3b51318fe05fce338719b56a70d44f1436ff5311
kate
  Tue Dec 5 12:37:26 2017 -0800
Fix problems with computing centers and position starts (esp. noticeable for SNPs). Also some cleanup. refs #17512

diff --git src/hg/inc/longRange.h src/hg/inc/longRange.h
index 0e0a557..bb91f1b 100644
--- src/hg/inc/longRange.h
+++ src/hg/inc/longRange.h
@@ -1,50 +1,57 @@
 /* longRange - Long Range Interaction Format functions */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 #ifndef LONGRANGE_H
 #define LONGRANGE_H
 
 #include "common.h"
 #include "cheapcgi.h"
 #include "cart.h"
 #include "trackDb.h"
 #include "bed.h"
 
 #define LONG_HEIGHT "heightPer"
 #define LONG_MINHEIGHT 20
 #define LONG_MAXHEIGHT 300
 #define LONG_DEFHEIGHT "200"
 #define LONG_MINSCORE "minScore"
 #define LONG_DEFMINSCORE "0"
 
 struct longRange
 {
 struct longRange *next;
-char *name;
-unsigned s;
-unsigned sw;
-int sOrient;
-char *sChrom;
+char *name;     // for longTabix, Wash U field 4 (other region pos + interaction value)
+                //      Unused in GB
+
+// info for 'start' (lower genomic coords) region
+unsigned s;     // position of 'center', 0-based
+unsigned sw;    // width in bp
+int sOrient;    // strand
+char *sChrom;   // chrom
+
+// info for 'end' (higher genomic coords) region
 unsigned e;
 unsigned ew;
 int eOrient;
 char *eChrom;
-unsigned height;
-double score;
-unsigned id;
-// Ensembl extension -- RGB color can be supplied instead of score
-boolean hasColor;
-unsigned rgb;
+
+boolean hasColor; // Ensembl extension to Wash U format -- 
+                 //        RGB color can be supplied instead of score
+unsigned rgb;   // RGB color for display
+double score;   // interaction numeric value; e.g. strength of interaction
+
+unsigned id;    // unique integer identifier of an item in a longTabix file (not interaction id)
+                // Required in Wash U spec. Unsed at UCSC, except for details page
 };
 
 void longRangeCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed);
 /* Complete track controls for long range interaction. */
 
 struct longRange *parseLongTabix(struct bed *beds, unsigned *maxWidth, double minScore);
 /* Parse longTabix format into longRange structures */
 
 struct asObject *longTabixAsObj();
 /* Return asObject describing fields of longTabix file. */
 
 #endif//def LONGRANGE_H