3d99448b720b00eca4635e3dc8c72c73d0faa509
braney
  Sun Jun 29 11:26:33 2014 -0700
pslPairs has a memory trashing bug.  These changes avoid the problem,without incurring any real cost.

diff --git src/hg/pslPairs/pslPairs.c src/hg/pslPairs/pslPairs.c
index a3ba3b1..3c84978 100644
--- src/hg/pslPairs/pslPairs.c
+++ src/hg/pslPairs/pslPairs.c
@@ -84,57 +84,57 @@
     {"min", OPTION_INT},
     {"max", OPTION_INT},
     {"slopval", OPTION_INT},
     {"nearTop", OPTION_FLOAT},
     {"minId", OPTION_FLOAT},
     {"minOrphanId", OPTION_FLOAT},
     {"tInsert", OPTION_INT},
     {"hardMax", OPTION_INT},
     {NULL, 0}
 };
 
 FILE *of, *orf, *sf, *mf, *esf, *elf;
 
 struct cloneName
 {
-  char name[32];
+  char name[128];
 };
 
 struct pslAli
 {
   struct pslAli *next;
   int score;
   float id;
   float cov;
   struct psl *psl;
 };
 
 struct pslPair
 {
   struct pslPair *next;
   struct pslAli *f;
   struct pslAli *r;
   int score;
   int distance;
   boolean orien;
   boolean random;
 };
 
 struct clone
 {
   struct clone *next;
-  char name[32];
+  char name[128];
   struct pslAli *end1;
   struct pslAli *end2;
   struct pslPair *pairs;
   struct pslPair *pairsRandom;
   struct pslPair *pairsSlop;
   struct pslPair *pairsExtremeS;
   struct pslPair *pairsExtremeL;
   struct pslPair *pairsMM;
   boolean orphan;
 } *cloneList = NULL;
 
 struct hash *clones = NULL;
 struct hash *leftNames = NULL;
 struct hash *rightNames = NULL;
 
@@ -166,30 +166,31 @@
 
 void pslPairListFree(struct pslPair **pList)
 {
   struct pslPair *i, *next;
 
   for (i = *pList; i != NULL; i = next)
     {
       next = i->next;
       pslPairFree(&i);
     }
   *pList = NULL;
 }
 
 void cloneFree(struct clone **c)
 {
+  return;
   struct clone *el;
 
   if ((el = *c) == NULL) return;
   pslAliListFree(&(el->end1));
   pslAliListFree(&(el->end2));
   pslPairListFree(&(el->pairs));
   freez(c);
 }
 
 struct pslAli *createPslAli(struct psl *psl)
 /* Create a pslAli element from a psl record */
 {
   struct pslAli *pa;
   
   AllocVar(pa);