0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd
max
  Fri Sep 20 13:18:01 2024 -0700
Revert "more features to hubtools: search in both parent and subdirs, better docs"

This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.

diff --git src/hg/lib/encode/encodePeak.c src/hg/lib/encode/encodePeak.c
index 8d1662d..247bf2a 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;