,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, no target 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_72
@@ -2150,7 +2150,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_73
@@ -2186,7 +2186,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, no target 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_75
@@ -2216,7 +2216,7 @@
 Right      0     0     0     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_76
@@ -2248,7 +2248,7 @@
 Right      6     5     1     0     0     0     0     0     0     0     0     0     0
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_77
@@ -2282,7 +2282,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_78
@@ -2316,7 +2316,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_79
@@ -2350,7 +2350,7 @@
 Right      6     5     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_80
@@ -2384,7 +2384,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_81
@@ -2418,7 +2418,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_82
@@ -2451,7 +2451,7 @@
 Right     10     9     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_83
@@ -2480,7 +2480,7 @@
 Right     10     9     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, no target 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_84
@@ -2513,7 +2513,7 @@
 Right     10     9     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_85
@@ -2546,7 +2546,7 @@
 Right      3     2     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_86
@@ -2580,7 +2580,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_71
@@ -2616,7 +2616,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_72
@@ -2648,7 +2648,7 @@
 Right      3     2     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 3, unacceptable product size 2, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_73
@@ -2676,7 +2676,7 @@
 Right      3     2     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 2, unacceptable product size 2, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_74
@@ -2708,7 +2708,7 @@
 Right      3     2     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 2, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_75
@@ -2740,7 +2740,7 @@
 Right      2     1     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 2, unacceptable product size 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_76
@@ -2772,7 +2772,7 @@
 Right      2     1     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 2, unacceptable product size 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_77
@@ -2813,7 +2813,7 @@
 Right     28    26     0     0     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 4, unacceptable product size 2, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_78
@@ -2854,7 +2854,7 @@
 Right     28    26     0     0     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 4, unacceptable product size 2, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_79
@@ -2895,7 +2895,7 @@
 Right     28    26     0     0     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 4, unacceptable product size 1, ok 3
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_80
@@ -2936,7 +2936,7 @@
 Right     28    26     0     0     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 4, unacceptable product size 1, ok 3
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_81
@@ -2968,7 +2968,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_82
@@ -2996,7 +2996,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, high any compl 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_83
@@ -3028,7 +3028,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_84
@@ -3056,7 +3056,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, high end compl 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_85
@@ -3088,7 +3088,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 200, ok 200
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_86
@@ -3122,7 +3122,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_87
@@ -3160,7 +3160,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_89
@@ -3195,7 +3195,7 @@
 Right     10     9     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_91
@@ -3219,7 +3219,7 @@
 Right     10     9     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 0, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_92
@@ -3254,7 +3254,7 @@
 Right      5     2     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 9, unacceptable product size 8, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_93
@@ -3289,7 +3289,7 @@
 Right      5     0     0     0     0     0     0     0     0     0     0     0     5
 Pair Stats:
 considered 5, unacceptable product size 4, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_94
@@ -3324,7 +3324,7 @@
 Right      5     0     0     0     0     0     0     0     0     0     0     0     5
 Pair Stats:
 considered 5, unacceptable product size 4, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_95
@@ -3359,7 +3359,7 @@
 Right      5     4     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 5, unacceptable product size 4, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_96
@@ -3394,7 +3394,7 @@
 Right      5     0     0     0     0     0     0     0     0     0     0     0     5
 Pair Stats:
 considered 5, unacceptable product size 4, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_97
@@ -3429,7 +3429,7 @@
 Right      5     0     0     0     0     0     0     0     0     0     0     0     5
 Pair Stats:
 considered 5, unacceptable product size 4, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR test_098
@@ -3461,7 +3461,7 @@
 Right      5     0     0     0     0     0     0     0     0     0     0     0     5
 Pair Stats:
 considered 5, unacceptable product size 4, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR test_099
@@ -3485,7 +3485,7 @@
 Right      5     0     0     0     0     0     0     0     0     0     0     0     5
 Pair Stats:
 considered 5, unacceptable product size 4, high product Tm 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR test_100
@@ -3516,7 +3516,7 @@
 Right      5     0     0     0     0     0     0     0     0     0     0     0     5
 Pair Stats:
 considered 5, unacceptable product size 4, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR test_101
@@ -3548,7 +3548,7 @@
 Right      5     0     0     0     0     0     0     0     0     0     0     0     5
 Pair Stats:
 considered 5, unacceptable product size 4, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR test_102
@@ -3572,7 +3572,7 @@
 Right      5     0     0     0     0     0     0     0     0     0     0     0     5
 Pair Stats:
 considered 5, unacceptable product size 4, low product Tm 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR test_103
@@ -3603,6 +3603,6 @@
 Right      5     0     0     0     0     0     0     0     0     0     0     0     5
 Pair Stats:
 considered 5, unacceptable product size 4, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 

Modified: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/empty_1.out2
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/empty_1.out2	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/empty_1.out2	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,52 +1,38 @@
 
-Copyright (c) 1996,1997,1998,1999,2000,2001,2004
-        Whitehead Institute for Biomedical Research. All rights reserved.
+Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
+modification, are permitted provided that the following conditions are
+met:
 
-1.      Redistributions must reproduce the above copyright notice, this
-list of conditions and the following disclaimer in the  documentation
-and/or other materials provided with the distribution.  Redistributions of
-source code must also reproduce this information in the source code itself.
+   * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+   * Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following disclaimer
+in the documentation and/or other materials provided with the
+distribution.
+   * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
 
-2.      If the program is modified, redistributions must include a notice
-(in the same places as above) indicating that the redistributed program is
-not identical to the version distributed by Whitehead Institute.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-3.      All advertising materials mentioning features or use of this
-software  must display the following acknowledgment:
-        This product includes software developed by the
-        Whitehead Institute for Biomedical Research.
 
-4.      The name of the Whitehead Institute may not be used to endorse or
-promote products derived from this software without specific prior written
-permission.
-
-We also request that use of this software be cited in publications as 
-
-  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.
-  Code available at
-  http://fokker.wi.mit.edu/primer3/.
-
-THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS'' AND  ANY
-EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE  IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE  ARE
-DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE  FOR ANY
-DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL  DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS  OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)  HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
-LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
-OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGE.
-
-
 USAGE: ../src/primer3_core [-format_output] [-2x_compat] [-strict_tags]
-This is primer3 (primer3 release 1.0)
+This is primer3 (primer3 release 1.0b)
 Input must be provided on standard input.
 For example:
 $ primer3_core < my_input_file

Deleted: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no=.in
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no=.in	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no=.in	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,3 +0,0 @@
-PRIMER_SEQUENCE_ID=without_eq
-AGTCGATCGTAGCTAGCTAGCTAGCTGACTGATGCTAGCTAGCTGATCGATCGTAGCTAGCTAGCTGATCGTAGCTAGCTAGCTGACTGATCATCTAGCTAGCTGATCATCGTAGCTAGCTCTATTTTATCGTAGCTAGCTATCATCTAGCTAGC
-=

Deleted: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no=.out
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no=.out	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no=.out	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,4 +0,0 @@
-PRIMER_SEQUENCE_ID=without_eq
-AGTCGATCGTAGCTAGCTAGCTAGCTGACTGATGCTAGCTAGCTGATCGATCGTAGCTAGCTAGCTGATCGTAGCTAGCTAGCTGACTGATCATCTAGCTAGCTGATCATCGTAGCTAGCTCTATTTTATCGTAGCTAGCTATCATCTAGCTAGC
-PRIMER_ERROR=Missing SEQUENCE tag; Input line with no '=': AGTCGATCGTAGCTAGCTAGCTAGCTGACTGATGCTAGCTAGCTGATCGATCGTAGCTAGCTAGCTGATCGTAGCTAGCTAGCTGACTGATCATCTAGCTAGCTGATCATCGTAGCTAGCTCTATTTTATCGTAGCTAGCTATCATCTAGCTAGC
-=

Deleted: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no=.out2
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no=.out2	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no=.out2	2006-09-22 14:39:44 UTC (rev 122)
@@ -1 +0,0 @@
-../src/primer3_core: Input line with no '=': AGTCGATCGTAGCTAGCTAGCTAGCTGACTGATGCTAGCTAGCTGATCGATCGTAGCTAGCTAGCTGATCGTAGCTAGCTAGCTGACTGATCATCTAGCTAGCTGATCATCGTAGCTAGCTCTATTTTATCGTAGCTAGCTATCATCTAGCTAGC

Added: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_equal.in
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_equal.in	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_equal.in	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1,3 @@
+PRIMER_SEQUENCE_ID=without_eq
+AGTCGATCGTAGCTAGCTAGCTAGCTGACTGATGCTAGCTAGCTGATCGATCGTAGCTAGCTAGCTGATCGTAGCTAGCTAGCTGACTGATCATCTAGCTAGCTGATCATCGTAGCTAGCTCTATTTTATCGTAGCTAGCTATCATCTAGCTAGC
+=

Added: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_equal.out
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_equal.out	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_equal.out	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1,4 @@
+PRIMER_SEQUENCE_ID=without_eq
+AGTCGATCGTAGCTAGCTAGCTAGCTGACTGATGCTAGCTAGCTGATCGATCGTAGCTAGCTAGCTGATCGTAGCTAGCTAGCTGACTGATCATCTAGCTAGCTGATCATCGTAGCTAGCTCTATTTTATCGTAGCTAGCTATCATCTAGCTAGC
+PRIMER_ERROR=Missing SEQUENCE tag; Input line with no '=': AGTCGATCGTAGCTAGCTAGCTAGCTGACTGATGCTAGCTAGCTGATCGATCGTAGCTAGCTAGCTGATCGTAGCTAGCTAGCTGACTGATCATCTAGCTAGCTGATCATCGTAGCTAGCTCTATTTTATCGTAGCTAGCTATCATCTAGCTAGC
+=

Added: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_equal.out2
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_equal.out2	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_equal.out2	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1 @@
+../src/primer3_core: Input line with no '=': AGTCGATCGTAGCTAGCTAGCTAGCTGACTGATGCTAGCTAGCTGATCGATCGTAGCTAGCTAGCTGATCGTAGCTAGCTAGCTGACTGATCATCTAGCTAGCTGATCATCGTAGCTAGCTCTATTTTATCGTAGCTAGCTATCATCTAGCTAGC

Deleted: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal=.in
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal=.in	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal=.in	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,11 +0,0 @@
-PRIMER_SEQUENCE_ID=example
-SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
-TARGET=37,21
-PRIMER_OPT_SIZE=18
-PRIMER_MIN_SIZE=15
-PRIMER_MAX_SIZE=21
-PRIMER_NUM_NS_ACCEPTED=1
-PRIMER_PRODUCT_SIZE_RANGE=75-100
-PRIMER_FILE_FLAG=1
-PRIMER_PICK_INTERNAL_OLIGO=1
-PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=37,21

Deleted: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal=.out
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal=.out	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal=.out	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,13 +0,0 @@
-PRIMER_SEQUENCE_ID=example
-SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
-TARGET=37,21
-PRIMER_OPT_SIZE=18
-PRIMER_MIN_SIZE=15
-PRIMER_MAX_SIZE=21
-PRIMER_NUM_NS_ACCEPTED=1
-PRIMER_PRODUCT_SIZE_RANGE=75-100
-PRIMER_FILE_FLAG=1
-PRIMER_PICK_INTERNAL_OLIGO=1
-PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=37,21
-PRIMER_ERROR=Final record not terminated by '='
-=

Deleted: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal=.out2
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal=.out2	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal=.out2	2006-09-22 14:39:44 UTC (rev 122)
@@ -1 +0,0 @@
-../src/primer3_core: Final record not terminated by '='

Added: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal_equal.in
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal_equal.in	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal_equal.in	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1,11 @@
+PRIMER_SEQUENCE_ID=example
+SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
+TARGET=37,21
+PRIMER_OPT_SIZE=18
+PRIMER_MIN_SIZE=15
+PRIMER_MAX_SIZE=21
+PRIMER_NUM_NS_ACCEPTED=1
+PRIMER_PRODUCT_SIZE_RANGE=75-100
+PRIMER_FILE_FLAG=1
+PRIMER_PICK_INTERNAL_OLIGO=1
+PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=37,21

Added: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal_equal.out
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal_equal.out	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal_equal.out	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1,13 @@
+PRIMER_SEQUENCE_ID=example
+SEQUENCE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
+TARGET=37,21
+PRIMER_OPT_SIZE=18
+PRIMER_MIN_SIZE=15
+PRIMER_MAX_SIZE=21
+PRIMER_NUM_NS_ACCEPTED=1
+PRIMER_PRODUCT_SIZE_RANGE=75-100
+PRIMER_FILE_FLAG=1
+PRIMER_PICK_INTERNAL_OLIGO=1
+PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=37,21
+PRIMER_ERROR=Final record not terminated by '='
+=

Added: trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal_equal.out2
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal_equal.out2	                        (rev 0)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_global_err/no_terminal_equal.out2	2006-09-22 14:39:44 UTC (rev 122)
@@ -0,0 +1 @@
+../src/primer3_core: Final record not terminated by '='

Modified: trunk/packages/primer3/branches/upstream/current/test/primer_internal1_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_internal1_formatted_output	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_internal1_formatted_output	2006-09-22 14:39:44 UTC (rev 122)
@@ -33,7 +33,7 @@
 Intl      60    57     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 4, unacceptable product size 1, no internal oligo 2, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_01
@@ -71,7 +71,7 @@
 Intl      60    57     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 2, unacceptable product size 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_02
@@ -109,7 +109,7 @@
 Intl      60    57     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_05
@@ -147,7 +147,7 @@
 Intl      60    57     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 4, unacceptable product size 3, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_11
@@ -174,7 +174,7 @@
 Intl      60    59     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 8, unacceptable product size 6, no internal oligo 2, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_11
@@ -219,7 +219,7 @@
 Intl      60    52     0     0     0     0     0     0     0     0     0     0     8
 Pair Stats:
 considered 10, unacceptable product size 8, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_12
@@ -264,7 +264,7 @@
 Intl      60    52     0     0     0     0     0     0     0     0     0     0     8
 Pair Stats:
 considered 10, unacceptable product size 8, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_13
@@ -302,7 +302,7 @@
 Intl      60    23     0     0     0     0     0     0     0     0     0     0    37
 Pair Stats:
 considered 4, unacceptable product size 3, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_14
@@ -340,7 +340,7 @@
 Intl      60    25     0     0     0     0     0     0     0     0     0     0    35
 Pair Stats:
 considered 6, unacceptable product size 5, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_15
@@ -378,7 +378,7 @@
 Intl      60    25     0     0     0     0     0     0     0     0     0     0    35
 Pair Stats:
 considered 6, unacceptable product size 5, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_16
@@ -404,7 +404,7 @@
 Intl      35     0     0     0     0     0     0     0     0     0     0     0    35
 Pair Stats:
 considered 4, no internal oligo 4, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_17
@@ -431,7 +431,7 @@
 Intl      60     0     0     0    29     0     0     0     0     0     0     0    31
 Pair Stats:
 considered 16, unacceptable product size 4, no internal oligo 12, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_18
@@ -465,7 +465,7 @@
 Intl      87    39     0    40     0     0     0     0     0     0     0     0     8
 Pair Stats:
 considered 81, unacceptable product size 49, no internal oligo 32, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_19
@@ -527,7 +527,7 @@
 Intl      91    84     0     5     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 18, unacceptable product size 3, no internal oligo 8, ok 7
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_20
@@ -599,7 +599,7 @@
 Intl     226   175     0    47     0     0     0     0     0     0     0     0     4
 Pair Stats:
 considered 23, no internal oligo 15, ok 8
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_21
@@ -662,7 +662,7 @@
 Intl     152    57     0     0     0     0     1    93     0     0     0     0     1
 Pair Stats:
 considered 323, unacceptable product size 223, no internal oligo 87, ok 13
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_22
@@ -700,7 +700,7 @@
 Intl      60    57     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_23
@@ -743,7 +743,7 @@
 Intl      56    53     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_24
@@ -784,7 +784,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_25
@@ -827,7 +827,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_26
@@ -868,7 +868,7 @@
 Intl      56    53     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_27
@@ -903,7 +903,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, no internal oligo 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_28
@@ -938,7 +938,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, no internal oligo 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_29
@@ -979,7 +979,7 @@
 Intl      56    53     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_30
@@ -1020,7 +1020,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_31
@@ -1063,7 +1063,7 @@
 Intl      56    53     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_32
@@ -1106,7 +1106,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_33
@@ -1147,7 +1147,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_34

Modified: trunk/packages/primer3/branches/upstream/current/test/primer_internal_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_internal_formatted_output	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_internal_formatted_output	2006-09-22 14:39:44 UTC (rev 122)
@@ -33,7 +33,7 @@
 Intl      60    57     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 4, unacceptable product size 1, no internal oligo 2, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_01
@@ -71,7 +71,7 @@
 Intl      60    57     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 2, unacceptable product size 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_02
@@ -109,7 +109,7 @@
 Intl      60    57     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_05
@@ -147,7 +147,7 @@
 Intl      60    57     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 4, unacceptable product size 3, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_11
@@ -174,7 +174,7 @@
 Intl      60    59     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 8, unacceptable product size 6, no internal oligo 2, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_11
@@ -219,7 +219,7 @@
 Intl      60    52     0     0     0     0     0     0     0     0     0     0     8
 Pair Stats:
 considered 10, unacceptable product size 8, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_12
@@ -264,7 +264,7 @@
 Intl      60    52     0     0     0     0     0     0     0     0     0     0     8
 Pair Stats:
 considered 10, unacceptable product size 8, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_13
@@ -302,7 +302,7 @@
 Intl      60    23     0     0     0     0     0     0     0     0     0     0    37
 Pair Stats:
 considered 4, unacceptable product size 3, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_14
@@ -340,7 +340,7 @@
 Intl      60    25     0     0     0     0     0     0     0     0     0     0    35
 Pair Stats:
 considered 6, unacceptable product size 5, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_15
@@ -378,7 +378,7 @@
 Intl      60    25     0     0     0     0     0     0     0     0     0     0    35
 Pair Stats:
 considered 6, unacceptable product size 5, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_16
@@ -404,7 +404,7 @@
 Intl      35     0     0     0     0     0     0     0     0     0     0     0    35
 Pair Stats:
 considered 4, no internal oligo 4, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_17
@@ -431,7 +431,7 @@
 Intl      60     0     0     0    29     0     0     0     0     0     0     0    31
 Pair Stats:
 considered 16, unacceptable product size 4, no internal oligo 12, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_18
@@ -465,7 +465,7 @@
 Intl      87    39     0    40     0     0     0     0     0     0     0     0     8
 Pair Stats:
 considered 81, unacceptable product size 49, no internal oligo 32, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_19
@@ -527,7 +527,7 @@
 Intl      91    84     0     5     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 18, unacceptable product size 3, no internal oligo 8, ok 7
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_20
@@ -599,7 +599,7 @@
 Intl     226   175     0    47     0     0     0     0     0     0     0     0     4
 Pair Stats:
 considered 23, no internal oligo 15, ok 8
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_21
@@ -662,7 +662,7 @@
 Intl     152    57     0     0     0     0     1    93     0     0     0     0     1
 Pair Stats:
 considered 323, unacceptable product size 223, no internal oligo 87, ok 13
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_22
@@ -700,7 +700,7 @@
 Intl      60    57     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_23
@@ -743,7 +743,7 @@
 Intl      56    53     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_24
@@ -784,7 +784,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_25
@@ -827,7 +827,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_26
@@ -868,7 +868,7 @@
 Intl      56    53     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_27
@@ -903,7 +903,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, no internal oligo 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_28
@@ -938,7 +938,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, no internal oligo 1, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_29
@@ -979,7 +979,7 @@
 Intl      56    53     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_30
@@ -1020,7 +1020,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_31
@@ -1063,7 +1063,7 @@
 Intl      56    53     0     0     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_32
@@ -1106,7 +1106,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_33
@@ -1147,7 +1147,7 @@
 Intl      56    53     0     1     0     0     0     0     0     0     0     0     2
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR boundary_test_34

Modified: trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary1_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary1_formatted_output	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary1_formatted_output	2006-09-22 14:39:44 UTC (rev 122)
@@ -39,7 +39,7 @@
 Intl     163     0     0     0     0     0     0     0     0     0   121     0     0    42
 Pair Stats:
 considered 381, unacceptable product size 369, no internal oligo 11, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR pair_0
@@ -67,7 +67,7 @@
 Intl     144     0     0     0     0     0     0     0     0     0     0     0     0   144
 Pair Stats:
 considered 32, unacceptable product size 32, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR pair_1
@@ -111,6 +111,6 @@
 Intl     163     0     0     0     0     0     0     0     0     0   121     0     0    42
 Pair Stats:
 considered 6889, unacceptable product size 3403, no internal oligo 11, high mispriming library similarity 3474, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 

Modified: trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary2_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary2_formatted_output	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_boundary2_formatted_output	2006-09-22 14:39:44 UTC (rev 122)
@@ -39,7 +39,7 @@
 Intl     163     0     0     0     0     0     0     0     0     0   121     0     0    42
 Pair Stats:
 considered 381, unacceptable product size 369, no internal oligo 11, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR pair_0
@@ -67,6 +67,6 @@
 Intl     144     0     0     0     0     0     0     0     0     0     0     0     0   144
 Pair Stats:
 considered 32, unacceptable product size 32, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 

Modified: trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_formatted_output	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_mispriming_formatted_output	2006-09-22 14:39:44 UTC (rev 122)
@@ -64,7 +64,7 @@
 Right   1012    19     0    58    25     0     0   702     0     0     0     0     0   208
 Pair Stats:
 considered 23, unacceptable product size 17, ok 6
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR exon2
@@ -130,7 +130,7 @@
 Right    827     0     0    72   314     0   236     0     0     0     0     0     0   205
 Pair Stats:
 considered 14, unacceptable product size 8, ok 6
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR exon2
@@ -204,7 +204,7 @@
 Intl    3079     0     0     0   316     0   517   178     0     0     0    23     0  2045
 Pair Stats:
 considered 14, unacceptable product size 8, ok 6
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR exon1
@@ -281,7 +281,7 @@
 Intl    3237    27     0     0    32     0    23  1880     0     0     0     0     0  1275
 Pair Stats:
 considered 29, unacceptable product size 18, high mispriming library similarity 2, ok 9
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR exon2
@@ -355,7 +355,7 @@
 Intl    3079     0     0     0   316     0   517   178     0     0     0    23     0  2045
 Pair Stats:
 considered 116, unacceptable product size 66, tm diff too large 5, high mispriming library similarity 38, ok 7
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR exon2
@@ -401,6 +401,6 @@
 Intl    3079     0     0     0   316     0   517   178     0     0     0    23     0  2045
 Pair Stats:
 considered 12459, unacceptable product size 6872, tm diff too large 4075, high mispriming library similarity 1512, ok 0
-primer3 release 1.0
+primer3 release 1.0b
 
 

Modified: trunk/packages/primer3/branches/upstream/current/test/primer_must_use_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_must_use_formatted_output	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_must_use_formatted_output	2006-09-22 14:39:44 UTC (rev 122)
@@ -34,7 +34,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR high_tm
@@ -74,7 +74,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR high_tm_and_self_any
@@ -114,7 +114,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR high_tm_and_self_any_and_target
@@ -154,7 +154,7 @@
 Right      3     0     0     0     0     0     0     2     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR high_tm_and_self_any_and_excl_region
@@ -196,7 +196,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR high_tm_and_self_any_and_incl_region
@@ -236,7 +236,7 @@
 Statistics
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR left_high_tm_and_self_any_and_right_bad_gc
@@ -272,7 +272,7 @@
 Statistics
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR left_high_tm_and_self_any_and_right_bad_gc_and_target
@@ -308,7 +308,7 @@
 Statistics
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR internal_too_short
@@ -351,7 +351,7 @@
 Statistics
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR internal_too_cold
@@ -390,7 +390,7 @@
 Statistics
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR internal_too_cold2
@@ -433,7 +433,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR mispriming
@@ -476,6 +476,6 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 

Modified: trunk/packages/primer3/branches/upstream/current/test/primer_position_penalty_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_position_penalty_formatted_output	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_position_penalty_formatted_output	2006-09-22 14:39:44 UTC (rev 122)
@@ -60,7 +60,7 @@
 Right   3504     0   289     0     0     0   655  1723     0     0     0     0     0   837
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR AT3_X2
@@ -143,7 +143,7 @@
 Right   6657     0   289     0   114     0  1327  3439     0     2     0    19     0  1467
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR AT3_X3
@@ -217,7 +217,7 @@
 Right   5254     0   289     0   103     0  1706  1557     0     0     0     0     0  1599
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR AT3_X3'
@@ -288,7 +288,7 @@
 Right   4294     0   289     0   209     0   512  2472     0     0     0    25     0   787
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR AT3_X4
@@ -371,7 +371,7 @@
 Right   7004     0   289     0     0     0  1493  3474     0     0     0     0     0  1748
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR AT3_X5
@@ -439,7 +439,7 @@
 Right   3744     0   289     0     0     0   874  1504     0     8     0     0     0  1069
 Pair Stats:
 considered 21, high end compl 20, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR AT3_X6
@@ -510,7 +510,7 @@
 Right   4414     0   289     0   103     0  1578  1288     0     0    14     0     0  1142
 Pair Stats:
 considered 3, high end compl 2, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X1
@@ -578,7 +578,7 @@
 Right   4274     0   289     0     0     0   375  2978     0     0     0     0     0   632
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X2
@@ -640,7 +640,7 @@
 Right   2584     0   289     0     1     0    95  1901     0     0     0     0     0   298
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X3
@@ -711,7 +711,7 @@
 Right   4444     0   289     0     0     0   400  2950     0     0     0     0     0   805
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X4
@@ -779,7 +779,7 @@
 Right   3804     0   289     0     0     0   348  2565     0     0     0     0     0   602
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X5
@@ -847,7 +847,7 @@
 Right   3974     0   289     0    34     0   889  1971     0     0     0     0     0   791
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X6
@@ -915,7 +915,7 @@
 Right   3794     0   289     0     0     0   274  2616     2     3     0     0     0   610
 Pair Stats:
 considered 40, high end compl 38, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X7
@@ -983,7 +983,7 @@
 Right   3593     0   289     0    15     0   752  1654     0     0     0    22     0   861
 Pair Stats:
 considered 102, high any compl 81, high end compl 20, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X8
@@ -1051,7 +1051,7 @@
 Right   3861     0   289     0     8     0   269  2629     0     0     0    22     0   644
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X9
@@ -1116,7 +1116,7 @@
 Right   4589     0   154     0     0     0   711  2838     0     0     0     0     0   886
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X10
@@ -1169,7 +1169,7 @@
 Right   1498     0   226     0     0     0   153   792     0     0     0    22     0   305
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X11
@@ -1222,7 +1222,7 @@
 Right   2741     0   116     0    42     0   336  1775     0     0     0     0     0   472
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X12
@@ -1290,7 +1290,7 @@
 Right   3774     0   289     0     0     0   619  2094     0     0     0     0     0   772
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X13
@@ -1355,7 +1355,7 @@
 Right   3434     0   289     0     0     0   586  1682     0     0     0     0     0   877
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X14
@@ -1411,7 +1411,7 @@
 Right   1454     0   289     0     0     0    83   882     0     0     0     0     0   200
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X15
@@ -1476,7 +1476,7 @@
 Right   3758     0   245     0     1     0   356  2464     0     0     3    22     0   667
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR CETP_X16
@@ -1544,7 +1544,7 @@
 Right   3637     0   289     0     3     0   299  2316     0     0     0    25     0   705
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X1
@@ -1612,7 +1612,7 @@
 Right   4194     0   289     0     8     0   235  3082     0     0     2     0     0   578
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X2
@@ -1683,7 +1683,7 @@
 Right   4704     0   289     0    96     0   191  3583     0     4     0     0     0   541
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X3
@@ -1748,7 +1748,7 @@
 Right   3344     0   289     0     1     0   379  2040     0     0     0     0     0   635
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X4
@@ -1813,7 +1813,7 @@
 Right   3497     0   289     0   107     0   371  2132     0     0     0    18     0   580
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X5
@@ -1881,7 +1881,7 @@
 Right   4154     0   289     0    14     0   310  2916     0     0     0     0     0   625
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X6
@@ -1952,7 +1952,7 @@
 Right   4464     0   289     0    40     0   325  3245     0     0     0     0     0   565
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X7
@@ -2032,7 +2032,7 @@
 Right   5938     0   289     0    51     0   580  3983     0     0     0    44     0   991
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X8
@@ -2103,7 +2103,7 @@
 Right   4384     0   289     0    97     0   244  3201     0     0     0     0     0   553
 Pair Stats:
 considered 14, high end compl 12, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X9
@@ -2174,7 +2174,7 @@
 Right   4248     0   289     0    80     0   415  2693     0     0     0    23     0   748
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X10
@@ -2245,7 +2245,7 @@
 Right   4621     0   289     0     8     0   474  3110     0     0     0    22     0   718
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X11
@@ -2316,7 +2316,7 @@
 Right   4762     0   289     0   176     0   739  2528     0     0     0    13     0  1017
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X12
@@ -2390,7 +2390,7 @@
 Right   4914     0   289     0    83     0   976  2660     0     0     0     0     0   906
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X13
@@ -2458,7 +2458,7 @@
 Right   3804     0   289     0     0     0   873  1715     0     5     0     0     0   922
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2_X14
@@ -2526,7 +2526,7 @@
 Right   3944     0   289     0    74     0   898  1848     0     2     0     0     0   833
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2R_X1
@@ -2576,7 +2576,7 @@
 Right    951     0   226     0   209     0     0   510     0     0     0     0     0     6
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2R_X2-seg1
@@ -2644,7 +2644,7 @@
 Right   6710     0     0     0     4     0  1540  3376     0     0     2     0     0  1788
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F2R_X2-seg2
@@ -2715,7 +2715,7 @@
 Right   6997     0     0     0   109     0  2483  2360     0     0     0    22     0  2023
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F3_X1
@@ -2783,7 +2783,7 @@
 Right   4094     0   289     0   716     0   101  2783     0     0     0     0     0   205
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F3_X2
@@ -2851,7 +2851,7 @@
 Right   4214     0   289     0   232     0  1968   682     0     0     0     0     0  1043
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F3_X3
@@ -2925,7 +2925,7 @@
 Right   5005     0   289     0   185     0  1231  1945     0     0     0    11     0  1344
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F3_X4
@@ -2996,7 +2996,7 @@
 Right   4770     0   289     0   176     0  1330  1913     0     0     0    21     0  1041
 Pair Stats:
 considered 36, high end compl 33, ok 3
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F3_X5
@@ -3067,7 +3067,7 @@
 Right   4397     0   289     0    28     0  1323  1565     0     4     0    44     0  1144
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F3_X6
@@ -3138,7 +3138,7 @@
 Right   4311     0   289     0    51     0  1766   895     0     0     0    22     0  1288
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F5_X10
@@ -3188,7 +3188,7 @@
 Right   2435     0    50     0     0     0  1068   632     0     0     0     0     0   685
 Pair Stats:
 considered 18, high end compl 16, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F7_X1
@@ -3256,7 +3256,7 @@
 Right   3734     0   289     0    17     0   289  2735     0     1     0     0     0   403
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F7_X2
@@ -3324,7 +3324,7 @@
 Right   3601     0   289     0    16     0   390  2278     0     0     0    22     0   606
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F7_X2'
@@ -3395,7 +3395,7 @@
 Right   4704     0   289     0  1078     0   138  2874     0     0     0     0     0   325
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F7_X3
@@ -3460,7 +3460,7 @@
 Right   3344     0   289     0     0     0   284  2312     8    13     7     0     0   431
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F7_X4
@@ -3528,7 +3528,7 @@
 Right   4234     0   289     0    81     0   378  2891     0     0     0     0     0   595
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F7_X5
@@ -3599,7 +3599,7 @@
 Right   4504     0   289     0     1     0   499  3030     0     0     2     0     0   683
 Pair Stats:
 considered 20, high any compl 8, high end compl 10, ok 2
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F7_X6
@@ -3667,7 +3667,7 @@
 Right   3894     0   289     0    11     0   463  2371     0     1     0    44     0   715
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F7_X7
@@ -3738,7 +3738,7 @@
 Right   4181     0   289     0    10     0   236  3155     0     5     0    22     0   464
 Pair Stats:
 considered 126, high any compl 28, high end compl 97, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR F7_X8
@@ -3830,7 +3830,7 @@
 Right   9054     0   289     0    79     0  1105  6374     0     1     0     0     0  1206
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HCF2_X2
@@ -3940,7 +3940,7 @@
 Right  12144     0   289     0    15     0  3651  4687     0     7     0     0     0  3495
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HCF2_X3
@@ -4017,7 +4017,7 @@
 Right   5393     0   289     0    28     0  1331  2335    19     7     0    67     0  1317
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HCF2_X4
@@ -4088,7 +4088,7 @@
 Right   4238     0   289     0    20     0   420  2770     0     0     0    44     0   695
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HCF2_X5
@@ -4195,7 +4195,7 @@
 Right  11432     0   289     0    57     0  2518  5947     0    12     0    20     0  2589
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X1
@@ -4239,7 +4239,7 @@
 Right   1490     0    65     0     0     0   478   584     0     0     0     0     0   363
 Pair Stats:
 considered 11, high end compl 10, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X2
@@ -4277,7 +4277,7 @@
 Right    770     0     0     0    11     0   448    81     7     1     0     0     0   222
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X3
@@ -4315,7 +4315,7 @@
 Right    530     0     0     0     1     0   416     4     0     0     0     0     0   109
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X4
@@ -4353,7 +4353,7 @@
 Right    500     0     0     0     0     0   123   202     0     0     0     0     0   175
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X5
@@ -4391,7 +4391,7 @@
 Right    710     0     0     0     0     0   202   248     0     1     1     0     0   258
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X6
@@ -4429,7 +4429,7 @@
 Right    720     0     0     0     0     0   181   338     0     0     0     0     0   201
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X7
@@ -4467,7 +4467,7 @@
 Right    820     0     0     0     3     0   237   349     0     0     0     0     0   231
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X8
@@ -4508,7 +4508,7 @@
 Right   1260     0     0     0     0     0   530   315     0     0    20     0     0   395
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X9
@@ -4555,7 +4555,7 @@
 Right   1977     0     0     0     0     0  1125   203     0     0     0    22     0   627
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X10
@@ -4593,7 +4593,7 @@
 Right    550     0     0     0     0     0   227   116     0     0     0     0     0   207
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X11
@@ -4631,7 +4631,7 @@
 Right    540     0     0     0     0     0   181   215     0     0     0     0     0   144
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X12
@@ -4675,7 +4675,7 @@
 Right   1600     0     0     0     0     0   707   324     0     0     0     0     0   569
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X13
@@ -4716,7 +4716,7 @@
 Right   1240     0     0     0     1     0   280   628     0     0     0     0     0   331
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X14
@@ -4757,7 +4757,7 @@
 Right   1230     0     0     0     0     0   122   805     0     0     0     0     0   303
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X15
@@ -4795,7 +4795,7 @@
 Right    710     0     0     0     0     0   172   343     0     0     0     0     0   195
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X16
@@ -4836,7 +4836,7 @@
 Right   1360     0     0     0     0     0   616   248     0     1     0     0     0   495
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X17
@@ -4877,7 +4877,7 @@
 Right   1060     0     0     0     1     0   217   601     0     0     0     0     0   241
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X18
@@ -4918,7 +4918,7 @@
 Right   1240     0     0     0    18     0   504   411     0     0     0     0     0   307
 Pair Stats:
 considered 62, high end compl 59, ok 3
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X19
@@ -4959,7 +4959,7 @@
 Right   1200     0     0     0     0     0   167   784     0     0     0     0     0   249
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR HMGCR_X20
@@ -5000,6 +5000,6 @@
 Right   1150     0     0     0    42     0   311   512    26     3     0    20     0   236
 Pair Stats:
 considered 1, ok 1
-primer3 release 1.0
+primer3 release 1.0b
 
 

Modified: trunk/packages/primer3/branches/upstream/current/test/primer_task_formatted_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_task_formatted_output	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_task_formatted_output	2006-09-22 14:39:44 UTC (rev 122)
@@ -44,7 +44,7 @@
 Right      1     0     0     0     0     0     0     0     0     0     0     0     1
 Pair Stats:
 considered 3, ok 3
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR pcr_primers_and_io
@@ -113,7 +113,7 @@
 Intl     393   280     0     0     0     0    30    46     0     0     3     0    34
 Pair Stats:
 considered 7, ok 7
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR left_only
@@ -152,7 +152,7 @@
          sid  many   tar  excl   bad    GC   too   too   any    3'  poly   end      
         ered    Ns   get   reg   GC% clamp   low  high compl compl     X  stab    ok
 Left    1121    38    23     0     0     0    42   866     0     0     0     0   152
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR right_only
@@ -191,7 +191,7 @@
          sid  many   tar  excl   bad    GC   too   too   any    3'  poly   end      
         ered    Ns   get   reg   GC% clamp   low  high compl compl     X  stab    ok
 Right    623    27    36     0     5     0   230   145     0     6     0     0   174
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR hyb_probe_only
@@ -228,7 +228,7 @@
          sid  many   tar  excl   bad    GC   too   too   any    3'  poly   end      
         ered    Ns   get   reg   GC% clamp   low  high compl compl     X  stab    ok
 Intl    1040    27     0    33     0     0    44   804     0     0     0     0   132
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR left_only
@@ -253,7 +253,7 @@
          sid  many   tar  excl   bad    GC   too   too   any    3'  poly   end      
         ered    Ns   get   reg   GC% clamp   low  high compl compl     X  stab    ok
 Left       1     0     0     0     0     0     0     0     0     0     0     0     1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR right_only
@@ -278,7 +278,7 @@
          sid  many   tar  excl   bad    GC   too   too   any    3'  poly   end      
         ered    Ns   get   reg   GC% clamp   low  high compl compl     X  stab    ok
 Left       1     0     0     0     0     0     0     0     0     0     0     0     1
-primer3 release 1.0
+primer3 release 1.0b
 
 
 PRIMER PICKING RESULTS FOR hyb_probe_only
@@ -303,6 +303,6 @@
          sid  many   tar  excl   bad    GC   too   too   any    3'  poly   end      
         ered    Ns   get   reg   GC% clamp   low  high compl compl     X  stab    ok
 Left       1     0     0     0     0     0     0     0     0     0     0     0     1
-primer3 release 1.0
+primer3 release 1.0b
 
 

Deleted: trunk/packages/primer3/branches/upstream/current/test/primer_template_mispriming_input
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_template_mispriming_input	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_template_mispriming_input	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,158 +0,0 @@
-PRIMER_SEQUENCE_ID=template_mis_1
-PRIMER_NUM_RETURN=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
-=
-PRIMER_SEQUENCE_ID=template_mis_2
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTG
-=
-PRIMER_SEQUENCE_ID=template_mis_3
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCC
-=
-PRIMER_SEQUENCE_ID=template_mis_4
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCCACSCCCCCCCCCCCCCCCCA
-=
-PRIMER_SEQUENCE_ID=template_mis_5
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCCACTCCCCCCCCCCCCCCCCA
-=
-PRIMER_SEQUENCE_ID=template_mis_6
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-PRIMER_PRODUCT_SIZE_RANGE=36-300
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCACCCCCCCCACCCCCCCCCCCCCCCCCC
-=
-PRIMER_SEQUENCE_ID=template_mis_7
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-PRIMER_PRODUCT_SIZE_RANGE=36-300
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
-=
-PRIMER_SEQUENCE_ID=template_mis_8
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=11
-PRIMER_MAX_POLY_X=40
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-PRIMER_PRODUCT_SIZE_RANGE=36-300
-PRIMER_MAX_GC=100
-PRIMER_MAX_TM=100
-PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
-COMMENT=Should succeed
-=
-PRIMER_SEQUENCE_ID=template_mis_9
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=9
-PRIMER_MAX_POLY_X=40
-PRIMER_SELF_END=100
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-PRIMER_PRODUCT_SIZE_RANGE=36-300
-PRIMER_MAX_GC=100
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
-COMMENT=Should succeed
-=
-PRIMER_SEQUENCE_ID=template_mis_10
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=6.7
-PRIMER_MAX_POLY_X=40
-PRIMER_SELF_END=100
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-PRIMER_PRODUCT_SIZE_RANGE=36-300
-PRIMER_MAX_GC=100
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
-COMMENT=Should fail
-=

Deleted: trunk/packages/primer3/branches/upstream/current/test/primer_template_mispriming_output
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_template_mispriming_output	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_template_mispriming_output	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,386 +0,0 @@
-PRIMER_SEQUENCE_ID=template_mis_1
-PRIMER_NUM_RETURN=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
-PRIMER_PAIR_PENALTY=0.9341
-PRIMER_LEFT_PENALTY=0.323851
-PRIMER_RIGHT_PENALTY=0.610234
-PRIMER_LEFT_SEQUENCE=Gatgcgtacgatccatgcta
-PRIMER_RIGHT_SEQUENCE=tagcggcctagtgtgtgtgt
-PRIMER_LEFT=20,20
-PRIMER_RIGHT=131,20
-PRIMER_LEFT_TM=59.676
-PRIMER_RIGHT_TM=59.390
-PRIMER_LEFT_GC_PERCENT=50.000
-PRIMER_RIGHT_GC_PERCENT=55.000
-PRIMER_LEFT_SELF_ANY=8.00
-PRIMER_RIGHT_SELF_ANY=4.00
-PRIMER_LEFT_SELF_END=2.00
-PRIMER_RIGHT_SELF_END=0.00
-PRIMER_LEFT_END_STABILITY=7.5000
-PRIMER_RIGHT_END_STABILITY=6.4000
-PRIMER_LEFT_TEMPLATE_MISPRIMING=6.0000
-PRIMER_RIGHT_TEMPLATE_MISPRIMING=7.0000
-PRIMER_PAIR_COMPL_ANY=4.00
-PRIMER_PAIR_COMPL_END=2.00
-PRIMER_PRODUCT_SIZE=112
-PRIMER_PAIR_TEMPLATE_MISPRIMING=13.00
-=
-PRIMER_SEQUENCE_ID=template_mis_2
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTG
-PRIMER_WARNING=Left primer is unacceptable: High self complementarity
-PRIMER_RIGHT_EXPLAIN=considered 1240, low tm 698, high tm 374, high any compl 13, high end compl 34, ok 121
-PRIMER_PAIR_EXPLAIN=considered 242, ok 242
-PRIMER_PAIR_PENALTY=2600.1166
-PRIMER_LEFT_PENALTY=0.102704
-PRIMER_RIGHT_PENALTY=0.013916
-PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_SEQUENCE=gatatCAGTGTGTACATGGCGG
-PRIMER_LEFT=32,23
-PRIMER_RIGHT=197,22
-PRIMER_LEFT_TM=62.054
-PRIMER_RIGHT_TM=60.278
-PRIMER_LEFT_GC_PERCENT=43.478
-PRIMER_RIGHT_GC_PERCENT=50.000
-PRIMER_LEFT_SELF_ANY=12.00
-PRIMER_RIGHT_SELF_ANY=6.00
-PRIMER_LEFT_SELF_END=3.00
-PRIMER_RIGHT_SELF_END=1.00
-PRIMER_LEFT_END_STABILITY=6.5000
-PRIMER_RIGHT_END_STABILITY=12.9000
-PRIMER_LEFT_TEMPLATE_MISPRIMING=23.0000
-PRIMER_RIGHT_TEMPLATE_MISPRIMING=17.0000
-PRIMER_PAIR_COMPL_ANY=4.00
-PRIMER_PAIR_COMPL_END=2.00
-PRIMER_PRODUCT_SIZE=166
-PRIMER_PAIR_TEMPLATE_MISPRIMING=26.00
-=
-PRIMER_SEQUENCE_ID=template_mis_3
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCC
-PRIMER_WARNING=Left primer is unacceptable: High self complementarity; Right primer is unacceptable: Unacceptable GC content/Tm too high/Long poly-X
-PRIMER_PAIR_EXPLAIN=considered 2, ok 2
-PRIMER_PAIR_PENALTY=2601.0969
-PRIMER_LEFT_PENALTY=0.102704
-PRIMER_RIGHT_PENALTY=0.994170
-PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGG
-PRIMER_LEFT=32,23
-PRIMER_RIGHT=240,18
-PRIMER_LEFT_TM=62.054
-PRIMER_RIGHT_TM=79.883
-PRIMER_LEFT_GC_PERCENT=43.478
-PRIMER_RIGHT_GC_PERCENT=100.000
-PRIMER_LEFT_SELF_ANY=12.00
-PRIMER_RIGHT_SELF_ANY=0.00
-PRIMER_LEFT_SELF_END=3.00
-PRIMER_RIGHT_SELF_END=0.00
-PRIMER_LEFT_END_STABILITY=6.5000
-PRIMER_RIGHT_END_STABILITY=12.4000
-PRIMER_LEFT_TEMPLATE_MISPRIMING=23.0000
-PRIMER_RIGHT_TEMPLATE_MISPRIMING=3.0000
-PRIMER_PAIR_COMPL_ANY=2.00
-PRIMER_PAIR_COMPL_END=0.00
-PRIMER_PRODUCT_SIZE=209
-PRIMER_PAIR_TEMPLATE_MISPRIMING=26.00
-=
-PRIMER_SEQUENCE_ID=template_mis_4
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCCACSCCCCCCCCCCCCCCCCA
-PRIMER_WARNING=Unrecognized base in input sequence; Left primer is unacceptable: High self complementarity; Right primer is unacceptable: Unacceptable GC content/Tm too high/Long poly-X
-PRIMER_PAIR_EXPLAIN=considered 2, ok 2
-PRIMER_PAIR_PENALTY=2701.0969
-PRIMER_LEFT_PENALTY=0.102704
-PRIMER_RIGHT_PENALTY=0.994170
-PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGG
-PRIMER_LEFT=23,23
-PRIMER_RIGHT=231,18
-PRIMER_LEFT_TM=62.054
-PRIMER_RIGHT_TM=79.883
-PRIMER_LEFT_GC_PERCENT=43.478
-PRIMER_RIGHT_GC_PERCENT=100.000
-PRIMER_LEFT_SELF_ANY=12.00
-PRIMER_RIGHT_SELF_ANY=0.00
-PRIMER_LEFT_SELF_END=3.00
-PRIMER_RIGHT_SELF_END=0.00
-PRIMER_LEFT_END_STABILITY=6.5000
-PRIMER_RIGHT_END_STABILITY=12.4000
-PRIMER_LEFT_TEMPLATE_MISPRIMING=23.0000
-PRIMER_RIGHT_TEMPLATE_MISPRIMING=16.0000
-PRIMER_PAIR_COMPL_ANY=2.00
-PRIMER_PAIR_COMPL_END=0.00
-PRIMER_PRODUCT_SIZE=209
-PRIMER_PAIR_TEMPLATE_MISPRIMING=27.00
-=
-PRIMER_SEQUENCE_ID=template_mis_5
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCCACTCCCCCCCCCCCCCCCCA
-PRIMER_WARNING=Left primer is unacceptable: High self complementarity; Right primer is unacceptable: Unacceptable GC content/Tm too high/Long poly-X
-PRIMER_PAIR_EXPLAIN=considered 2, ok 2
-PRIMER_PAIR_PENALTY=2701.0969
-PRIMER_LEFT_PENALTY=0.102704
-PRIMER_RIGHT_PENALTY=0.994170
-PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGG
-PRIMER_LEFT=23,23
-PRIMER_RIGHT=231,18
-PRIMER_LEFT_TM=62.054
-PRIMER_RIGHT_TM=79.883
-PRIMER_LEFT_GC_PERCENT=43.478
-PRIMER_RIGHT_GC_PERCENT=100.000
-PRIMER_LEFT_SELF_ANY=12.00
-PRIMER_RIGHT_SELF_ANY=0.00
-PRIMER_LEFT_SELF_END=3.00
-PRIMER_RIGHT_SELF_END=0.00
-PRIMER_LEFT_END_STABILITY=6.5000
-PRIMER_RIGHT_END_STABILITY=12.4000
-PRIMER_LEFT_TEMPLATE_MISPRIMING=23.0000
-PRIMER_RIGHT_TEMPLATE_MISPRIMING=16.0000
-PRIMER_PAIR_COMPL_ANY=2.00
-PRIMER_PAIR_COMPL_END=0.00
-PRIMER_PRODUCT_SIZE=209
-PRIMER_PAIR_TEMPLATE_MISPRIMING=27.00
-=
-PRIMER_SEQUENCE_ID=template_mis_6
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-PRIMER_PRODUCT_SIZE_RANGE=36-300
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCACCCCCCCCACCCCCCCCCCCCCCCCCC
-PRIMER_WARNING=Left primer is unacceptable: High self complementarity; Right primer is unacceptable: Unacceptable GC content/Tm too high/Long poly-X
-PRIMER_PAIR_EXPLAIN=considered 1, ok 1
-PRIMER_PAIR_PENALTY=1901.0969
-PRIMER_LEFT_PENALTY=0.102704
-PRIMER_RIGHT_PENALTY=0.994170
-PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGG
-PRIMER_LEFT=0,23
-PRIMER_RIGHT=67,18
-PRIMER_LEFT_TM=62.054
-PRIMER_RIGHT_TM=79.883
-PRIMER_LEFT_GC_PERCENT=43.478
-PRIMER_RIGHT_GC_PERCENT=100.000
-PRIMER_LEFT_SELF_ANY=12.00
-PRIMER_RIGHT_SELF_ANY=0.00
-PRIMER_LEFT_SELF_END=3.00
-PRIMER_RIGHT_SELF_END=0.00
-PRIMER_LEFT_END_STABILITY=6.5000
-PRIMER_RIGHT_END_STABILITY=12.4000
-PRIMER_LEFT_TEMPLATE_MISPRIMING=3.0000
-PRIMER_RIGHT_TEMPLATE_MISPRIMING=16.0000
-PRIMER_PAIR_COMPL_ANY=2.00
-PRIMER_PAIR_COMPL_END=0.00
-PRIMER_PRODUCT_SIZE=68
-PRIMER_PAIR_TEMPLATE_MISPRIMING=19.00
-=
-PRIMER_SEQUENCE_ID=template_mis_7
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-PRIMER_PRODUCT_SIZE_RANGE=36-300
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
-PRIMER_WARNING=Left primer is unacceptable: High self complementarity; Right primer is unacceptable: Unacceptable GC content/Tm too high/Long poly-X
-PRIMER_PAIR_EXPLAIN=considered 1, ok 1
-PRIMER_PAIR_PENALTY=1276.0969
-PRIMER_LEFT_PENALTY=0.102704
-PRIMER_RIGHT_PENALTY=0.994170
-PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATGat
-PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGG
-PRIMER_LEFT=0,23
-PRIMER_RIGHT=67,18
-PRIMER_LEFT_TM=62.054
-PRIMER_RIGHT_TM=79.883
-PRIMER_LEFT_GC_PERCENT=43.478
-PRIMER_RIGHT_GC_PERCENT=100.000
-PRIMER_LEFT_SELF_ANY=12.00
-PRIMER_RIGHT_SELF_ANY=0.00
-PRIMER_LEFT_SELF_END=3.00
-PRIMER_RIGHT_SELF_END=0.00
-PRIMER_LEFT_END_STABILITY=6.5000
-PRIMER_RIGHT_END_STABILITY=12.4000
-PRIMER_LEFT_TEMPLATE_MISPRIMING=3.0000
-PRIMER_RIGHT_TEMPLATE_MISPRIMING=9.7500
-PRIMER_PAIR_COMPL_ANY=2.00
-PRIMER_PAIR_COMPL_END=0.00
-PRIMER_PRODUCT_SIZE=68
-PRIMER_PAIR_TEMPLATE_MISPRIMING=12.75
-=
-PRIMER_SEQUENCE_ID=template_mis_8
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=11
-PRIMER_MAX_POLY_X=40
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-PRIMER_PRODUCT_SIZE_RANGE=36-300
-PRIMER_MAX_GC=100
-PRIMER_MAX_TM=100
-PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
-COMMENT=Should succeed
-PRIMER_LEFT_EXPLAIN=considered 75, too many Ns 34, low tm 14, high any compl 7, ok 20
-PRIMER_PAIR_EXPLAIN=considered 20, high any compl 11, high end compl 5, ok 4
-PRIMER_PAIR_PENALTY=1076.0792
-PRIMER_LEFT_PENALTY=0.085063
-PRIMER_RIGHT_PENALTY=0.994170
-PRIMER_LEFT_SEQUENCE=CCCCCCCCAAAAAAAAAA
-PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGG
-PRIMER_LEFT=32,18
-PRIMER_RIGHT=67,18
-PRIMER_LEFT_TM=61.701
-PRIMER_RIGHT_TM=79.883
-PRIMER_LEFT_GC_PERCENT=44.444
-PRIMER_RIGHT_GC_PERCENT=100.000
-PRIMER_LEFT_SELF_ANY=0.00
-PRIMER_RIGHT_SELF_ANY=0.00
-PRIMER_LEFT_SELF_END=0.00
-PRIMER_RIGHT_SELF_END=0.00
-PRIMER_LEFT_END_STABILITY=7.6000
-PRIMER_RIGHT_END_STABILITY=12.4000
-PRIMER_LEFT_TEMPLATE_MISPRIMING=4.0000
-PRIMER_RIGHT_TEMPLATE_MISPRIMING=9.7500
-PRIMER_PAIR_COMPL_ANY=8.00
-PRIMER_PAIR_COMPL_END=0.00
-PRIMER_PRODUCT_SIZE=36
-PRIMER_PAIR_TEMPLATE_MISPRIMING=10.75
-=
-PRIMER_SEQUENCE_ID=template_mis_9
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=9
-PRIMER_MAX_POLY_X=40
-PRIMER_SELF_END=100
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-PRIMER_PRODUCT_SIZE_RANGE=36-300
-PRIMER_MAX_GC=100
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
-COMMENT=Should succeed
-PRIMER_LEFT_EXPLAIN=considered 75, too many Ns 34, low tm 14, high any compl 7, ok 20
-PRIMER_RIGHT_EXPLAIN=considered 177, too many Ns 22,high template mispriming score 5, ok 150
-PRIMER_PAIR_EXPLAIN=considered 3004, unacceptable product size 2784, high any compl 199, ok 21
-PRIMER_PAIR_PENALTY=776.1163
-PRIMER_LEFT_PENALTY=0.085063
-PRIMER_RIGHT_PENALTY=1.031264
-PRIMER_LEFT_SEQUENCE=CCCCCCCCAAAAAAAAAA
-PRIMER_RIGHT_SEQUENCE=GGGGGGGGGGGGGGGGGGTTTTT
-PRIMER_LEFT=32,18
-PRIMER_RIGHT=67,23
-PRIMER_LEFT_TM=61.701
-PRIMER_RIGHT_TM=80.625
-PRIMER_LEFT_GC_PERCENT=44.444
-PRIMER_RIGHT_GC_PERCENT=78.261
-PRIMER_LEFT_SELF_ANY=0.00
-PRIMER_RIGHT_SELF_ANY=0.00
-PRIMER_LEFT_SELF_END=0.00
-PRIMER_RIGHT_SELF_END=0.00
-PRIMER_LEFT_END_STABILITY=7.6000
-PRIMER_RIGHT_END_STABILITY=7.6000
-PRIMER_LEFT_TEMPLATE_MISPRIMING=4.0000
-PRIMER_RIGHT_TEMPLATE_MISPRIMING=6.7500
-PRIMER_PAIR_COMPL_ANY=8.00
-PRIMER_PAIR_COMPL_END=5.00
-PRIMER_PRODUCT_SIZE=36
-PRIMER_PAIR_TEMPLATE_MISPRIMING=7.75
-=
-PRIMER_SEQUENCE_ID=template_mis_10
-PRIMER_NUM_RETURN=1
-PRIMER_EXPLAIN_FLAG=1
-PRIMER_PICK_ANYWAY=1
-PRIMER_MAX_TEMPLATE_MISPRIMING=6.7
-PRIMER_MAX_POLY_X=40
-PRIMER_SELF_END=100
-PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
-PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
-PRIMER_WT_SIZE_GT=0
-PRIMER_WT_SIZE_LT=0
-PRIMER_WT_TM_GT=.05
-PRIMER_WT_TM_LT=.05
-PRIMER_LIBERAL_BASE=1
-PRIMER_PRODUCT_SIZE_RANGE=36-300
-PRIMER_MAX_GC=100
-SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
-COMMENT=Should fail
-PRIMER_LEFT_EXPLAIN=considered 75, too many Ns 34, low tm 14, high any compl 7,high template mispriming score 2, ok 18
-PRIMER_RIGHT_EXPLAIN=considered 177, too many Ns 22,high template mispriming score 19, ok 136
-PRIMER_PAIR_EXPLAIN=considered 2718, unacceptable product size 2710, high any compl 8, ok 0
-=

Deleted: trunk/packages/primer3/branches/upstream/current/test/primer_test.pl
===================================================================
--- trunk/packages/primer3/branches/upstream/current/test/primer_test.pl	2006-09-22 05:38:11 UTC (rev 121)
+++ trunk/packages/primer3/branches/upstream/current/test/primer_test.pl	2006-09-22 14:39:44 UTC (rev 122)
@@ -1,192 +0,0 @@
-# Regression test driver for primer3 executable.
-#
-# Usage: perl primer_test.pl [<primer3>]
-#
-# <primer3> defaults to primer3, in which case the executable
-# run is ../src/primer3.
-#
-# If <primer3> is specified, the executable run is 
-# ../src/<primer3>.
-#
-# Stderr difference tests for fatal errors are performed only
-# if <primer3> is 'primer3' (because the executable name
-# is part of the text written to stderr).
-
-$ENV{TC_SILENT} = '1';	# TestCenter proofed executables will not 
-                        # write extra stuff to std{err,out}, and
-                        # consequently will not cause spurious diff's.
-
-$ENV{TC_RESULTDIR} = './tc_results'; # Directory for testcenter results.
-    
-
-$exe = 'primer3_core';
-$exe = $ARGV[0] if defined $ARGV[0];
-$p1 =  "../src/$exe";
-$EXIT_STAT = 0;
-
-die "Cannot execute $p1" unless -x $p1;
-
-print STDERR "\n\n$0: testing $p1 ", `date`;
-
-test_fatal_errors($p1);
-
-my $cmd;
-for $test (
-           'primer_boundary',   # Put the quickest tests first.
-           'primer_internal',
-           'primer_boundary_formatted',
-           'primer_internal_formatted',
-	   'primer_start_codon',
-           'primer_boundary1',
-           'primer_internal1',
-	   'primer_task',
-	   'primer_task_formatted',
-           'primer_boundary1_formatted',
-           'primer_internal1_formatted',
-	   'primer_check',
-	   'primer_must_use',
-	   'primer_must_use_formatted',
-           'primer_syntax',
-           'primer_end_pathology',
-           'primer_num_best',
-	   'primer_quality_boundary',
-	   'primer_obj_fn',
-           'primer',
-           'primer1',
-           'primer_mispriming',
-           'primer_mispriming_formatted',
-           'primer_mispriming_boundary1',
-           'primer_mispriming_boundary1_formatted',
-           'primer_mispriming_boundary2',
-           'primer_mispriming_boundary2_formatted',
-           'primer_mispriming_long_lib',
-           'primer_rat',
-           'primer_human',
-           'primer_ch',
-           'long_seq',
-           'primer_position_penalty',
-           'primer_position_penalty_formatted',
-	   'primer_template_mispriming',
-	   'primer_lib_amb_codes',
-	   ) {
-    print STDERR "$test...";
-    $testx = $test;
-    $testx =~ s/_formatted$//;
-    $input = $testx . '_input';
-    $output = $test . '_output';
-    $tmp = $test . '_tmp';
-    if ($test ne 'primer_ch') {
-	die "Cannot read $input"  unless -r $input;
-	die "Cannot read $output"  unless -r $output;
-    }
-
-    if ($test eq 'primer' || $test eq 'primer1') {
-	$list_tmp = $test.'_list_tmp';
-	# We need to chdir below because primer3 puts the 'list' files
-        # in the current working directory.  Therefore we adjust
-	# the TestCenter result directory.
-	$cmd = "rm -f $list_tmp/*.*; "
-	    . "cd $list_tmp; ../$p1 -strict_tags <../$input >../$tmp";
-	$ENV{TC_COMMENT} = $cmd;
-	# Reset the TestCenter result directory.
-	$save_results = $ENV{TC_RESULTDIR};
-	$ENV{TC_RESULTDIR} = "../$save_results";
-	$r = system $cmd;
-	$ENV{TC_RESULTDIR} = $save_results;
-	$ENV{TC_COMMENT} = '';
-    } elsif ($test =~ /formatted$/) {
-	$cmd = "$p1 -strict_tags -format_output <$input >$tmp";
-	$ENV{TC_COMMENT} = $cmd;
-	$r = system $cmd;
-	$ENV{TC_COMMENT} = '';
-    } else {
-	# We do not distribute primer_ch_input.
-	unless ($test eq 'primer_ch' && !-e 'primer_ch_input') {
-	    $cmd = "$p1 -strict_tags <$input >$tmp";
-	    $ENV{TC_COMMENT} = $cmd;
-	    $r = system $cmd;
-	    $ENV{TC_COMMENT} = '';
-	}
-    }
-
-    unless ($r == 0) {
-	print STDERR "NON-0 EXIT: $r\n";
-	$EXIT_STAT = -1;
-	next;
-    }
-
-    $r = system "diff $output $tmp"
-	unless ($test eq 'primer_ch' && !-e 'primer_ch_input');
-
-    if ($r == 0) {
-	print STDERR "OK\n";
-    } else {
-	print STDERR "FAILED\n";
-	$EXIT_STAT = -1;
-    }
-    if ($test eq 'primer' || $test eq 'primer1') {
-	$list_tmp = $test.'_list_tmp';
-	$list_last = $test.'_list_last';
-	if  (-e "$list_tmp/.cvsignore") {
-	    $r = system "mv $list_tmp/.cvsignore ./saved.cvsignore; "
-		. "diff $list_last $list_tmp";
-	    system "mv ./saved.cvsignore $list_tmp/.cvsignore";
-	} else {
-	    $r = system "diff $list_tmp $list_last";
-	}
-	print STDERR "$test list files ";
-	if ($r == 0) {
-	    print STDERR "OK\n";
-	} else { 
-	    print STDERR "FAILED\n";
-	    $EXIT_STAT = -1;
-	}
-    }
-}
-
-unlink("./core") if -e "./core";
-print STDERR "DONE\n";
-exit ($EXIT_STAT);
-
-sub test_fatal_errors {
-    my $exe = $_[0];
-    my $skip_stderr = 0;
-    if ($exe ne '../src/primer3_core') {
-	print STDERR "Skipping comparisons of stderr because ",
-	"executable is not ../src/primer3_core";
-	$skip_stderr = 1;
-    }
-    my $inputs = `ls primer_global_err/*.in`;
-    my @inputs = split /\s/, $inputs;
-    my ($root, $cmd, $r);
-    my $problem = 0;
-    print STDERR "\ntesting fatal errors...";
-    for (@inputs) {
-	($root) = /(.*)\.in$/;
-	$cmd = "$exe <$_ > $root.tmp 2> $root.tmp2";
-	$ENV{TC_COMMENT} = $cmd;
-	system $cmd;
-	$ENV{TC_COMMENT} = '';
-	if ($? == 0) {
-	    $r = $? >> 8;
-	    print STDERR "\nErroneous 0 exit status ($?) from command $cmd\n";
-	    $problem = 1;
-	}
-	$r = system "diff $root.out $root.tmp";
-	if ($r != 0) {
-	    print STDERR
-		"Difference found between $root.out and $root.tmp\n\n";
-	    $problem = 1;
-	}
-	unless ($skip_stderr) {
-	    $r = system "diff $root.out2 $root.tmp2";
-	    if ($r != 0) {
-		print STDERR
-		    "\nDifference found between $root.out2 and $root.tmp2\n\n";
-		$problem = 1;
-	    }
-	}
-    }
-    print STDERR $problem ? "FAILED" : "OK" ,"\n";
-}
-