src/hg/pslPseudo/checkExp/checkExp.c 1.6

Index: src/hg/pslPseudo/checkExp/checkExp.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/pslPseudo/checkExp/checkExp.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 4 -r1.5 -r1.6
--- src/hg/pslPseudo/checkExp/checkExp.c	6 Dec 2004 23:30:36 -0000	1.5
+++ src/hg/pslPseudo/checkExp/checkExp.c	2 Aug 2009 21:26:09 -0000	1.6
@@ -288,9 +288,9 @@
 axt->symCount = symCount = strlen(t);
 axt->tSym = cloneString(t);
 if (strlen(q) != symCount)
     warn("Symbol count %d != %d inconsistent at t %s:%d and qName %s\n%s\n%s\n",
-    	symCount, strlen(q), psl->tName, psl->tStart, psl->qName, t, q);
+    	symCount, (int)strlen(q), psl->tName, psl->tStart, psl->qName, t, q);
 axt->qSym = cloneString(q);
 axt->score = axtScoreFilterRepeats(axt, ss);
 verbose(1,"axt score = %d\n",axt->score);
 //for (i=0; i<size ; i++) 
@@ -416,9 +416,9 @@
     }
 
 if (strlen(q->string) != strlen(t->string))
     warn("Symbol count(t) %d != %d inconsistent at t %s:%d and qName %s\n%s\n%s\n",
-    	strlen(t->string), strlen(q->string), psl->tName, psl->tStart, psl->qName, t->string, q->string);
+    	(int)strlen(t->string), (int)strlen(q->string), psl->tName, psl->tStart, psl->qName, t->string, q->string);
 if (psl->strand[0] == '-')
     {
     reverseComplement(q->string, q->stringSize);
     reverseComplement(t->string, t->stringSize);
@@ -648,8 +648,9 @@
                 {
                 int j = mAxt->tStart - mPsl->tStart;
                 verbose(5, "listLen = %d\n",slCount(&misMatchList));
                 if ((mf = matchFound(&misMatchList, (mPsl->tStart)+i)) != NULL)
+                    {
                     if (toupper(mf->retroBase) == toupper(mAxt->qSym[j+i]))
                         {
                         verbose (3,"match retro[%d] %d %c == %c parent %c %d\n",
                                 i,mf->retroLoc, mf->retroBase, mAxt->qSym[j+i], 
@@ -672,8 +673,9 @@
                                 mf->retroBase, mf->retroLoc);
                         scoreNeither++;
                         }
                 }
+                }
             verbose(2,"final score %s parent %d retro %d  neither %d\n",
                     mPsl->qName, scoreParent, scoreRetro, scoreNeither);
             fprintf(outFile,"%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%d\t%d\t%s\t%s\n",
                     ps->chrom, ps->chromStart, ps->chromEnd, ps->name, ps->score,