68315931f4a9ec4272a8df76e6a881339717ac16
braney
  Wed Jun 1 15:37:37 2016 -0700
changes to support longTabix files in hgIntegrator

diff --git src/hg/lib/longRange.c src/hg/lib/longRange.c
index 43e8f09..419fc92 100644
--- src/hg/lib/longRange.c
+++ src/hg/lib/longRange.c
@@ -1,119 +1,100 @@
 /*    longRange --- functions to provide UI for long range interaction
  *         graph.   Functions to retrieve long range information from
  *         bedTabix format.
  */
 
 /* Copyright (C) 2016 The Regents of the University of California 
  *  * See README in this or parent directory for licensing information. */
 
 #include "longRange.h"
 
-static char *longTabixAutoSqlString =
-"table longTabix\n"
-"\"Long Range Tabix file\"\n"
-"   (\n"
-"   string chrom;      \"Reference sequence chromosome or scaffold\"\n"
-"   uint   chromStart; \"Start position in chromosome\"\n"
-"   uint   chromEnd;   \"End position in chromosome\"\n"
-"   string interactingRegion;       \"(e.g. chrX:123-456,3.14, where chrX:123-456 is the coordinate of the mate, and 3.14 is the score of the interaction)\"\n"
-"   uint   id;      \"Unique Id\"\n"
-"   char[1] strand;    \"+ or -\"\n"
-"   )\n"
-;
-
-struct asObject *longTabixAsObj()
-// Return asObject describing fields of longTabix file
-{
-return asParseText(longTabixAutoSqlString);
-}
-
 void longRangeCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed)
 /* Complete track controls for long range interaction. */
 {
 char buffer[1024];
 safef(buffer, sizeof buffer, "%s.%s", tdb->track, LONG_HEIGHT );
 unsigned height = sqlUnsigned(cartUsualString(cart, buffer, LONG_DEFHEIGHT));
 printf("<BR><b>Track height:&nbsp;</b>");
 cgiMakeIntVar(buffer, height, 3);
 safef(buffer, sizeof buffer, "%s.%s", tdb->track, LONG_MINSCORE);
 double minScore = sqlDouble(cartUsualString(cart, buffer, LONG_DEFMINSCORE));
 printf("<BR><BR><b>Minimum score:&nbsp;</b>");
 cgiMakeDoubleVar(buffer, minScore, 0);
 }
 
 static char *getOther(struct bed *bed, unsigned *s, unsigned *e, double *score)
 /* parse the name field of longTabix to get the other location */
 {
 char *otherChrom = cloneString(bed->name);
 char *ptr = strchr(otherChrom, ':');
 if (ptr == NULL)
     errAbort("bad longTabix bed name %s\n", bed->name);
 *ptr++ = 0;
 *s = atoi(ptr);
 ptr = strchr(ptr, '-');
 if (ptr == NULL)
     errAbort("bad longTabix bed name %s\n", bed->name);
 ptr++;
 *e = atoi(ptr);
 ptr = strchr(ptr, ',');
 if (ptr == NULL)
     errAbort("bad longTabix bed name %s\n", bed->name);
 ptr++;
 *score = sqlDouble(ptr);
 
 return otherChrom;
 }
 
 struct longRange *parseLongTabix(struct bed *beds, unsigned *maxWidth, double minScore)
 /* Parse longTabix format into longRange structures */
 {
 struct longRange *longRangeList = NULL;
 *maxWidth = 1;
 for(; beds; beds=beds->next)
     {
     double score;
     unsigned otherS;
     unsigned otherE;
     char *otherChrom = getOther(beds, &otherS, &otherE, &score);
     if (score < minScore)
         continue;
 
     struct longRange *longRange;
     AllocVar(longRange);
     slAddHead(&longRangeList, longRange);
 
     unsigned otherCenter = (otherS + otherE)/2;
     unsigned otherWidth = otherE - otherS;
     unsigned thisWidth = beds->chromEnd - beds->chromStart;
     unsigned center = (beds->chromEnd + beds->chromStart) / 2;
 
     // don't have oriented feet at the moment
     longRange->sOrient = longRange->eOrient = 0;
     longRange->id = beds->score;
     longRange->score = score;
     longRange->name = beds->name;
     
     if (sameString(beds->chrom, otherChrom) && (otherCenter < center))
         {
         longRange->s = otherCenter;
         longRange->sw = otherWidth;
         longRange->sChrom = otherChrom;
         longRange->e = center;
         longRange->ew = thisWidth;
         longRange->eChrom = beds->chrom;
         }
     else
         {
         longRange->s = center;
         longRange->sw = thisWidth;
         longRange->sChrom = beds->chrom;
         longRange->e = otherCenter;
         longRange->ew = otherWidth;
         longRange->eChrom = otherChrom;
         }
     unsigned longRangeWidth = longRange->e - longRange->s;
     if (sameString(longRange->eChrom,longRange->sChrom) && ( longRangeWidth > *maxWidth))
         *maxWidth = longRangeWidth;
     }
 return longRangeList;
 }