From 23dbf95663e19316d1315f5a0319a3ed2dc97d9b Mon Sep 17 00:00:00 2001
From: "Marcus D. R. Klarqvist" <mk819@cam.ac.uk>
Date: Sun, 18 Feb 2018 14:14:55 +0000
Subject: [PATCH] release 0.3.3

---
 README.md                                 |  2 +-
 RELEASE.md                                | 14 +++++++-
 src/support/MagicConstants.h              |  2 +-
 src/tomahawk/two/TomahawkOutputReader.cpp | 39 +++++++++++++----------
 4 files changed, 38 insertions(+), 19 deletions(-)

diff --git a/README.md b/README.md
index 75748cb..c08fc2b 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
 [![Build Status](https://travis-ci.org/mklarqvist/tomahawk.svg?branch=master)](https://travis-ci.org/mklarqvist/tomahawk)
-[![Release](https://img.shields.io/badge/Release-beta_0.3.2-blue.svg)](https://github.com/mklarqvist/tomahawk/releases)
+[![Release](https://img.shields.io/badge/Release-beta_0.3.3-blue.svg)](https://github.com/mklarqvist/tomahawk/releases)
 [![License](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE)
 
 ![screenshot](tomahawk.png)
diff --git a/RELEASE.md b/RELEASE.md
index 6372730..68d5b2a 100644
--- a/RELEASE.md
+++ b/RELEASE.md
@@ -1,7 +1,16 @@
+# Release 0.3.3
+
+## Major Features And Improvements
+* None
+
+## Bug Fixes and Other Changes
+* Bug fixes
+   * Viewing sorted two files fixed for edge cases
+
 # Release 0.3.2
 
 ## Breaking Changes
-* Sorted files needs to be resorted. Using old sorted files does not break functionality
+* Using old sorted files does not break functionality but have to be resorted
 
 ## Major Features And Improvements
 * Sorting `two` files not correctly produces two indices used for fast queries
@@ -13,6 +22,9 @@
 
 # Release 0.3.1
 
+## Major Features And Improvements
+* None
+
 ## Bug Fixes and Other Changes
 * Bug fixes
    * Sort merge (`tomahawk sort -M`) now produces the correct output
diff --git a/src/support/MagicConstants.h b/src/support/MagicConstants.h
index d7e697b..77a4869 100644
--- a/src/support/MagicConstants.h
+++ b/src/support/MagicConstants.h
@@ -15,7 +15,7 @@ extern std::string INTERPRETED_COMMAND;
 
 // Versioning
 const float PROGRAM_VERSION_MAJOR = 0.3; // major
-const float PROGRAM_VERSION_MINOR = 2;
+const float PROGRAM_VERSION_MINOR = 3;
 
 const double ALLOWED_ROUNDING_ERROR = 0.001;
 
diff --git a/src/tomahawk/two/TomahawkOutputReader.cpp b/src/tomahawk/two/TomahawkOutputReader.cpp
index dc23061..57ab4de 100644
--- a/src/tomahawk/two/TomahawkOutputReader.cpp
+++ b/src/tomahawk/two/TomahawkOutputReader.cpp
@@ -553,25 +553,32 @@ bool TomahawkOutputReader::__viewRegion(void){
 		if(this->interval_tree == nullptr)
 			return false;
 
-		for(U32 i = 0; i < this->interval_tree_entries->size(); ++i){
-			// Find this overlap
-			std::pair<U32, U32> ret = this->getIndex().getContainer().findOverlap(this->interval_tree_entries->at(i).contigID, this->interval_tree_entries->at(i).start, this->interval_tree_entries->at(i).stop);
-			const U32 n_blocks_hits = ret.second - ret.first;
-			if(n_blocks_hits == 0)
-				return false;
-
-			for(U32 j = 0; j < n_blocks_hits; ++j){
-				if(!this->seekBlock(ret.first + j)){
-					std::cerr << "failed to seek block" << std::endl;
+		std::cerr << "meta: " << this->getIndex().getMetaContainer().size() << std::endl;
+		for(U32 i = 0; i < this->getIndex().getMetaContainer().size(); ++i){
+			std::cerr << this->interval_tree_entries[i].size() << std::endl;
+			for(U32 j = 0; j < this->interval_tree_entries[i].size(); ++j){
+				std::cerr << "here: " << this->interval_tree_entries[i].at(j) << std::endl;
+
+				// Find this overlap
+				std::pair<U32, U32> ret = this->getIndex().getContainer().findOverlap(this->interval_tree_entries[i].at(j).contigID, this->interval_tree_entries[i].at(j).start, this->interval_tree_entries[i].at(j).stop);
+				std::cerr << "ret: " << ret.first << "->" << ret.second << std::endl;
+				const U32 n_blocks_hits = ret.second - ret.first;
+				if(n_blocks_hits == 0)
 					return false;
-				}
 
-				if(!this->parseBlock())
-					return false;
+				for(U32 k = 0; k < n_blocks_hits; ++k){
+					if(!this->seekBlock(ret.first + k)){
+						std::cerr << "failed to seek block" << std::endl;
+						return false;
+					}
 
-				output_container_reference_type o(this->data_);
-				for(U32 i = 0; i < o.size(); ++i)
-					this->__checkRegionNoIndex(o[i]);
+					if(!this->parseBlock())
+						return false;
+
+					output_container_reference_type o(this->data_);
+					for(U32 l = 0; l < o.size(); ++l)
+						this->__checkRegionNoIndex(o[l]);
+				}
 			}
 		}
 	}