39e533cc9ffcb46d9c484dc09a387a031a739391
Merge parents 1c86690 f642bab
kate
  Mon Sep 24 16:35:53 2018 -0700
Updating from master

diff --cc src/hg/lib/interact.c
index 1d74ada,e27d480..43f4404
--- src/hg/lib/interact.c
+++ src/hg/lib/interact.c
@@@ -333,135 -333,139 +333,233 @@@
  if (aDist < 0)
      {
      if (bDist < 0)
          return 0;
      return 1;
      }
  if (bDist < 0)
      return -1;
  
  // same chromosome
  return aDist - bDist;
  }
  
  struct interact *interactLoadAndValidate(char **row)
  /* Load a interact from row fetched with select * from interact
-  * from database, validating fields.  Dispose of this with interactFree(). */
+  * from database, validating fields.  Dispose of this with interactFree(). 
+  * This currently differs from auto-gened only by it's handling of color field */
  // TODO: more validating
  {
  struct interact *ret;
  
  AllocVar(ret);
  ret->chrom = cloneString(row[0]);
  ret->chromStart = sqlUnsigned(row[1]);
  ret->chromEnd = sqlUnsigned(row[2]);
  ret->name = cloneString(row[3]);
  ret->score = sqlUnsigned(row[4]);
  ret->value = sqlDouble(row[5]);
  ret->exp = cloneString(row[6]);
- ret->color = bedParseColor(row[7]);
+ ret->color = bedParseColor(row[7]);     // handle #NNNNNN, and HTML color (as well as rgb)
  ret->sourceChrom = cloneString(row[8]);
  ret->sourceStart = sqlUnsigned(row[9]);
  ret->sourceEnd = sqlUnsigned(row[10]);
  ret->sourceName = cloneString(row[11]);
  ret->sourceStrand = cloneString(row[12]);
  ret->targetChrom = cloneString(row[13]);
  ret->targetStart = sqlUnsigned(row[14]);
  ret->targetEnd = sqlUnsigned(row[15]);
  ret->targetName = cloneString(row[16]);
  ret->targetStrand = cloneString(row[17]);
  return ret;
  }
  
 +void interactRegionCenters(struct interact *inter, int *sourceCenter, int *targetCenter)
 +/* Return genomic position of endpoint centers */
 +{
 +assert(sourceCenter);
 +assert(targetCenter);
 +*sourceCenter = interactRegionCenter(inter->sourceStart, inter->sourceEnd);
 +*targetCenter = interactRegionCenter(inter->targetStart, inter->targetEnd);
 +}
 +
 +struct bed *interactToBed(struct interact *inter)
 +/* Convert an interact to a BED12 (actually, BED15+label) */
 +{
 +struct bed *bed = NULL;
 +AllocVar(bed);
 +
 +bed->chrom = inter->chrom;
 +// expand extents to edges of endpoints
 +// NOTE: this should be changed in schema defn
 +//bed->chromStart = inter->chromStart;
 +bed->chromStart = min(inter->sourceStart, inter->targetStart);
 +//bed->chromEnd = inter->chromEnd;
 +bed->chromEnd = max(inter->sourceEnd, inter->targetEnd);
 +bed->thickStart = bed->chromStart;
 +bed->thickEnd = bed->chromEnd;
 +bed->name = inter->name;
 +bed->score = inter->score;
 +bed->itemRgb = inter->color;
 +AllocArray(bed->blockSizes, 2);
 +AllocArray(bed->chromStarts, 2);
 +
 +char *strand = "+";
 +if (differentString(inter->sourceChrom, inter->targetChrom))
 +    {
 +    // inter-chromosomal
 +    bed->blockCount = 1;
 +    bed->blockSizes[0] = inter->chromEnd - inter->chromStart;
 +    bed->chromStarts[0] = 0;
 +    if sameString(bed->chrom, inter->targetChrom)
 +        strand = "-";
 +    }
 +else 
 +    {
 +    // same chromosome
 +    int sourceCenter, targetCenter;
 +    interactRegionCenters(inter, &sourceCenter, &targetCenter);
 +    if (targetCenter < sourceCenter)
 +        {
 +        strand = "-";
 +        if (inter->sourceStart <= inter->targetEnd)
 +            {
 +            // overlapping - use thickStart/End to delineate
 +            bed->blockCount = 1;
 +            bed->blockSizes[0] = bed->chromEnd - bed->chromStart;
 +            bed->chromStarts[0] = 0;
 +            bed->thickStart = targetCenter;
 +            bed->thickEnd = sourceCenter;
 +            }
 +        else
 +            {
 +            bed->blockCount = 2;
 +            bed->blockSizes[1] = inter->sourceEnd - inter->sourceStart;
 +            bed->blockSizes[0] = inter->targetEnd - inter->targetStart;
 +            bed->chromStarts[1] = inter->sourceStart - bed->chromStart;
 +            bed->chromStarts[0] = 0;
 +            }
 +        }
 +    else
 +        {
 +        // forward direction
 +        if (inter->targetStart <= inter->sourceEnd)
 +            {
 +            // overlapping - use thickStart/End to delineate
 +            bed->blockCount = 1;
 +            bed->blockSizes[0] = bed->chromEnd - bed->chromStart;
 +            bed->chromStarts[0] = 0;
 +            bed->thickStart = sourceCenter;
 +            bed->thickEnd = targetCenter;
 +            }
 +        else
 +            {
 +            bed->blockCount = 2;
 +            bed->blockSizes[0] = inter->sourceEnd - inter->sourceStart;
 +            bed->blockSizes[1] = inter->targetEnd - inter->targetStart;
 +            bed->chromStarts[0] = 0;
 +            bed->chromStarts[1] = inter->targetStart - bed->chromStart;
 +            }
 +        }
 +    }
 +strcpy(bed->strand, strand);
 +bed->label = bed->name;
 +return bed;
 +}
 +
+ struct interact *interactLoadAllAndValidate(char *fileName) 
+ /* Load all interact from a whitespace-separated file.
+  * Dispose of this with interactFreeList(). */
+ {
+ struct interact *list = NULL, *el;
+ struct lineFile *lf = lineFileOpen(fileName, TRUE);
+ char *row[18];
+ while (lineFileRow(lf, row))
+     {
+     el = interactLoadAndValidate(row);
+     slAddHead(&list, el);
+     }
+ lineFileClose(&lf);
+ slReverse(&list);
+ return list;
+ }
+ 
+ void interactOutputCustom(struct interact *el, FILE *f, char sep, char lastSep) 
+ /* Print out interact.  Separate fields with sep. Follow last field with lastSep.
+  * Differs from auto-gen'ed by printing rgb color  */
+ {
+ if (sep == ',') fputc('"',f);
+ fprintf(f, "%s", el->chrom);
+ if (sep == ',') fputc('"',f);
+ fputc(sep,f);
+ fprintf(f, "%u", el->chromStart);
+ fputc(sep,f);
+ fprintf(f, "%u", el->chromEnd);
+ fputc(sep,f);
+ if (sep == ',') fputc('"',f);
+ fprintf(f, "%s", el->name);
+ if (sep == ',') fputc('"',f);
+ fputc(sep,f);
+ fprintf(f, "%u", el->score);
+ fputc(sep,f);
+ fprintf(f, "%g", el->value);
+ fputc(sep,f);
+ if (sep == ',') fputc('"',f);
+ fprintf(f, "%s", el->exp);
+ if (sep == ',') fputc('"',f);
+ fputc(sep,f);
+ 
+ // print rgb color
+ bedOutputRgb(f, el->color);
+ 
+ fputc(sep,f);
+ if (sep == ',') fputc('"',f);
+ fprintf(f, "%s", el->sourceChrom);
+ if (sep == ',') fputc('"',f);
+ fputc(sep,f);
+ fprintf(f, "%u", el->sourceStart);
+ fputc(sep,f);
+ fprintf(f, "%u", el->sourceEnd);
+ fputc(sep,f);
+ if (sep == ',') fputc('"',f);
+ fprintf(f, "%s", el->sourceName);
+ if (sep == ',') fputc('"',f);
+ fputc(sep,f);
+ if (sep == ',') fputc('"',f);
+ fprintf(f, "%s", el->sourceStrand);
+ if (sep == ',') fputc('"',f);
+ fputc(sep,f);
+ if (sep == ',') fputc('"',f);
+ fprintf(f, "%s", el->targetChrom);
+ if (sep == ',') fputc('"',f);
+ fputc(sep,f);
+ fprintf(f, "%u", el->targetStart);
+ fputc(sep,f);
+ fprintf(f, "%u", el->targetEnd);
+ fputc(sep,f);
+ if (sep == ',') fputc('"',f);
+ fprintf(f, "%s", el->targetName);
+ if (sep == ',') fputc('"',f);
+ fputc(sep,f);
+ if (sep == ',') fputc('"',f);
+ fprintf(f, "%s", el->targetStrand);
+ if (sep == ',') fputc('"',f);
+ fputc(lastSep,f);
+ }
+ 
+ void interactFixRange(struct interact *inter)
+ /* Set values for chromStart/chromEnd based on source and target start/ends */
+ {
+ int chromStart = min(inter->sourceStart, inter->targetStart);
+ int chromEnd = max(inter->sourceEnd, inter->targetEnd);
+ if (inter->chromStart != chromStart)
+     {
+     warn("Fixed chromStart: %d to %d. ", inter->chromStart, chromStart); 
+     inter->chromStart = chromStart;
+     }
+ if (inter->chromEnd != chromEnd)
+     {
+     warn("Fixed chromEnd: %d to %d. ", inter->chromEnd, chromEnd); 
+     inter->chromEnd = chromEnd;
+     }
+ }
++