ec099b026edcb192c203dd48341e979cdc8162ee
angie
  Mon Mar 26 15:22:38 2012 -0700
Track #7090 (ISCA update): Adding abbreviations for several morevariant origin terms from John Lopez (NCBI).

diff --git src/hg/hgTracks/gvfTrack.c src/hg/hgTracks/gvfTrack.c
index ddb1071..b3a874c 100644
--- src/hg/hgTracks/gvfTrack.c
+++ src/hg/hgTracks/gvfTrack.c
@@ -112,40 +112,47 @@
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 slSort(&list, gvfHierCmp);
 tg->items = list;
 }
 
 static char *gvfItemName(struct track *tg, void *item)
 /* ISCA requested that we append abbreviated variant origin to the item names. */
 {
 struct bed8Attrs *gvf = item;
 struct dyString *name = dyStringNew(0);
 int ix = stringArrayIx("var_origin", gvf->attrTags, gvf->attrCount);
 if (ix >= 0)
     {
     char *origin = gvf->attrVals[ix];
-    if (sameWord(origin, "Not tested"))
+    if (sameWord(origin, "Not tested") || sameWord(origin, "Not reported") ||
+	sameWord(origin, "Tested - inconclusive"))
 	dyStringPrintf(name, "%s_unk", gvf->name);
     else if (sameWord(origin, "De novo"))
 	dyStringPrintf(name, "%s_dnovo", gvf->name);
     else if (sameWord(origin, "Maternal"))
 	dyStringPrintf(name, "%s_mat", gvf->name);
     else if (sameWord(origin, "Paternal"))
 	dyStringPrintf(name, "%s_pat", gvf->name);
     else if (sameWord(origin, "Biparental"))
 	dyStringPrintf(name, "%s_bip", gvf->name);
+    else if (sameWord(origin, "Uniparental"))
+	dyStringPrintf(name, "%s_unip", gvf->name);
+    else if (sameWord(origin, "Germline"))
+	dyStringPrintf(name, "%s_germ", gvf->name);
+    else if (sameWord(origin, "Somatic"))
+	dyStringPrintf(name, "%s_som", gvf->name);
     else
 	dyStringPrintf(name, "%s_%s", gvf->name, origin);
     }
 else
     dyStringPrintf(name, "%s_unk", gvf->name);
 return dyStringCannibalize(&name);
 }
 
 void gvfMethods(struct track *tg)
 /* Load GVF variant data. */
 {
 bedMethods(tg);
 tg->canPack = TRUE;
 tg->loadItems = gvfLoad;
 tg->itemName = gvfItemName;