100ad514ee0c866afdb787202cae49270b6c8b1e
braney
  Thu Jul 26 12:45:30 2012 -0700
oops... wasn't dealing with CDS start and stop correctly on '-' strand
diff --git src/hg/pslToBed/pslToBed.c src/hg/pslToBed/pslToBed.c
index 0e25ea1..4be663e 100644
--- src/hg/pslToBed/pslToBed.c
+++ src/hg/pslToBed/pslToBed.c
@@ -54,35 +54,45 @@
 
 	assert(offsetInBlock < psl->blockSizes[blockNum]);
 
 	return psl->tStarts[blockNum] + offsetInBlock;
 	}
     }
 
 // we don't have any blocks with this query in it, just point
 // to the end
 return psl->tEnd;
 }
 
 static void setThick(struct psl *psl, struct bed *bed, struct cds *cds)
 // set thickStart and thickEnd based on CDS record
 {
-int thickStart, thickEnd;
+unsigned thickStart, thickEnd;
+unsigned cdsStart = cds->start - 1;
+unsigned cdsEnd = cds->end;
+
+if (psl->strand[0] == '-')
+    {
+    // if on negative strand, cds is from end
+    unsigned temp = cdsStart;
+    cdsStart = psl->qSize - cdsEnd;
+    cdsEnd = psl->qSize - temp;
+    }
 
 // we subtract one from start to convert to PSL coordinate system
-thickStart = getTargetForQuery(psl, cds->start - 1); 
-thickEnd = getTargetForQuery(psl, cds->end); 
+thickStart = getTargetForQuery(psl, cdsStart);
+thickEnd = getTargetForQuery(psl, cdsEnd);
 
 // if thickStart equals thickEnd, then there is no CDS
 if (thickStart == thickEnd)
     thickStart = thickEnd = 0;
 
 bed->thickStart = thickStart;
 bed->thickEnd = thickEnd;
 }
 
 void pslToBed(char *pslFile, char *bedFile, struct hash *cdsHash)
 /* pslToBed -- tranform a psl format file to a bed format file */
 {
 struct lineFile *pslLf = pslFileOpen(pslFile);
 FILE *bedFh = mustOpen(bedFile, "w");
 struct psl *psl;
@@ -105,34 +115,37 @@
 carefulClose(&bedFh);
 lineFileClose(&pslLf);
 }
 
 struct hash *getCdsHash(char *cdsFile)
 /* read CDS start and end for list of id's */
 {
 struct lineFile *lf = lineFileOpen(cdsFile, TRUE);
 char *row[2];
 struct hash *hash = newHash(0);
 while (lineFileRow(lf, row))
     {
     // lines are of the form of <start>..<end>
     struct cds *cds;
     AllocVar(cds);
-    cds->start = atoi(row[1]);
+    cds->start = atoi(row[1]);  // atoi will stop at '.'
     char *ptr = strchr(row[1], '.');	 // point to first '.'
     ptr+=2; // step past two '.'s
     cds->end = atoi(ptr);
+    if (cds->start > cds->end)
+	errAbort("CDS start(%d) is before end(%d) on line %d",
+		cds->start, cds->end, lf->lineIx);
     hashAdd(hash, row[0], cds);
     }
 lineFileClose(&lf);
 return hash;
 }
 
 int main(int argc, char* argv[])
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 char *cdsFile = optionVal("cds", NULL);
 struct hash *cdsHash = NULL;
 
 if (cdsFile != NULL)