src/hg/bedSplitOnChrom/bedSplitOnChrom.c 1.4

Index: src/hg/bedSplitOnChrom/bedSplitOnChrom.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/bedSplitOnChrom/bedSplitOnChrom.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/bedSplitOnChrom/bedSplitOnChrom.c	29 Sep 2009 00:54:16 -0000	1.3
+++ src/hg/bedSplitOnChrom/bedSplitOnChrom.c	30 Sep 2009 03:26:06 -0000	1.4
@@ -10,8 +10,9 @@
 
 int maxChromCount = 256;
 boolean nfCheck;    /* check for number of fields consistency */
 boolean doStrand;   /* append strand to file name */
+boolean doAppend;   /* append to rather than create files */
 
 void usage()
 /* Explain usage and exit. */
 {
@@ -19,15 +20,17 @@
   "bedSplitOnChrom - Split bed into a directory with one file per chromosome.\n"
   "usage:\n"
   "   bedSplitOnChrom inFile.bed outDir\n"
   "options:\n"
+  "   -append   append to rather than create files\n"
   "   -strand   append strand to file name\n"
   "   -noCheck  do not check to see if number of fields is same in every record\n"
   "   -maxChromCount=N Maximum number of different chromosomes, default %d\n"
   , maxChromCount);
 }
 
 static struct optionSpec options[] = {
+   {"append", OPTION_BOOLEAN},
    {"strand", OPTION_BOOLEAN},
    {"noCheck", OPTION_BOOLEAN},
    {"maxChromCount", OPTION_INT},
    {NULL, 0},
@@ -82,8 +85,9 @@
     if (differentString(chrom, lastChrom))
 	{
 	f = hashFindVal(fileHash, chrom);
 	strcpy(lastChrom, chrom);
+	verbose(2, "new chrom %s f %p\n", lastChrom,f);
 	}
 
     if (f == NULL)
         {
@@ -91,9 +95,10 @@
 	    errAbort("%s is the %dth chromosome, which is too many. "
 	             "Use maxChromCount option if need be.",
 		     chrom, fileHash->elCount+1);
 	safef(path, sizeof(path), "%s/%s.bed", outDir, chrom);
-	f = mustOpen(path, "w");
+	f = mustOpen(path, doAppend ? "a" : "w");
+	verbose(2, "opened %s f %p\n",path, f);
 	hashAdd(fileHash, chrom, f);
 	}
 
     /* Output line of bed file, starting with the three fields that are always there. */
@@ -135,7 +140,8 @@
 if (argc != 3)
     usage();
 nfCheck = !optionExists("noCheck");
 doStrand = optionExists("strand");
+doAppend = optionExists("append");
 bedSplitOnChrom(argv[1], argv[2]);
 return 0;
 }