src/shortReads/bwtMake/bananas.suffix 1.2

Index: src/shortReads/bwtMake/bananas.suffix
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/shortReads/bwtMake/bananas.suffix,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/shortReads/bwtMake/bananas.suffix	7 Nov 2008 23:54:52 -0000	1.1
+++ src/shortReads/bwtMake/bananas.suffix	24 Nov 2009 15:48:52 -0000	1.2
@@ -1,28 +1,56 @@
-0 s $        occ[s,0] = 0
-1 b ananas$  occ[b,1] = 0
-2 n anas$    occ[n,2] = 0
-3 n as$      occ[n,3] = 1
-4 $ bananas$ occ[$,4] = 1
-5 a nanas$   occ[a,5] = 0
-6 a nas$     occ[a,6] = 1
-7 a s$       occ[a,7] = 2
-
-offsets
-   $ - 0
-   a - 1
-   b - 4
-   n - 5
-   s - 7
+             occ[*,-1] = -1?
+1 s $        occ[s,0] = 1
+2 b ananas$  occ[b,1] = 1
+3 n anas$    occ[n,2] = 1
+4 n as$      occ[n,3] = 2
+5 $ bananas$ occ[$,4] = 1
+6 a nanas$   occ[a,5] = 1
+7 a nas$     occ[a,6] = 2
+8 a s$       occ[a,7] = 3
+
+offsets $ = 0,  a = 1,  b = 4,  n = 5,  s = 7
 
 reconstructing in reverse
-   letter = $,  nextPos = 0  <- start condition, always starts with last letter
-   letter = s,  nextPos = offsets[s] + occ[s,0] = 7+0 = 7
+   letter = $,  nextPos = 1  <- start condition, always starts with last letter
+   letter = s,  nextPos = offsets[s] + occ[s,1] = 7+1 = 8
+   letter = a,  nextPos = offsets[a] + occ[a,8] = 1+3 = 4
+   letter = n,  nextPos = offsets[n] + occ[n,4] = 5+2 = 7
    letter = a,  nextPos = offsets[a] + occ[a,7] = 1+2 = 3
    letter = n,  nextPos = offsets[n] + occ[n,3] = 5+1 = 6
    letter = a,  nextPos = offsets[a] + occ[a,6] = 1+1 = 2
-   letter = n,  nextPos = offsets[n] + occ[n,2] = 5+0 = 5
-   letter = a,  nextPos = offsets[a] + occ[a,5] = 1+0 = 1
-   letter = b,  nextPos = offsets[b] + occ[b,1] = 4+0 = 4
+   letter = b,  nextPos = offsets[b] + occ[b,2] = 4+0 = 4
+  
+search for 'ana'
+       start=1, end=8
+   c=a start=1+0+1=2, end=1+3=4
+   c=n start=5+0+1=6, end=5+2=7
+   c=a start=1+0+1=2, end=1+2=3
+       [2,3]
   
+search for 'sa'
+       start=1, end=8
+   c=a start=1+0+1=2, end=1+3=4
+   c=s start=7+1+1=9, end=7+1=8
+       [9,8] = []
+
+search for 'nn'
+       start=1, end=8
+   c=n start=5+0+1=6, end=5+2=7
+   c=n start=5+2+1=8, end=5+2=7
+       [8,7] = []
+   
+---------------------------------------------------------------
 search for 'ana'
+       start=0 end=7 i=2
+   c=a start=1+0=1  end=1+2=3
+   c=n start=5+0=5  end=5+1=6
+   c=a start=1+0=1  end=1+1=2
+   
+search for 'sa'
+       start=0 end=7 i=1
+   c=a start=1+0=1  end=1+2=3
+   c=s start=7+0=7  end=7+0=7
 
+search for 'b'
+	start=0 end=7 i=0
+    c=b start=4 end=4+1=5