2de160a334786c2168e379c5f02838f4aed40a3b
chmalee
  Thu Jul 27 12:20:35 2023 -0700
Fix two separate hgPcr related bugs. One, the primers entered by the user do not have to match the genome/transcript fully, and so when looking up the primers for showing mismatches we need to ensure we find them by relying on the psl qName rather than the primer file that holds the users input. Second, when clicking through to hgc, ensure that we check that the tStart and tEnd of the psl match what was clicked on so the right amplicon sequence can be shown, in the case that two separate searches that hit the same transcript are visible, refs #31784

diff --git src/hg/hgPcr/hgPcr.c src/hg/hgPcr/hgPcr.c
index 31f6dbd..f37fc3c 100644
--- src/hg/hgPcr/hgPcr.c
+++ src/hg/hgPcr/hgPcr.c
@@ -460,36 +460,34 @@
 printf("%s", "</CENTER></TD>\n");
 
 jsOnEventById("click", "Submit", "if ($('#wp_r').val()==='' || $('#wp_f').val()==='') "\
         "{ alert('Please specify at least a forward and reverse primer. Both input boxes need to be filled out.'); event.preventDefault(); }");
 
 printf("%s", "<TD><CENTER>\n");
 printf(" Min Good Match: ");
 cgiMakeIntVar("wp_good", minGood, 2);
 printf("%s", "</CENTER></TD>\n");
 
 printf("%s", "<TD><CENTER>\n");
 printf(" Flip Reverse Primer: ");
 cgiMakeCheckBox("wp_flipReverse", flipReverse);
 printf("%s", "</CENTER></TD>\n");
 
-#ifdef NOTNOW   // disabling until Chris gets back from vacation
 printf("%s", "<TD><CENTER>\n");
 printf(" Append to existing PCR result: ");
 cgiMakeCheckBox("wp_append", appendToResults);
 printf("%s", "</CENTER></TD>\n");
-#endif
 
 printf("</TR></TABLE><BR>");
 
 printf("</FORM>\n");
 
 /* Put up a second form who's sole purpose is to preserve state
  * when the user flips the genome button. */
 printf("<FORM ACTION=\"../cgi-bin/hgPcr\" METHOD=\"GET\" NAME=\"orgForm\">"
        "<input type=\"hidden\" name=\"wp_target\" value=\"\">\n"
        "<input type=\"hidden\" name=\"db\" value=\"\">\n"
        "<input type=\"hidden\" name=\"org\" value=\"\">\n"
        "<input type=\"hidden\" name=\"wp_f\" value=\"\">\n"
        "<input type=\"hidden\" name=\"wp_r\" value=\"\">\n"
        "<input type=\"hidden\" name=\"wp_size\" value=\"\">\n"
        "<input type=\"hidden\" name=\"wp_perfect\" value=\"\">\n"