Fixed compl_end calculation

src/libprimer3.cc

@@ -3958,7 +3958,7 @@ characterize_pair(p3retval *retval,
                   int update_stats) {
   char s1[MAX_PRIMER_LENGTH+1], s2[MAX_PRIMER_LENGTH+1],
     s1_rev[MAX_PRIMER_LENGTH+1], s2_rev[MAX_PRIMER_LENGTH+1];
-  double compl_end;
+  double compl_end, compl_end2;
   pair_stats *pair_expl = &retval->best_pairs.expl;
   int must_use = 0;
   double min_oligo_tm;
@@ -4294,16 +4294,21 @@ characterize_pair(p3retval *retval,
     if (!must_use) return PAIR_FAILED;
   }
    /* thermodynamic approach */
-   if (pa->thermodynamic_oligo_alignment==1 && 
-       ((compl_end = align_thermod(s2, s1_rev, thal_arg_to_use->end1)) > ppair->compl_end || 
-        (compl_end = align_thermod(s2, s1_rev, thal_arg_to_use->end2)) > ppair->compl_end)) {
-      if (compl_end > pa->p_args.max_self_end_th) {
+   if (pa->thermodynamic_oligo_alignment==1) {
+     compl_end = align_thermod(s2, s1_rev, thal_arg_to_use->end1);
+     compl_end2 = align_thermod(s2, s1_rev, thal_arg_to_use->end2);
+     if (compl_end2 > compl_end) {
+       compl_end = compl_end2;
+     }
+     if (compl_end > ppair->compl_end) {
+       if (compl_end > pa->p_args.max_self_end_th) {
          if (update_stats) {
             pair_expl->compl_end++; 
          }
          if (!must_use) return PAIR_FAILED;
-      }
-      ppair->compl_end = compl_end; /* Is this correct? even if end1 is bigger we write end2?? */
+       }
+       ppair->compl_end = compl_end;
+     }
    }
 
   /* ============================================================= */
@@ -4879,16 +4884,15 @@ recalc_pair_sec_struct(primer_pair *ppair,
           free(end3.sec_struct);
           end3.sec_struct = NULL;
         }
-        /* most likely wrong - should not be within this else */
-        thal((const unsigned char *) s2, (const unsigned char *) s1_rev, thal_arg_to_use->end2, THL_STRUCT, &end4); /* Triinu Please check */
-        if (ppair->compl_end < end4.temp) {
-          ppair->compl_end = end4.temp;
-          save_overwrite_sec_struct(&ppair->compl_end_struct, end4.sec_struct);
-        } else {
-          if (end4.sec_struct != NULL) {
-            free(end4.sec_struct);
-            end4.sec_struct = NULL;
-          }
+      }
+      thal((const unsigned char *) s2, (const unsigned char *) s1_rev, thal_arg_to_use->end2, THL_STRUCT, &end4); /* Triinu Please check */
+      if (ppair->compl_end < end4.temp) {
+        ppair->compl_end = end4.temp;
+        save_overwrite_sec_struct(&ppair->compl_end_struct, end4.sec_struct);
+      } else {
+        if (end4.sec_struct != NULL) {
+          free(end4.sec_struct);
+          end4.sec_struct = NULL;
         }
       }
     }

src/primer3_manual.htm

@@ -127,19 +127,24 @@ <h2><a id="citationRequest">3. CITING PRIMER3</a></h2>
 * Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M and Rozen SG.<br>
 Primer3--new capabilities and interfaces.<br>
 Nucleic Acids Res. 2012 Aug 1;40(15):e115.<br>
-<br>
 The paper is available at
 <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424584/">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424584/</a><br>
 <br>
 and <br>
 <br>
 * Koressaar T and Remm M.<br>
 Enhancements and modifications of primer design program Primer3.<br>
-Bioinformatics 2007;23(10):1289-91.<br>
-<br>
-The papers is available at<br>
+Bioinformatics 2007;23(10):1289-1291.<br>
+The paper is available at
 <a href="https://www.ncbi.nlm.nih.gov/pubmed/17379693">https://www.ncbi.nlm.nih.gov/pubmed/17379693</a><br>
 <br>
+If you use masker function, please cite:<br>
+* Koressaar T, Lepamets M, Kaplinski L, Raime K, Andreson R and Remm M.<br>
+Primer3_masker: integrating masking of template sequence with primer design software.<br>
+Bioinformatics 2018;34(11):1937-1938.<br>
+The paper is available at
+<a href="https://www.ncbi.nlm.nih.gov/pubmed/29360956">https://www.ncbi.nlm.nih.gov/pubmed/29360956</a><br>
+<br>
 Source code available at <a href="https://github.com/primer3-org/primer3">https://github.com/primer3-org/primer3</a>.</p>
 <h2><a id="licenseExplain">4. FAIR USE OF PRIMER3</a></h2>
 <p>
@@ -501,6 +506,11 @@ <h2><a id="installMac">8. INSTALLATION INSTRUCTIONS - Mac OSX</a></h2>
 <br>
 The first option is just a shortcut to the second.</p>
 <h2><a id="installWindows">9. INSTALLATION INSTRUCTIONS - WINDOWS</a></h2>
+<p>Functionality warning<br>
+=====================<br>
+<br>
+The windows version does not support the masker functionality.
+</p>
 <p>How to install this software<br>
 ============================<br>
 <br>
@@ -520,8 +530,8 @@ <h2><a id="installWindows">9. INSTALLATION INSTRUCTIONS - WINDOWS</a></h2>
 Compile Primer3<br>
 ---------------<br>
 <br>
-1. Download and install MinGW64 from<br>
-   https://sourceforge.net/projects/mingw-w64/files/latest/download
+1. Download and install TDM-GCC MinGW Compiler from<br>
+   https://sourceforge.net/projects/tdm-gcc/
 2. Open the windows command line and change to the src folder in
    Primer3<br>
 3. Run: mingw32-make TESTOPTS=--windows<br>

test/primer1_th_output

@@ -559,7 +559,7 @@ PRIMER_RIGHT_1_HAIRPIN_TH=0.00
 PRIMER_LEFT_1_END_STABILITY=3.5100
 PRIMER_RIGHT_1_END_STABILITY=3.7200
 PRIMER_PAIR_1_COMPL_ANY_TH=38.19
-PRIMER_PAIR_1_COMPL_END_TH=35.05
+PRIMER_PAIR_1_COMPL_END_TH=39.91
 PRIMER_PAIR_1_PRODUCT_SIZE=100
 PRIMER_PAIR_2_PENALTY=1.129499
 PRIMER_LEFT_2_PENALTY=0.024450
@@ -659,7 +659,7 @@ PRIMER_RIGHT_0_HAIRPIN_TH=0.00
 PRIMER_LEFT_0_END_STABILITY=3.0200
 PRIMER_RIGHT_0_END_STABILITY=4.0000
 PRIMER_PAIR_0_COMPL_ANY_TH=10.52
-PRIMER_PAIR_0_COMPL_END_TH=9.69
+PRIMER_PAIR_0_COMPL_END_TH=10.76
 PRIMER_PAIR_0_PRODUCT_SIZE=159
 PRIMER_PAIR_1_PENALTY=0.227271
 PRIMER_LEFT_1_PENALTY=0.179947
@@ -785,7 +785,7 @@ PRIMER_RIGHT_0_HAIRPIN_TH=32.27
 PRIMER_LEFT_0_END_STABILITY=3.3200
 PRIMER_RIGHT_0_END_STABILITY=3.3200
 PRIMER_PAIR_0_COMPL_ANY_TH=17.42
-PRIMER_PAIR_0_COMPL_END_TH=6.65
+PRIMER_PAIR_0_COMPL_END_TH=10.45
 PRIMER_PAIR_0_PRODUCT_SIZE=109
 PRIMER_PAIR_1_PENALTY=0.200309
 PRIMER_LEFT_1_PENALTY=0.099786
@@ -807,7 +807,7 @@ PRIMER_RIGHT_1_HAIRPIN_TH=32.27
 PRIMER_LEFT_1_END_STABILITY=5.5400
 PRIMER_RIGHT_1_END_STABILITY=3.3200
 PRIMER_PAIR_1_COMPL_ANY_TH=21.31
-PRIMER_PAIR_1_COMPL_END_TH=18.43
+PRIMER_PAIR_1_COMPL_END_TH=21.14
 PRIMER_PAIR_1_PRODUCT_SIZE=180
 PRIMER_PAIR_2_PENALTY=0.200309
 PRIMER_LEFT_2_PENALTY=0.099786
@@ -829,7 +829,7 @@ PRIMER_RIGHT_2_HAIRPIN_TH=32.27
 PRIMER_LEFT_2_END_STABILITY=3.9300
 PRIMER_RIGHT_2_END_STABILITY=3.3200
 PRIMER_PAIR_2_COMPL_ANY_TH=20.46
-PRIMER_PAIR_2_COMPL_END_TH=19.79
+PRIMER_PAIR_2_COMPL_END_TH=22.80
 PRIMER_PAIR_2_PRODUCT_SIZE=182
 PRIMER_PAIR_3_PENALTY=0.295718
 PRIMER_LEFT_3_PENALTY=0.252674
@@ -941,7 +941,7 @@ PRIMER_RIGHT_1_HAIRPIN_TH=0.00
 PRIMER_LEFT_1_END_STABILITY=3.5100
 PRIMER_RIGHT_1_END_STABILITY=3.7200
 PRIMER_PAIR_1_COMPL_ANY_TH=38.19
-PRIMER_PAIR_1_COMPL_END_TH=35.05
+PRIMER_PAIR_1_COMPL_END_TH=39.91
 PRIMER_PAIR_1_PRODUCT_SIZE=100
 PRIMER_PAIR_2_PENALTY=1.129499
 PRIMER_LEFT_2_PENALTY=0.024450