src/hg/utils/bedExtendRanges/bedExtendRanges.c 1.3

Index: src/hg/utils/bedExtendRanges/bedExtendRanges.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/bedExtendRanges/bedExtendRanges.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/utils/bedExtendRanges/bedExtendRanges.c	7 Oct 2008 00:04:41 -0000	1.2
+++ src/hg/utils/bedExtendRanges/bedExtendRanges.c	6 Apr 2009 18:13:51 -0000	1.3
@@ -1,183 +1,206 @@
 /* bedExtendRanges - extend bed item sizes. */
 #include "common.h"
 #include "options.h"
 #include "linefile.h"
 #include "obscure.h"
 #include "hash.h"
 #include "jksql.h"
 #include "dystring.h"
 #include "chromInfo.h"
 #include "hdb.h"
 #include "portable.h"
 
 static char const rcsid[] = "$Id$";
 
 static boolean strictTab = FALSE;	/* Separate on tabs. */
 static struct hash *chromHash = NULL;
+char *host = NULL;
+char *user = NULL;
+char *password = NULL;
 
 static struct optionSpec optionSpecs[] = {
     {"tab", OPTION_BOOLEAN},
+    {"host", OPTION_STRING},
+    {"user", OPTION_STRING},
+    {"password", OPTION_STRING},
     {NULL, 0}
 };
 
 /* Command line switches. */
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bedExtendRanges - extend length of entries in bed 6+ data to be at least the given length,\n"
   "taking strand directionality into account.\n\n"
   "usage:\n"
   "   bedExtendRanges database length files(s)\n\n"
   "options:\n"
+  "   -host\tmysql host\n"
+  "   -user\tmysql user\n"
+  "   -password\tmysql password\n"
   "   -tab\t\tSeparate by tabs rather than space\n"
   "   -verbose=N - verbose level for extra information to STDERR\n\n"
   "example:\n\n"
   "   bedExtendRanges hg18 250 stdin\n\n"
+  "   bedExtendRanges -user=genome -host=mysql.cse.ucsc.edu hg18 250 stdin\n\n"
   "will transform:\n"
   "    chr1 500 525 . 100 +\n" 
   "    chr1 1000 1025 . 100 -\n" 
   "to:\n"
   "    chr1 500 750 . 100 +\n"
   "    chr1 775 1025 . 100 -\n"
   );
 }
 
 static struct hash *loadAllChromInfo(char *database)
 /* Load up all chromosome infos. */
 {
 struct chromInfo *el;
 struct sqlConnection *conn = NULL;
 struct sqlResult *sr = NULL;
 struct hash *ret;
 char **row;
+boolean localDb = TRUE;
 
-conn = hAllocConn(database);
+if(host)
+    {
+    conn = sqlConnectRemote(host, user, password, database);
+    localDb = FALSE;
+    }
+else
+    {
+    conn = hAllocConn(database);
+    }
 ret = newHash(0);
 
 sr = sqlGetResult(conn, "select * from chromInfo");
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = chromInfoLoad(row);
     verbose(4, "Add hash %s value %u (%#lx)\n", el->chrom, el->size, (unsigned long)&el->size);
     hashAdd(ret, el->chrom, (void *)(& el->size));
     }
 sqlFreeResult(&sr);
-hFreeConn(&conn);
+if(localDb)
+    hFreeConn(&conn);
 return ret;
 }
 
 static unsigned chromosomeSize(char *chromosome)
 /* Return full extents of chromosome.  Warn and fill in if none. */
 {
 struct hashEl *el = hashLookup(chromHash,chromosome);
 
 if (el == NULL)
     errAbort("Couldn't find size of chromosome %s (note: chrom names are case sensitive)", chromosome);
 return *(unsigned *)el->val;
 }
 
 static void processOneFile(char *fileName, int bedSize, int length)
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *words[64], *line;
 int wordCount;
 
 verbose(1, "Reading %s\n", lf->fileName);
 while (lineFileNextReal(lf, &line))
     {
     int i;
     char *dupe = cloneString(line);
     if (strictTab)
 	wordCount = chopTabs(line, words);
     else
 	wordCount = chopLine(line, words);
     /* ignore empty lines	*/
     if (0 == wordCount)
 	continue;
     lineFileExpectAtLeast(lf, bedSize, wordCount);
 
     char *chrom = words[0];
     // use signed for chromStart b/c calculations below may (temorarily) yield a negative number.
     int chromStart = lineFileNeedNum(lf, words, 1);
     unsigned chromEnd = lineFileNeedNum(lf, words, 2);
     char *name = words[3];
     int score = lineFileNeedNum(lf, words, 4);
     char *strand = words[5];
     
     if (chromEnd < 1)
         errAbort("ERROR: line %d:'%s'\nchromEnd is less than 1\n",
 		     lf->lineIx, dupe);
     if (chromStart > chromEnd)
         errAbort("ERROR: line %d:'%s'\nchromStart after chromEnd (%d > %d)\n",
                  lf->lineIx, dupe, chromStart, chromEnd);
 
     int delta = length - (chromEnd - chromStart);
     if(delta && delta > 0)
         {
         if(sameString(strand, "+"))
             chromEnd += delta;
         else if (sameString(strand, "-"))
             chromStart -= delta;
         else
             {
             chromStart -= delta / 2;
             chromEnd += delta / 2 + delta % 2;
             }
         }
     chromStart = max(0, chromStart);
     unsigned size = chromosomeSize(chrom);
     // XXXX special-case chrM?
     chromEnd = min(chromEnd, size);
 
     char sep = strictTab ? '\t' : ' ';
     printf("%s%c%d%c%d%c%s%c%d%c%s", chrom, sep, chromStart, sep, chromEnd, sep, name, sep, score, sep, strand);
     // print out remaining (unprocessed) fields.
     for(i=6;i<wordCount;i++)
         {
         printf("%c%s", sep, words[i]);
         }
     printf("\n");
     freeMem(dupe);
     }
 }
 
 static void bedExtendRanges(char *database, int length,
 	int count, char *files[])
 /* bedExtendRanges - process each file to extend ranges. */
 {
 int i;
 
 chromHash = loadAllChromInfo(database);
 
 if (verboseLevel() > 2)
     {
     struct hashCookie cookie;
     struct hashEl *el;
 
     cookie = hashFirst(chromHash);
 
     verbose(3,"chrom\tsize\n");
     while ((el = hashNext(&cookie)) != NULL)
 	{
 	unsigned size;
 	size = chromosomeSize(el->name);
 	verbose(3,"%s\t%u\n", el->name, size);
 	}
     }
 
 for (i=0; i<count; ++i)
     processOneFile(files[i], 6, length);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, optionSpecs);
 if (argc < 3)
     usage();
 strictTab = optionExists("tab");
+host = optionVal("host", NULL);
+user = optionVal("user", NULL);
+password = optionVal("password", NULL);
 
 bedExtendRanges(argv[1], atoi(argv[2]), argc-3, argv+3);
 return 0;
 }