be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

diff --git src/hg/hgPhyloPlace/hgPhyloPlace.c src/hg/hgPhyloPlace/hgPhyloPlace.c
index f3fb03e..ca2ac83 100644
--- src/hg/hgPhyloPlace/hgPhyloPlace.c
+++ src/hg/hgPhyloPlace/hgPhyloPlace.c
@@ -149,31 +149,32 @@
 webEndJWest();
 }
 
 #define CHECK_FILE_INPUT_JS "{ var $fileInput = $('input[name="seqFileVar"]');  " \
     "if ($fileInput && $fileInput[0] && $fileInput[0].files && !$fileInput[0].files.length) {" \
       " alert('Please choose a file first, then click the upload button.');" \
       " return false; " \
     "} else { return true; } }"
 
 static void inputForm()
 /* Ask the user for FASTA or VCF. */
 {
 printf("<form action='%s' name='mainForm' method=POST enctype='multipart/form-data'>\n\n",
        "hgPhyloPlace");
 cartSaveSession(cart);
-cgiMakeHiddenVar("db", "wuhCor1");
+char *db = "wuhCor1";
+cgiMakeHiddenVar("db", db);
 puts("  <div class='gbControl col-md-12'>");
 puts("<div class='readableWidth'>");
 puts("<p>Upload your SARS-CoV-2 sequence (FASTA or VCF file) to find the most similar\n"
      "complete, high-coverage samples from \n"
      "<a href='https://www.gisaid.org/' target='_blank'>GISAID</a>\n"
      "and your sequence's placement in the phylogenetic tree generated by the\n"
      "<a href='https://github.com/roblanf/sarscov2phylo' target='_blank'>sarscov2phylo</a>\n"
      "pipeline.\n"
      "Placement is performed by\n"
      "<a href='https://github.com/yatisht/usher' target=_blank>"
      "Ultrafast Sample placement on Existing tRee (UShER)</a> "
      "(<a href='https://www.biorxiv.org/content/10.1101/2020.09.26.314971v1' target=_blank>"
      "Turakhia <em>et al.</em></a>).  UShER also generates local subtrees to show samples "
      "in the context of the most closely related sequences.  The subtrees can be visualized "
      "as Genome Browser custom tracks and/or using "
@@ -189,39 +190,52 @@
      "<p>We do not store your information "
      "(aside from the information necessary to display results)\n"
      "and will not share it with others unless you choose to share your Genome Browser view.</p>\n"
      "<p>In order to enable rapid progress in SARS-CoV-2 research and genomic contact tracing,\n"
      "please share your SARS-CoV-2 sequences by submitting them to an "
      "<a href='https://ncbiinsights.ncbi.nlm.nih.gov/2020/08/17/insdc-covid-data-sharing/' "
      "target=_blank>INSDC</a> member institution\n"
      "(<a href='https://submit.ncbi.nlm.nih.gov/sarscov2/' target=_blank>NCBI</a>,\n"
      "<a href='https://www.covid19dataportal.org/submit-data' target=_blank>EMBL-EBI</a>\n"
      "or <a href='https://www.ddbj.nig.ac.jp/ddbj/websub.html' target=_blank>DDBJ</a>)\n"
      "and <a href='https://www.gisaid.org/' target=_blank>GISAID</a>.\n"
      "</p>\n");
 puts("</div>");
 puts("  </div>");
 puts("  <div class='gbControl col-md-12'>");
+printf("<p>Select your FASTA or VCF file: ");
 printf("<input type='file' id='%s' name='%s' "
        "accept='.fa, .fasta, .vcf, .vcf.gz, .fa.gz, .fasta.gz'>",
        seqFileVar, seqFileVar);
+struct treeChoices *treeChoices = loadTreeChoices(db);
+if (treeChoices)
+    {
+    puts("</p><p>");
+    printf("Phylogenetic tree version: ");
+    char *phyloPlaceTree = cartOptionalString(cart, "phyloPlaceTree");
+    cgiMakeDropListWithVals("phyloPlaceTree", treeChoices->descriptions, treeChoices->protobufFiles,
+                            treeChoices->count, phyloPlaceTree);
+    }
+puts("</p><p>");
 printf("Number of samples per subtree showing sample placement: ");
 int subtreeSize = cartUsualInt(cart, "subtreeSize", 50);
 cgiMakeIntVarWithLimits("subtreeSize", subtreeSize,
  "Number of samples in subtree showing neighborhood of placement",
  5, 10, 1000);
+puts("</p><p>");
 cgiMakeOnClickSubmitButton(CHECK_FILE_INPUT_JS, "submit", "upload");
+puts("</p>");
 puts("  </div>");
 puts("</form>");
 }
 
 static void exampleForm()
 /* Let the user try Russ's example. */
 {
 printf("<form action='%s' name='exampleForm' method=POST>\n\n",
        "hgPhyloPlace");
 cartSaveSession(cart);
 cgiMakeHiddenVar("db", "wuhCor1");
 puts("  <div class='gbControl col-md-12'>");
 puts("If you don't have a local file, you can try an "
      "<a href='https://github.com/russcd/USHER_DEMO/' target=_blank>example</a>: ");
 cgiMakeButton("submit", "try example");
@@ -305,32 +319,34 @@
      "  </div>\n"
      "</div>\n"
      "<div class='row'>\n");
 // Form submits subtree custom tracks to hgTracks
 printf("<form action='%s' name='resultsForm' method=%s>\n\n",
        hgTracksName(), cartUsualString(cart, "formMethod", "POST"));
 cartSaveSession(cart);
 puts("  <div class='gbControl col-md-12'>");
 
 if (lf != NULL)
     {
     // Use trackLayout to get hgTracks parameters relevant to displaying trees:
     struct trackLayout tl;
     trackLayoutInit(&tl, cart);
     // Do our best to place the user's samples, make custom tracks if successful:
+    char *phyloPlaceTree = cartOptionalString(cart, "phyloPlaceTree");
     int subtreeSize = cartUsualInt(cart, "subtreeSize", 50);
-    char *ctFile = phyloPlaceSamples(lf, db, measureTiming, subtreeSize, tl.fontHeight);
+    char *ctFile = phyloPlaceSamples(lf, db, phyloPlaceTree, measureTiming, subtreeSize,
+                                     tl.fontHeight);
     if (ctFile)
         {
         cgiMakeHiddenVar(CT_CUSTOM_TEXT_VAR, ctFile);
         if (tl.leftLabelWidthChars < 0 || tl.leftLabelWidthChars == leftLabelWidthDefaultChars)
             cgiMakeHiddenVar(leftLabelWidthVar, leftLabelWidthForLongNames);
         cgiMakeButton("submit", "view in Genome Browser");
         puts("  </div>");
         puts("</form>");
         }
     else
         {
         puts("  </div>");
         puts("</form>");
         // Let the user upload something else and try again:
         inputForm();