ff9313091f342ffe62a124427b5c9d6a516faaea
hiram
  Thu Oct 15 15:03:07 2015 -0700
fixup gcc warnings for -Wunused-but-set-variable refs #16121

diff --git src/hg/hgc/mafClick.c src/hg/hgc/mafClick.c
index 21cf3f2..9118366 100644
--- src/hg/hgc/mafClick.c
+++ src/hg/hgc/mafClick.c
@@ -91,35 +91,36 @@
 char *summaryLine = needMem(lineSize+1);
 char *referenceText;
 int startChars, sizeChars, srcSizeChars;
 boolean haveInserts = FALSE;
 struct mafComp *masterMc = maf->components;
 
 startChars = sizeChars = srcSizeChars = 0;
 
 for (mc = maf->components; mc != NULL; mc = mc->next)
     {
     /* Figure out length of source (species) field. */
     /*if (mc->size != 0)*/
 	{
 	char dbOnly[128];
 	int len;
-	char *chrom, *org;
+//	char *chrom;  unused variable
+	char *org;
 
 	memset(dbOnly, 0, sizeof(dbOnly));
 	safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
-	chrom = chopPrefix(dbOnly);
+//	chrom = chopPrefix(dbOnly);  unused variable
 
 	if ((org = hOrganism(dbOnly)) == NULL)
 	    len = strlen(dbOnly);
 	else
 	    len = strlen(org);
 	if (srcChars < len)
 	    srcChars = len;
 
 	len = digitsBaseTen(mc->start);
 	if (startChars < len)
 	    startChars = len;
 	len = digitsBaseTen(mc->size);
 	if (sizeChars < len)
 	    sizeChars = len;
 	len = digitsBaseTen(mc->srcSize);
@@ -854,35 +855,36 @@
 char *summaryLine = needMem(lineSize+1);
 char *referenceText;
 int startChars, sizeChars, srcSizeChars;
 boolean haveInserts = FALSE;
 struct mafComp *masterMc = maf->components;
 
 startChars = sizeChars = srcSizeChars = 0;
 
 for (mc = maf->components; mc != NULL; mc = mc->next)
     {
     /* Figure out length of source (species) field. */
     /*if (mc->size != 0)*/
 	{
 	char dbOnly[128];
 	int len;
-	char *chrom, *org;
+//	char *chrom;  unused variable
+	char *org;
 
 	memset(dbOnly, 0, sizeof(dbOnly));
 	safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
-	chrom = chopPrefix(dbOnly);
+	// chrom = chopPrefix(dbOnly);  unused variable
 
 	if ((org = hOrganism(dbOnly)) == NULL)
 	    len = strlen(dbOnly);
 	else
 	    len = strlen(org);
 	if (srcChars < len)
 	    srcChars = len;
 
 	len = digitsBaseTen(mc->start);
 	if (startChars < len)
 	    startChars = len;
 	len = digitsBaseTen(mc->size);
 	if (sizeChars < len)
 	    sizeChars = len;
 	len = digitsBaseTen(mc->srcSize);
@@ -904,38 +906,38 @@
 
 for (lineStart = 0; lineStart < maf->textSize; lineStart = lineEnd)
     {
     int size;
     lineEnd = lineStart + lineSize;
     if (lineEnd >= maf->textSize)
         lineEnd = maf->textSize;
     size = lineEnd - lineStart;
     initSummaryLine(summaryLine, size, '*');
     for (mc = maf->components; mc != NULL; mc = mc->next)
         {
 	char dbOnly[128], *chrom;
 	int s = mc->start;
 	int e = s + mc->size;
 	char *org;
-	char *revComp = "";
-	char strand = mc->strand;
+//	char *revComp = "";  unused variable
 	struct dyString *dy = newDyString(512);
 #ifdef REVERSESTRAND
+	char strand = mc->strand;
 	if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
 	    strand = (strand == '+') ? '-' : '+';
 #endif
-	if (strand == '-') revComp = "&hgSeq.revComp=on";
+//	if (strand == '-') revComp = "&hgSeq.revComp=on";  unused variable
 
 	dyStringClear(dy);
 
 	safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
 	chrom = chopPrefix(dbOnly);
 	if ((org = hOrganism(dbOnly)) == NULL)
 	    org = dbOnly;
 
 	if (mc->strand == '-')
 	    reverseIntRange(&s, &e, mc->srcSize);
 
 
 	if (mc->text != NULL)
 	    {
 	    fprintf(f, "    ");
@@ -998,59 +1000,60 @@
 #ifdef ADDMATCHLINE
     if (lineStart == 0)
 	fprintf(f, "    %-*s %s\n", srcChars, "", summaryLine);
     else
 	fprintf(f, "%-*s %s\n", srcChars, "", summaryLine);
 #else
     fprintf(f, "\n");
 #endif
     }
 
 if (haveInserts)
     {
     fprintf(f, "<B>Inserts between block %d and %d in window</B>\n",blockNo, blockNo+1);
     for (mc = maf->components; mc != NULL; mc = mc->next)
 	{
-	char dbOnly[128], *chrom;
+	char dbOnly[128];
+	// char *chrom;  unused variable
 	int s = mc->start + mc->size;
 	int e = s + mc->rightLen;
 	char *org;
 
 	if (mc->text == NULL)
 	    continue;
 
 	if (mc->strand == '-')
 	    reverseIntRange(&s, &e, mc->srcSize);
 
 	safef(dbOnly, sizeof(dbOnly), "%s", mc->src);
-	chrom = chopPrefix(dbOnly);
+	// chrom = chopPrefix(dbOnly);  unused variable
 
 	if ((org = hOrganism(dbOnly)) == NULL)
 	    org = dbOnly;
 
 	if (mc->rightStatus == MAF_INSERT_STATUS)
 	    {
 	    if (hDbIsActive(dbOnly))
 		{
-		char *revComp = "";
-		char strand = mc->strand;
 #ifdef REVERSESTRAND
+		char strand = mc->strand;
 		if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE))
 		    strand = (strand == '+') ? '-' : '+';
 #endif
-		if (strand == '-') revComp = "&hgSeq.revComp=on";
 		/*
+		char *revComp = "";
+		if (strand == '-') revComp = "&hgSeq.revComp=on";
 		linkToOtherBrowser(dbOnly, chrom, s, e);
 		fprintf(f,"B");
 		fprintf(f, "</A>");
 		fprintf(f, " ");
 
 		printf("<A TARGET=\"_blank\" HREF=\"%s?o=%d&g=getDna&i=%s&c=%s&l=%d&r=%d&db=%s%s\">D</A> ",  hgcName(),
 		   s, cgiEncode(chrom),
 		   chrom,  s, e, dbOnly,revComp);
 		*/
 		fprintf(f, "    ");
 		}
 	    else
 		fprintf(f, "    ");
 
 	    fprintf(f, "%*s %dbp\n", srcChars, org,mc->rightLen);