src/hg/gigAssembler/checkQa/checkQa.c 1.3

Index: src/hg/gigAssembler/checkQa/checkQa.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/gigAssembler/checkQa/checkQa.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/gigAssembler/checkQa/checkQa.c	6 May 2003 07:22:15 -0000	1.2
+++ src/hg/gigAssembler/checkQa/checkQa.c	7 Jul 2009 18:44:58 -0000	1.3
@@ -1,95 +1,95 @@
 /* checkQa - make sure that .fa and .qa files are in correspondence. */
 
 #include "common.h"
 #include "portable.h"
 #include "linefile.h"
 #include "qaSeq.h"
 
 static char const rcsid[] = "$Id$";
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
  "checkQa - make sure that .fa and .qa files are in correspondence.\n"
  "usage:\n"
  "    checkQa dirs qaDir faDir\n"
  "This checks that all the .fa files in faDir have corresponding\n"
  ".qa files in qaDir.\n"
  "    checkQa files qaFile faFile\n"
  "This checks that qaFile and faFile go together\n"
  "    checkQa top dir1 dir2 ... dirN\n"
  "This checks that all the files in dir1/fa and dir1/qa go together.\n"
  "Likewise for dir2, dir3, etc.");
 }
 
 void qaFiles(char *qaName, char *faName)
 /* Check that qaName and faName agree. */
 {
 struct qaSeq *qaList = qaReadBoth(qaName, faName);
 qaSeqFreeList(&qaList);
 }
 
 void qaDirs(char *qaDir, char *faDir)
 /* check that all the files in faDir have quality
  * files in faDir. */
 {
 char qaName[512];
 char faName[512];
 char cloneName[512];
 int ix = 0;
 struct slName *el, *list;
-struct qaSeq *qaList, *qa;
+struct qaSeq *qaList;
 
 printf("Comparing %s and %s\n", qaDir, faDir);
 list = listDir(faDir, "*.fa");
 for (el = list; el != NULL; el = el->next)
     {
     strcpy(cloneName, el->name);
     chopSuffix(cloneName);
     sprintf(qaName, "%s/%s.qa", qaDir, cloneName);
     sprintf(faName, "%s/%s.fa", faDir, cloneName);
     if (!fileExists(qaName))
         warn("%s doesn't exist", qaName);
     qaList = qaReadBoth(qaName, faName);
     qaSeqFreeList(&qaList);
     if ((++ix & 0x3f) == 0)
           {
 	  printf(".");
 	  fflush(stdout);
 	  }
     }
 printf("\n");
 }
 
 void qaFromTop(int dirCount, char *dirs[])
 /* Check fa and qa subdirectories against each other. */
 {
 int i;
 char faDir[512], qaDir[512];
 for (i=0; i<dirCount; ++i)
      {
      sprintf(qaDir, "%s/qa", dirs[i]);
      sprintf(faDir, "%s/fa", dirs[i]);
      qaDirs(qaDir, faDir);
      }
 }
 
 int main(int argc, char *argv[])
 /* Process command line . */
 {
 char *command;
 
 if (argc < 3)
     usage();
 command = argv[1];
 if (sameWord(command, "dirs"))
     qaDirs(argv[2], argv[3]);
 else if (sameWord(command, "files"))
     qaFiles(argv[2], argv[3]);
 else if (sameWord(command, "top"))
     qaFromTop(argc-2, argv+2);
 else
     usage();
 return 0;
 }