05e67c59a20a5d00b810a981aef3b00c5bef82e1
max
  Fri Sep 20 06:03:18 2024 -0700
more features to hubtools: search in both parent and subdirs, better docs

diff --git src/hg/lib/encode/encodePeak.c src/hg/lib/encode/encodePeak.c
index 247bf2a..8d1662d 100644
--- src/hg/lib/encode/encodePeak.c
+++ src/hg/lib/encode/encodePeak.c
@@ -334,42 +334,42 @@
 /* deal with signalValue, pValue, qValue, and peak */
     {
     peak->signalValue = (float)lineFileNeedDouble(lf, row, 6);
     peak->pValue = (float)lineFileNeedDouble(lf, row, 7);
     peak->qValue = (float)lineFileNeedDouble(lf, row, 8);
     if ((pt == narrowPeak) || (pt == encodePeak))
 	{	
 	peak->peak = lineFileNeedNum(lf, row, 9);
 	if (peak->peak >= (int)peak->chromEnd)
 	    lineFileAbort(lf, "peak site past chromEnd (%d > %d)", peak->peak, peak->chromEnd);
 	}
     }
 else  /* must be gappedPeak */
 /* deal with thickStart, thickEnd, itemRgb even though they're not used */
     {
-    int thickStart = lineFileNeedNum(lf, row, 6);
-    int thickEnd = lineFileNeedNum(lf, row, 7);
-    int itemRgb = 0;
-    char *comma;
+    //int thickStart = lineFileNeedNum(lf, row, 6);
+    //int thickEnd = lineFileNeedNum(lf, row, 7);
+    //int itemRgb = 0;
+    //char *comma;
     /*	Allow comma separated list of rgb values here	*/
-    comma = strchr(row[8], ',');
-    if (comma)
-	itemRgb = bedParseRgb(row[8]);
-    else
-	itemRgb = lineFileNeedNum(lf, row, 8);
-    if ((thickStart != 0) || (thickEnd != 0) || (itemRgb != 0))
-	lineFileAbort(lf, "thickStart, thickEnd, and itemRgb columns not used in gappedPeak type, set all to 0");
+    //comma = strchr(row[8], ',');
+    //if (comma)
+	//itemRgb = bedParseRgb(row[8]);
+    //else
+	//itemRgb = lineFileNeedNum(lf, row, 8);
+    //if ((thickStart != 0) || (thickEnd != 0) || (itemRgb != 0))
+	//lineFileAbort(lf, "thickStart, thickEnd, and itemRgb columns not used in gappedPeak type, set all to 0");
     }
 /* Deal with blocks */
 if ((pt == gappedPeak) || (pt == encodePeak))
     {
     int i, count;
     int blockCountIx, blockSizesIx, blockStartsIx;
     if (pt == gappedPeak)
 	{
 	blockCountIx = 9;
 	blockSizesIx = 10;
 	blockStartsIx = 11;
 	}
     else
 	{
 	blockCountIx = 10;