5e88a1196c6be3d47f925d8d31e401ef0a65c1fc
braney
  Fri Nov 10 14:40:51 2017 -0800
add support for bigNarrowPeak in hubs and custom tracks

diff --git src/hg/hgc/encodeClick.c src/hg/hgc/encodeClick.c
index 405e530..ba8dbfa 100644
--- src/hg/hgc/encodeClick.c
+++ src/hg/hgc/encodeClick.c
@@ -39,75 +39,42 @@
     }
 return TRUE;
 }
 
 static void rAddMatching(struct trackDb *tdb, struct slPair *selGroupList, struct slName **pList)
 /* Add track and any descendents that match selGroupList to pList */
 {
 if (selGroupListMatch(tdb, selGroupList))
     slNameAddHead(pList, tdb->track);
 struct trackDb *sub;
 for (sub = tdb->subtracks; sub != NULL; sub = sub->next)
     rAddMatching(sub, selGroupList, pList);
 }
 #endif//def UNUSED
 
-void doEncodePeak(struct trackDb *tdb, struct customTrack *ct, char *item)
-/*  details for encodePeak type tracks. */
-{
-struct sqlConnection *conn;
-struct sqlResult *sr;
-enum encodePeakType peakType;
-char **row;
-char *db;
-char *table = tdb->table;
-char *chrom = cartString(cart,"c");
-int start = cgiInt("o");
-int end = cgiInt("t");
-int rowOffset;
-boolean firstTime = TRUE;
-/* connect to DB */
-if (ct)
-    {
-    db = CUSTOM_TRASH;
-    table = ct->dbTableName;
-    }
-else
-    db = database;
-conn = hAllocConn(db);
-peakType = encodePeakInferTypeFromTable(db, table, tdb->type);
-if (peakType == 0)
-    errAbort("unrecognized peak type from table %s", tdb->table);
-genericHeader(tdb, NULL);  // genericClickHandlerPlus gets there first anyway (maybe except for encodePeak custom tracks).
-sr = hOrderedRangeQuery(conn, table, chrom, start, end,
-			NULL, &rowOffset);
-while((row = sqlNextRow(sr)) != NULL)
+static void printPeak(char **row, int rowOffset, char *item, char *chrom, int start, int end, enum encodePeakType peakType)
 {
 char **rowPastOffset = row + rowOffset;
 if ((sqlUnsigned(rowPastOffset[1]) != start) ||  (sqlUnsigned(rowPastOffset[2]) != end))
-	continue;
+    return;
 if (!sameString(rowPastOffset[3], item))
-	continue;
+    return;
 
 float signal = -1;
 float pValue = -1;
 float qValue = -1;
 
-    if (firstTime)
-	firstTime = FALSE;
-    else // print separator
-	printf("<BR>\n");
 
 /* Name */
 if (rowPastOffset[3][0] != '.')
     printf("<B>Name:</B> %s<BR>\n", rowPastOffset[3]);
 /* Position */
 printf("<B>Position:</B> "
    "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\n",
    hgTracksPathAndSettings(), database, chrom, start+1, end, chrom, start+1, end);
 /* Print peak base */
 if ((peakType == narrowPeak) || (peakType == encodePeak))
     {
     int peak = sqlSigned(rowPastOffset[9]);
     if (peak > -1)
         printf("<B>Peak point:</B> %d<BR>\n", start + peak + 1); // one based
     }
@@ -123,30 +90,99 @@
     qValue = sqlFloat(rowPastOffset[8]);
     }
 else
     {
     signal = sqlFloat(rowPastOffset[12]);
     pValue = sqlFloat(rowPastOffset[13]);
     qValue = sqlFloat(rowPastOffset[14]);
     }
 if (signal >= 0)
     printf("<B>Signal value:</B> %.3f<BR>\n", signal);
 if (pValue >= 0)
     printf("<B>P-value (-log10):</B> %.3f<BR>\n", pValue);
 if (qValue >= 0)
     printf("<B>Q-value (FDR): </B> %.3f<BR>\n", qValue);
 }
+
+void doBigEncodePeak(struct trackDb *tdb, struct customTrack *ct, char *item)
+/*  details for encodePeak type tracks. */
+{
+enum encodePeakType peakType = narrowPeak;
+char *chrom = cartString(cart,"c");
+int start = cgiInt("o");
+int end = cgiInt("t");
+boolean firstTime = TRUE;
+//peakType = encodePeakInferTypeFromTable(db, table, tdb->type);
+if (peakType == 0)
+    errAbort("unrecognized peak type from table %s", tdb->table);
+genericHeader(tdb, NULL);  // genericClickHandlerPlus gets there first anyway (maybe except for encodePeak custom tracks).
+char *fileName = bbiNameFromSettingOrTable(tdb, NULL, tdb->table);
+struct bbiFile *bbi = bigBedFileOpen(fileName);
+struct lm *lm = lmInit(0);
+struct bigBedInterval *bb, *bbList =  bigBedIntervalQuery(bbi, chrom, start, end, 0, lm);
+int fieldCount = 10;
+char *bedRow[fieldCount];
+char startBuf[16], endBuf[16];
+
+for (bb = bbList; bb != NULL; bb = bb->next)
+    {
+    bigBedIntervalToRow(bb, chrom, startBuf, endBuf, bedRow, ArraySize(bedRow));
+    if (firstTime)
+        firstTime = FALSE;
+    else // print separator
+        printf("<BR>\n");
+    printPeak(bedRow, 0, item, chrom, start, end, peakType);
+    }
+}
+
+void doEncodePeak(struct trackDb *tdb, struct customTrack *ct, char *item)
+/*  details for encodePeak type tracks. */
+{
+struct sqlConnection *conn;
+struct sqlResult *sr;
+enum encodePeakType peakType;
+char **row;
+char *db;
+char *table = tdb->table;
+char *chrom = cartString(cart,"c");
+int start = cgiInt("o");
+int end = cgiInt("t");
+int rowOffset;
+boolean firstTime = TRUE;
+/* connect to DB */
+if (ct)
+    {
+    db = CUSTOM_TRASH;
+    table = ct->dbTableName;
+    }
+else
+    db = database;
+conn = hAllocConn(db);
+peakType = encodePeakInferTypeFromTable(db, table, tdb->type);
+if (peakType == 0)
+    errAbort("unrecognized peak type from table %s", tdb->table);
+genericHeader(tdb, NULL);  // genericClickHandlerPlus gets there first anyway (maybe except for encodePeak custom tracks).
+sr = hOrderedRangeQuery(conn, table, chrom, start, end,
+			NULL, &rowOffset);
+while((row = sqlNextRow(sr)) != NULL)
+    {
+    if (firstTime)
+        firstTime = FALSE;
+    else // print separator
+        printf("<BR>\n");
+    printPeak(row, rowOffset, item, chrom, start, end, peakType);
+    }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 int encodeFiveCInterCmp(const void *va, const void *vb)
 /* reverse sort on bed nine's reserved field which in this */
 /* case is the where the strength of the interaction is stored */
 {
 const struct bed *a = *((struct bed **)va);
 const struct bed *b = *((struct bed **)vb);
 return b->itemRgb - a->itemRgb;
 }
 
 void doEncodeFiveC(struct sqlConnection *conn, struct trackDb *tdb)
 /* Print details for 5C track */