a3106f988783aede6481d2e3b685706e109747c1
kent
  Thu May 21 11:49:42 2015 -0700
Removing some unused code.

diff --git src/jkOwnLib/ffSeedExtend.c src/jkOwnLib/ffSeedExtend.c
index e0baaf4..98f5ee9 100644
--- src/jkOwnLib/ffSeedExtend.c
+++ src/jkOwnLib/ffSeedExtend.c
@@ -819,52 +819,30 @@
     }
 if (score >= 3* matchScore)
     score += matchScore;
 return score;
 }
 
 static void grabAroundIntron(char *hpStart, int iPos, int iSize,
 	int modPeelSize, char *hSeq)
 /* Grap sequence on either side of intron. */
 {
 memcpy(hSeq, hpStart, iPos);
 memcpy(hSeq+iPos, hpStart+iPos+iSize, modPeelSize - iPos);
 hSeq[modPeelSize] = 0;
 }
 
-#ifdef UNTESTED
-struct ffAli *removeFf(struct ffAli *ff, struct ffAli *ffList)
-/* Remove ffAli and free it.  Return resulting list. */
-{
-struct ffAli *right = ff->right;
-struct ffAli *left;
-if (ff == ffList)
-    {
-    if (right != NULL)
-	right->left = NULL;
-    freeMem(ff);
-    return right;
-    }
-left = ff->left;
-left->right = right;
-if (right != NULL)
-    right->left = left;
-freeMem(ff);
-return ffList;
-}
-#endif /* UNTESTED */
-
 static struct ffAli *hardRefineSplice(struct ffAli *left, struct ffAli *right,
 	struct dnaSeq *qSeq, struct dnaSeq *tSeq, struct ffAli *ffList, 
 	int orientation)
 /* Do difficult refinement of splice site.  See if
  * can get nice splice sites without breaking too much.  */
 {
 /* Strategy: peel back about 6 bases on either side of intron.
  * Then try positioning the intron at each position in the
  * peeled area and assessing score. */
 int peelSize = 12;
 char nSeq[12+1], hSeq[12+1+1];
 char nSym[25], hSym[25];
 int symCount;
 int seqScore, spliceScore, score, maxScore = 0;
 int nGap = right->nStart - left->nEnd;