e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/utils/bedRemoveOverlap/bedRemoveOverlap.c src/utils/bedRemoveOverlap/bedRemoveOverlap.c
index 633d1d6..02afa14 100644
--- src/utils/bedRemoveOverlap/bedRemoveOverlap.c
+++ src/utils/bedRemoveOverlap/bedRemoveOverlap.c
@@ -1,150 +1,153 @@
 /* bedRemoveOverlap - Remove overlapping records from a (sorted) bed file.  Gets rid of the 
  * smaller of overlapping records.. */
+
+/* Copyright (C) 2011 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bedRemoveOverlap - Remove overlapping records from a (sorted) bed file.  Gets rid of\n"
   "`the smaller of overlapping records.\n"
   "usage:\n"
   "   bedRemoveOverlap in.bed out.bed\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 boolean isCommentLine(char *line)
 /* Return TRUE if line is a BED comment - blank or starting with '#' */
 {
 char *s = skipLeadingSpaces(line);
 char c = s[0];
 return c == '#' || c == 0;
 }
 
 void bedRemoveOverlap(char *input, char *output)
 /* bedRemoveOverlap - Remove overlapping records from a (sorted) bed file.  Gets rid of 
  * the smaller of overlapping records.. */
 {
 struct lineFile *lf = lineFileOpen(input, TRUE);
 FILE *f = mustOpen(output, "w");
 char *prevChrom = NULL;
 unsigned int prevStart = 0, prevEnd = 0;
 char *row[1024];
 int wordCount;
 int maxLineSize = 1024*1024;
 char *prevLine = needMem(maxLineSize);
 char *curLine = needMem(maxLineSize);
 int lineSize;
 char *line;
 boolean firstTime = TRUE;
 while (lineFileNext(lf, &line, &lineSize))
     {
     /* Skip comments and make sure other lines not too long. */
     if (isCommentLine(line))
         continue;
     if (lineSize >= maxLineSize)
         errAbort("Line too long (%d chars, max is %d) line %d of %s", lineSize, 
 	    maxLineSize, lf->lineIx, lf->fileName);
 
     /* Swap existing prevLine and curLine buffers. */
     char *tmp = prevLine;
     prevLine = curLine;
     curLine = tmp;
 
     /* Save current line for use next time through loop. */
     strcpy(curLine, line);
 
     /* Parse current line. */
     wordCount = chopLine(line, row);
     if (wordCount == ArraySize(row))
          errAbort("Too many fields (%d max is %lu) line %d of %s", wordCount, (unsigned long)ArraySize(row),
 	     lf->lineIx, lf->fileName);
     char *chrom = row[0];
     unsigned int start = lineFileNeedNum(lf, row, 1);
     unsigned int end = lineFileNeedNum(lf, row, 2);
 
     if (firstTime)
         {
 	/* First time through the loop don't output anything. */
 	firstTime = FALSE;
 	prevChrom = cloneString(chrom);
 	}
     else
         {
 	/* Check to see if we are on a new chromosome. */
 	int cmp = strcmp(chrom, prevChrom);
 	if (cmp != 0)
 	    {
 	    if (cmp < 0)
 	       errAbort("%s not sorted line %d, %s before %s", 
 		    lf->fileName, lf->lineIx, prevChrom, chrom);
 	    fprintf(f, "%s\n", prevLine);
 	    freeMem(prevChrom);
 	    prevChrom = cloneString(chrom);
 	    }
 	else
 	    {
 	    if (prevStart > start)
 	        errAbort("File not sorted line %d of %s", lf->lineIx, lf->fileName);
 	    if (rangeIntersection(start, end, prevStart, prevEnd) > 0)
 	        {
 		/* Detected overlap.  Don't overlap anything this time through.
 		 * instead dummy things up so bigger piece of overlap gets put
 		 * out next time. */
 		int curSize = end - start;
 		int prevSize = prevEnd - prevStart;
 		if (prevSize > curSize)
 		    {
 		    verbose(2, "%s:%d-%d overlaps %s:%d-%d.  Skipping %s:%d-%d line %d of %s\n",
 		    	prevChrom, prevStart, prevEnd, chrom, start, end, chrom, start, end,
 			lf->lineIx, lf->fileName);
 		    start = prevStart;
 		    end = prevEnd;
 		    strcpy(curLine, prevLine);
 		    }
 		else
 		    {
 		    verbose(2, "%s:%d-%d overlaps %s:%d-%d.  Skipping %s:%d-%d line %d of %s\n",
 		    	prevChrom, prevStart, prevEnd, chrom, start, end, 
 			prevChrom, prevStart, prevEnd, lf->lineIx, lf->fileName);
 		    /* This last bit is only needed for last line of file... */
 		    prevStart = start;
 		    prevEnd = end;
 		    strcpy(prevLine, curLine);
 		    }
 		}
 	    else
 		fprintf(f, "%s\n", prevLine);
 	    }
 	}
     prevStart = start;
     prevEnd = end;
     }
 
 /* Print last line if any. */
 if (!firstTime)
     fprintf(f, "%s\n", curLine);
    
 
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 bedRemoveOverlap(argv[1], argv[2]);
 return 0;
 }