Merge pull request #126 from brentp/contingency-order

fix #117 by re-ordering contingency table. 

docs/content/tools/fisher.rst

@@ -43,8 +43,8 @@ can do this with ``fisher`` as:
     # Contingency Table
     #_________________________________________
     #           | not in -b    | in -b        |
-    # not in -a | 475          | 15           |
-    #     in -a | 5            | 5            |
+    # not in -a | 475          | 5           |
+    #     in -a | 15           | 5            |
     #_________________________________________
     # p-values for fisher's exact test
     left    right   two-tail    ratio

src/fisher/Fisher.cpp

@@ -38,10 +38,10 @@ bool Fisher::calculate() {
     long long genomeSize = _context->getGenomeFile()->getGenomeSize();
     // bases covered by neither a nor b
     long long n11 = genomeSize - _queryLen - _dbLen + _intersectionVal;
-    // bases covered only by -a
-    long long n12 = _queryLen - _intersectionVal;
     // bases covered only by -b
-    long long n21 = _dbLen - _intersectionVal;
+    long long n12 = _dbLen - _intersectionVal;
+    // bases covered only by -a
+    long long n21 = _queryLen - _intersectionVal;
     // bases covered by both
     long long n22 = _intersectionVal;