From 17a8ec10b3ca3c4ac0f3dca26c4106213a999584 Mon Sep 17 00:00:00 2001
From: Daniel Mapleson <daniel.mapleson@tgac.ac.uk>
Date: Fri, 7 Apr 2017 15:08:35 +0100
Subject: [PATCH] Fixed a bug which was causing a seg fault when using the comp
 tool with bin sizes larger than the default value.

---
 configure.ac                      | 2 +-
 doc/source/conf.py                | 4 ++--
 lib/include/kat/comp_counters.hpp | 4 ++++
 lib/include/kat/sparse_matrix.hpp | 2 +-
 lib/src/comp_counters.cc          | 4 ++++
 src/comp.cc                       | 3 +--
 6 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/configure.ac b/configure.ac
index 36f4416b..8e70640d 100644
--- a/configure.ac
+++ b/configure.ac
@@ -4,7 +4,7 @@
 
 # Autoconf initialistion.  Sets package name version and contact details
 AC_PREREQ([2.68])
-AC_INIT([kat],[2.3.2],[https://github.com/TGAC/KAT/issues],[kat],[https://github.com/TGAC/KAT])
+AC_INIT([kat],[2.3.3],[https://github.com/TGAC/KAT/issues],[kat],[https://github.com/TGAC/KAT])
 AC_CONFIG_SRCDIR([src/kat.cc])
 AC_CONFIG_AUX_DIR([build-aux])
 AC_CONFIG_MACRO_DIR([m4])
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 0816bdf2..a7d5e020 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -52,9 +52,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2.3.2'
+version = '2.3.3'
 # The full version, including alpha/beta/rc tags.
-release = '2.3.2'
+release = '2.3.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/lib/include/kat/comp_counters.hpp b/lib/include/kat/comp_counters.hpp
index e482a88a..5ce341d4 100644
--- a/lib/include/kat/comp_counters.hpp
+++ b/lib/include/kat/comp_counters.hpp
@@ -57,6 +57,8 @@ class CompCounters {
     path hash3_path;
 
     CompCounters();
+	
+	CompCounters(const size_t _dm_size);
 
     CompCounters(const path& _hash1_path, const path& _hash2_path, const path& _hash3_path, const size_t _dm_size);
 
@@ -92,6 +94,8 @@ class ThreadedCompCounters {
 public:
 
     ThreadedCompCounters();
+	
+	ThreadedCompCounters(const size_t _dm_size);
 
     ThreadedCompCounters(const path& _hash1_path, const path& _hash2_path, const path& _hash3_path, const size_t _dm_size);
 
diff --git a/lib/include/kat/sparse_matrix.hpp b/lib/include/kat/sparse_matrix.hpp
index 7e9423c0..fed458a9 100644
--- a/lib/include/kat/sparse_matrix.hpp
+++ b/lib/include/kat/sparse_matrix.hpp
@@ -323,7 +323,7 @@ class ThreadedSparseMatrix {
     }
 
     const SM64& mergeThreadedMatricies() {
-        // Merge matrix
+		// Merge matrix
         for (int i = 0; i < width; i++) {
             for (int j = 0; j < height; j++) {
                 for (int k = 0; k < threads; k++) {
diff --git a/lib/src/comp_counters.cc b/lib/src/comp_counters.cc
index a219fb5d..37ab8ffa 100644
--- a/lib/src/comp_counters.cc
+++ b/lib/src/comp_counters.cc
@@ -39,6 +39,8 @@ using kat::DistanceMetric;
 
 kat::CompCounters::CompCounters() : CompCounters("", "", "", DEFAULT_NB_BINS) {}
 
+kat::CompCounters::CompCounters(const size_t _dm_size) : CompCounters("", "", "", _dm_size) {}
+
 kat::CompCounters::CompCounters(const path& _hash1_path, const path& _hash2_path, const path& _hash3_path, const size_t _dm_size) :
         hash1_path(_hash1_path), hash2_path(_hash2_path), hash3_path(_hash3_path) {
 
@@ -208,6 +210,8 @@ void kat::CompCounters::printCounts(ostream &out) {
 
 kat::ThreadedCompCounters::ThreadedCompCounters() : ThreadedCompCounters("", "", "", DEFAULT_NB_BINS) {}
 
+kat::ThreadedCompCounters::ThreadedCompCounters(const size_t _dm_size) : ThreadedCompCounters("", "", "", _dm_size) {}
+
 kat::ThreadedCompCounters::ThreadedCompCounters(const path& _hash1_path, const path& _hash2_path, const path& _hash3_path, const size_t _dm_size) {
     final_matrix = CompCounters(_hash1_path, _hash2_path, _hash3_path, _dm_size);            
 }
diff --git a/src/comp.cc b/src/comp.cc
index 8664fe6f..41813776 100644
--- a/src/comp.cc
+++ b/src/comp.cc
@@ -253,7 +253,6 @@ void kat::Comp::merge() {
 
     cout << "Merging results ...";
     cout.flush();
-
     // Merge results from the threads
     main_matrix.mergeThreadedMatricies();
     if (doThirdHash()) {
@@ -390,7 +389,7 @@ void kat::Comp::compare() {
 
 void kat::Comp::compareSlice(int th_id) {
 
-    shared_ptr<CompCounters> cc = make_shared<CompCounters>();
+    shared_ptr<CompCounters> cc = make_shared<CompCounters>(std::min(this->d1Bins, this->d2Bins));
 
     // Setup iterator for this thread's chunk of hash1
     LargeHashArray::eager_iterator hash1Iterator = input[0].hash->eager_slice(th_id, threads);