src/hg/overlapSelect/coordCols.c 1.3

Index: src/hg/overlapSelect/coordCols.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/overlapSelect/coordCols.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/overlapSelect/coordCols.c	24 Jul 2006 19:36:08 -0000	1.2
+++ src/hg/overlapSelect/coordCols.c	31 Jul 2009 18:09:23 -0000	1.3
@@ -1,73 +1,75 @@
 /* coordCols - parsing of file by specifying coordinate columns */
 #include "common.h"
 #include "coordCols.h"
 #include "rowReader.h"
 #include "sqlNum.h"
 
+static char const rcsid[] = "$Id$";
+
 static void invalidSpec(char *optName, char* spec)
 /* generate an error, msg can be null */
 {
 errAbort("invalid coord column spec for %s: %s", optName, spec);
 }
 
 struct coordCols coordColsParseSpec(char *optName, char* spec)
 /* parse coordinate specified in an option. Can be in the form
  *   - chromCol - chrom in this column followed by start and end.
  *   - chromCol,startCol,endCol - chrom, start, and end in specified
  *     columns.
  *   - chromCol,startCol,endCol,strandCol - chrom, start, end, and
  *     strand in specified columns.
  */
 {
 char buf[128];
 int numWords;
 char *words[4];
 struct coordCols cols;
 ZeroVar(&cols);
 cols.strandCol = -1;
 
 if (strlen(spec) > sizeof(buf)-1)
     invalidSpec(optName, spec);
 strcpy(buf, spec);
 numWords = chopString(buf, ",", words, ArraySize(words));
 switch (numWords) {
 case 1:
     cols.chromCol = sqlUnsigned(words[0]);
     cols.startCol = cols.chromCol + 1;
     cols.endCol = cols.chromCol + 2;
     break;
 case 4:
     cols.strandCol = sqlUnsigned(words[3]);
 case 3:
     cols.chromCol = sqlUnsigned(words[0]);
     cols.startCol = sqlUnsigned(words[1]);
     cols.endCol = sqlUnsigned(words[2]);
     break;
 default:
     invalidSpec(optName, spec);
 }
 cols.minNumCols = cols.chromCol;
 cols.minNumCols = max(cols.minNumCols, cols.startCol);
 cols.minNumCols = max(cols.minNumCols, cols.endCol);
 if (cols.strandCol >= 0)
     cols.minNumCols = max(cols.minNumCols, cols.strandCol);
 cols.minNumCols++;
 
 return cols;
 }
 
 struct coordColVals coordColParseRow(struct coordCols* cols,
                                      struct rowReader *rr)
 /* parse coords from a row */
 {
 struct coordColVals colVals;
 ZeroVar(&colVals);
 rowReaderExpectAtLeast(rr, cols->minNumCols);
 colVals.chrom = rr->row[cols->chromCol];
 colVals.start = sqlUnsigned(rr->row[cols->startCol]);
 colVals.end = sqlUnsigned(rr->row[cols->endCol]);
 if (cols->strandCol >= 0)
     colVals.strand = rr->row[cols->strandCol][0];
 return colVals;
 }