Allowing revcomp makes no sense

primer3-org · Aug 5, 2024 · 027eb29 · 027eb29
1 parent 8cc57fe
commit 027eb29
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Showing 3 changed files with 61 additions and 4 deletions.
diff --git a/src/libprimer3.cc b/src/libprimer3.cc
@@ -7345,7 +7345,7 @@ _pr_data_control(const p3_global_settings *pa,
                             "Specified right primer not in Included Region");
       else if (sa->left_input) {
         if (strcmp(sa->left_input, s1) == 0)
-          pr_append_new_chunk(warning,
+          pr_append_new_chunk(nonfatal_err,
                             "Specified left and right primer are reverse complementary");
         if (strcmp(sa->left_input, sa->right_input) == 0)
           pr_append_new_chunk(warning,

diff --git a/test/primer_new_tasks_formatted_output b/test/primer_new_tasks_formatted_output
@@ -2287,7 +2287,7 @@ Left     954     0     0     0   939     0     0     0     0     0     0     0
 Right    954     0     0     0   951     0     0     0     0     0     0     0     0     3
 Pair Stats:
 considered 0, ok 0
-libprimer3 release 2.2.3
+libprimer3 release 2.6.1
 
 
 PRIMER PICKING RESULTS FOR rev_comp_primers
@@ -2296,5 +2296,34 @@ INPUT PROBLEM: Specified left and right primer are reverse complementary
 
 PRIMER PICKING RESULTS FOR identical_primers
 
-INPUT PROBLEM: Specified left and right primer are identical
+No mispriming library specified
+Using 1-based sequence positions
+WARNING: Specified left and right primer are identical
+
+OLIGO            start  len      tm     gc%   any    3' seq
+LEFT PRIMER          1   23   62.46   47.83  2.00  1.00 CACCCCCATCAAACTCTTACTCA
+RIGHT PRIMER        60   23   62.46   47.83  2.00  1.00 CACCCCCATCAAACTCTTACTCA
+SEQUENCE SIZE: 60
+INCLUDED REGION SIZE: 60
+
+PRODUCT SIZE: 60, PAIR ANY COMPL: 2.00, PAIR 3' COMPL: 1.00
+
+    1 CACCCCCATCAAACTCTTACTCANNNNNNNNNNNNNNTGAGTAAGAGTTTGATGGGGGTG
+      >>>>>>>>>>>>>>>>>>>>>>>              <<<<<<<<<<<<<<<<<<<<<<<
+
+KEYS (in order of precedence):
+>>>>>> left primer
+<<<<<< right primer
+
+
+Statistics
+         con   too    in    in   not          no    tm    tm  high  high        high      
+         sid  many   tar  excl    ok   bad    GC   too   too   any    3'  poly   end      
+        ered    Ns   get   reg   reg   GC% clamp   low  high compl compl     X  stab    ok
+Left       1     0     0     0     0     0     0     0     0     0     0     0     0     1
+Right      1     0     0     0     0     0     0     0     0     0     0     0     0     1
+Pair Stats:
+considered 1, primer in pair overlaps a primer in a better pair 1, ok 1
+libprimer3 release 2.6.1
+
 
diff --git a/test/primer_new_tasks_output b/test/primer_new_tasks_output
@@ -1898,5 +1898,33 @@ SEQUENCE_ID=identical_primers
 PRIMER_TASK=check_primers
 SEQUENCE_PRIMER=CACCCCCATCAAACTCTTACTCA
 SEQUENCE_PRIMER_REVCOMP=CACCCCCATCAAACTCTTACTCA
-PRIMER_ERROR=Specified left and right primer are identical
+PRIMER_WARNING=Specified left and right primer are identical
+PRIMER_LEFT_EXPLAIN=considered 1, ok 1
+PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
+PRIMER_PAIR_EXPLAIN=considered 1, primer in pair overlaps a primer in a better pair 1, ok 1
+PRIMER_LEFT_NUM_RETURNED=1
+PRIMER_RIGHT_NUM_RETURNED=1
+PRIMER_INTERNAL_NUM_RETURNED=0
+PRIMER_PAIR_NUM_RETURNED=1
+PRIMER_PAIR_0_PENALTY=10.914698
+PRIMER_LEFT_0_PENALTY=5.457349
+PRIMER_RIGHT_0_PENALTY=5.457349
+PRIMER_LEFT_0_SEQUENCE=CACCCCCATCAAACTCTTACTCA
+PRIMER_RIGHT_0_SEQUENCE=CACCCCCATCAAACTCTTACTCA
+PRIMER_LEFT_0=1,23
+PRIMER_RIGHT_0=60,23
+PRIMER_LEFT_0_TM=62.457
+PRIMER_RIGHT_0_TM=62.457
+PRIMER_LEFT_0_GC_PERCENT=47.826
+PRIMER_RIGHT_0_GC_PERCENT=47.826
+PRIMER_LEFT_0_SELF_ANY=2.00
+PRIMER_RIGHT_0_SELF_ANY=2.00
+PRIMER_LEFT_0_SELF_END=1.00
+PRIMER_RIGHT_0_SELF_END=1.00
+PRIMER_LEFT_0_END_STABILITY=6.4000
+PRIMER_RIGHT_0_END_STABILITY=6.4000
+PRIMER_PAIR_0_COMPL_ANY=2.00
+PRIMER_PAIR_0_COMPL_END=1.00
+PRIMER_PAIR_0_PRODUCT_SIZE=60
+PRIMER_PAIR_0_PRODUCT_TM=64.9
 =