src/hg/gigAssembler/gapper/gapper.c 1.4

Index: src/hg/gigAssembler/gapper/gapper.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/gigAssembler/gapper/gapper.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/gigAssembler/gapper/gapper.c	5 Sep 2003 21:30:42 -0000	1.3
+++ src/hg/gigAssembler/gapper/gapper.c	7 Jul 2009 18:44:59 -0000	1.4
@@ -308,9 +308,8 @@
 {
 int lineSize, wordCount;
 char *line, *words[20];
 boolean gotEnd = FALSE;
-char *lastCtgName = "";
 char *acc, *bac;
 struct gContig *contig = NULL;
 struct gContigRef *contigRef;
 struct hashEl *hel;
@@ -402,9 +401,9 @@
     if (wordCount != 5 && wordCount != 4)
 	errAbort("Odd start line %d of %s\n", in->lineIx, in->fileName);
     s = strrchr(words[2], '.');
     if (s == NULL)
-	errAbort("Couldn't find chromosome line %d of 5s\n", in->lineIx, in->fileName);
+	errAbort("Couldn't find chromosome line %d of %5s\n", in->lineIx, in->fileName);
     s += 1;
     strncpy(chromName, s, sizeof(chromName));
     if (!sameString(chromName, lastChromName))
 	{
@@ -691,11 +690,9 @@
 struct bConnect *bcList = NULL, *bc;
 bits32 count;
 bits32 i;
 char s[256];
-int slen;
 struct hashEl *hel;
-struct gClone *clone;
 
 mustReadOne(f, count);
 for (i=0; i<count; ++i)
     {
@@ -811,9 +808,9 @@
 int tot = 0;
 
 mustReadOne(f, sig);
 if (sig != bcTempSig)
-    errAbort("%s isn't a valid gapPreProc file\n");
+    errAbort("%s isn't a valid gapPreProc file\n", fileName);
 mustReadOne(f, count);
 for (i=0; i<count; ++i)
     {
     fastReadString(f, s);
@@ -1423,12 +1420,8 @@
 {
 struct joinedBarges *jb;
 char *jbName;
 struct joinedClones *jc;
-int selfSingleCount = 0;
-int selfDoubleCount = 0;
-int otherSingleCount = 0;
-int otherDoubleCount = 0;
 struct gBarge *bargeA, *bargeB;
 struct hashEl *hel;
 struct connectPair *cp;