a44421a79fb36cc2036fe116b97ea3bc9590cd0c
braney
  Fri Dec 2 09:34:39 2011 -0800
removed rcsid (#295)
diff --git src/hg/affyTransciptome/nmerParasolGenome.c src/hg/affyTransciptome/nmerParasolGenome.c
index dcbc618..af08a30 100644
--- src/hg/affyTransciptome/nmerParasolGenome.c
+++ src/hg/affyTransciptome/nmerParasolGenome.c
@@ -1,72 +1,71 @@
 #include "common.h"
 #include "hdb.h"
 #include "jksql.h"
 
-static char const rcsid[] = "$Id: nmerParasolGenome.c,v 1.2 2003/05/06 07:22:13 kate Exp $";
 
 struct slName *chromNames = NULL;
 char *dirName = NULL;
 
 int chunkSize = 0;
 
 void usage() 
 {
 errAbort("nmerParasolGenome - creates a series of parasol jobs to span the entire genome\n"
 	 "for nmerAlign. Must be run from a machine that has the genome database\n"
 	 "as it is used for getting chromsomes names, files, and sizes.\n"
 	 "usage:\n\t"
 	 "nmerParasolGenome <genome {hg12,hg13,etc}> <chunkSize> <fastaFile.fa> <oligoSize> <outputDir>\n");
 }
 
 void getChromNamesAndDirForDb(char *db)
 {
 struct sqlConnection *conn = hConnectCentral();
 char query[512];
 char buff[512];
 char *tmpMark = NULL;
 int buffSize = 512;
 
 snprintf(query, sizeof(query), "select nibPath from dbDb where name='%s'", db);
 if(sqlQuickQuery(conn, query, buff, buffSize) == NULL)
     errAbort("Coun't find nib dir for genome %s\n", db);
 dirName = needMem(buffSize*sizeof(char));
 tmpMark = strrchr(buff, '/');
 if(tmpMark != NULL)
     *tmpMark = '\0';
 snprintf(dirName, buffSize, "%s/mixedNib/", buff);
 chromNames = hAllChromNames();
 hDisconnectCentral(&conn);
 }
 
 void writeOutJobs(char *fastaFile, int size, int oligoSize, char *outDir)
 {
 struct slName *chromName = NULL;
 char buff[512];
 FILE *out = mustOpen("parasol.spec", "w");
 for(chromName = chromNames; chromName != NULL; chromName = chromName->next) 
     {
     int chromSize = hChromSize(chromName->name);
     int mark = 0;
     while(mark + chunkSize < chromSize) 
 	{
 	fprintf(out, "nmerAlign %d %d %s%s.nib %s %s/%s:%d-%d.nmer nmerSize=%d\n", 
 		mark, mark+chunkSize, dirName, chromName->name, fastaFile, outDir, chromName->name, mark, mark+chunkSize, oligoSize);
 	mark += chunkSize - 25;
 	}
     fprintf(out, "nmerAlign %d %d %s%s.nib %s %s/%s:%d-%d.nmer nmerSize=%d\n", 
 		mark, chromSize , dirName, chromName->name, fastaFile, outDir, chromName->name, mark, chromSize, oligoSize);
     }
 }
 
 int main(int argc, char *argv[])
 {
 int oligoSize = 0;
 if(argc != 6)
     usage();
 hSetDb(argv[1]);
 chunkSize = atoi(argv[2]);
 oligoSize = atoi(argv[4]);
 getChromNamesAndDirForDb(argv[1]);
 writeOutJobs(argv[3], chunkSize, oligoSize, argv[5]);
 return 0;
 }