From 51ef360166bccd2981fc82fdb157b950820fbd67 Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Wed, 8 Oct 2014 15:11:33 -0600
Subject: [PATCH] fix #117 by re-ordering contingency table. thanks
@thomasgilgenast for a clear report
---
docs/content/tools/fisher.rst | 4 ++--
src/fisher/Fisher.cpp | 6 +++---
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/docs/content/tools/fisher.rst b/docs/content/tools/fisher.rst
index efc6814a..239328dd 100644
--- a/docs/content/tools/fisher.rst
+++ b/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
diff --git a/src/fisher/Fisher.cpp b/src/fisher/Fisher.cpp
index 38eb23b4..874da58b 100644
--- a/src/fisher/Fisher.cpp
+++ b/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;
--
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