src/hg/mouseStuff/netSplit/netSplit.c 1.6

Index: src/hg/mouseStuff/netSplit/netSplit.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/mouseStuff/netSplit/netSplit.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/hg/mouseStuff/netSplit/netSplit.c	26 Aug 2005 21:02:12 -0000	1.5
+++ src/hg/mouseStuff/netSplit/netSplit.c	23 Sep 2009 18:42:23 -0000	1.6
@@ -1,60 +1,60 @@
 /* netSplit - Split a genome net file into chromosome net files. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "portable.h"
 #include "chainNet.h"
 
 static char const rcsid[] = "$Id$";
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "netSplit - Split a genome net file into chromosome net files\n"
   "usage:\n"
   "   netSplit in.net outDir\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 void netSplit(char *inNet, char *outDir)
 /* netSplit - Split a genome net file into chromosome net files. */
 {
 char fileName[512], tpath[512], cmd[512];
 struct lineFile *lf = lineFileOpen(inNet, TRUE);
 FILE *f, *meta ;
 struct chainNet *net;
 bool metaOpen = TRUE;
 safef(tpath, sizeof(tpath), "%s/meta.tmp", outDir);
 
 makeDir(outDir);
 meta = mustOpen(tpath,"w");
 lineFileSetMetaDataOutput(lf, meta);
 while ((net = chainNetRead(lf)) != NULL)
     {
     safef(fileName, sizeof(fileName), "%s/%s.net", outDir, net->name);
     if (metaOpen)
         fclose(meta);
     metaOpen = FALSE;
     safef(cmd,sizeof(cmd), "cat %s | sort -u > %s", tpath, fileName);
-    system(cmd);
+    mustSystem(cmd);
     f = mustOpen(fileName, "a");
     printf("Writing %s\n", fileName);
     chainNetWrite(net, f);
     carefulClose(&f);
     chainNetFree(&net);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionHash(&argc, argv);
 if (argc != 3)
     usage();
 netSplit(argv[1], argv[2]);
 return 0;
 }