34ae341f397c44bda8ce0e2d59dcc3d18b5e519e
angie
  Thu Aug 20 10:38:14 2020 -0700
Use the new vcfParseGenotypesGtOnly for speed in haplotype displays.

diff --git src/hg/hgTracks/vcfTrack.c src/hg/hgTracks/vcfTrack.c
index f04efae..7ad70b3 100644
--- src/hg/hgTracks/vcfTrack.c
+++ src/hg/hgTracks/vcfTrack.c
@@ -1517,31 +1517,33 @@
 #define GENE_SIZE_FUDGE 2500000
 
 static boolean vcfHapClusterDrawInit(struct track *tg, struct vcfFile *vcff, struct hvGfx *hvg,
                                      enum hapColorMode *retHapColorMode,
                                      struct seqWindow **retGSeqWin, struct txInfo **retTxiList)
 /* Parse vcff's genotypes and get ready to draw haplotypes.  Return FALSE if nothing to draw. */
 {
 if (vcff->records == NULL)
     return FALSE;
 undefYellow = hvGfxFindRgb(hvg, &undefinedYellowColor);
 if (retHapColorMode)
     *retHapColorMode = getColorMode(tg->tdb);
 pushWarnHandler(ignoreEm);
 struct vcfRecord *rec;
 for (rec = vcff->records;  rec != NULL;  rec = rec->next)
-    vcfParseGenotypes(rec);
+    {
+    vcfParseGenotypesGtOnly(rec);
+    }
 popWarnHandler();
 if (*retHapColorMode == functionMode)
     {
     if (!exprBedColorsMade)
         {
         makeRedGreenShades(hvg);
         // Make darkerShadesOfGreenOnWhite for local use
         static struct rgbColor white  = {255, 255, 255};
         static struct rgbColor darkerGreen  = {0, 210, 0};
         hvGfxMakeColorGradient(hvg, &white, &darkerGreen,  EXPR_DATA_SHADES,
                                darkerShadesOfGreenOnWhite);
         }
     int gStart = winStart - GENE_SIZE_FUDGE;
     if (gStart < 0)
         gStart = 0;