Merge pull request #18 from mklarqvist/fast-mode

Release 0.5.1 and 0.5.2
mklarqvist · May 25, 2018 · 15dce8f · 15dce8f
2 parents 8f3209f + 9f67323
commit 15dce8f
Show file tree

Hide file tree

Showing 46 changed files with 205,315 additions and 1,568 deletions.
diff --git a/.settings/language.settings.xml b/.settings/language.settings.xml
@@ -5,7 +5,7 @@
 			<provider copy-of="extension" id="org.eclipse.cdt.ui.UserLanguageSettingsProvider"/>
 			<provider-reference id="org.eclipse.cdt.core.ReferencedProjectsLanguageSettingsProvider" ref="shared-provider"/>
 			<provider class="org.eclipse.cdt.managedbuilder.language.settings.providers.GCCBuildCommandParser" id="org.eclipse.cdt.managedbuilder.core.GCCBuildCommandParser" keep-relative-paths="false" name="CDT GCC Build Output Parser" parameter="(g?cc)|([gc]\+\+)|(clang)" prefer-non-shared="true"/>
-			<provider class="org.eclipse.cdt.internal.build.crossgcc.CrossGCCBuiltinSpecsDetector" console="false" env-hash="1364303945936347282" id="org.eclipse.cdt.build.crossgcc.CrossGCCBuiltinSpecsDetector" keep-relative-paths="false" name="CDT Cross GCC Built-in Compiler Settings" parameter="${COMMAND} ${FLAGS} -E -P -v -dD &quot;${INPUTS}&quot;" prefer-non-shared="true">
+			<provider class="org.eclipse.cdt.internal.build.crossgcc.CrossGCCBuiltinSpecsDetector" console="false" env-hash="-1884500886375924948" id="org.eclipse.cdt.build.crossgcc.CrossGCCBuiltinSpecsDetector" keep-relative-paths="false" name="CDT Cross GCC Built-in Compiler Settings" parameter="${COMMAND} ${FLAGS} -E -P -v -dD &quot;${INPUTS}&quot;" prefer-non-shared="true">
 				<language-scope id="org.eclipse.cdt.core.gcc"/>
 				<language-scope id="org.eclipse.cdt.core.g++"/>
 			</provider>

diff --git a/Makefile b/Makefile
@@ -28,7 +28,7 @@ src/tomahawk/two \
 -include src/algorithm/subdir.mk
 -include src/subdir.mk
 
-LD_LIB_FLAGS := -fPIC -Wl,-rpath,$(CWD),-soname,ltomahawk.so.1 
+LD_LIB_FLAGS := -fPIC -Wl,-rpath,"./",-soname,ltomahawk.so.1 
 
 # Inject git information
 BRANCH := $(shell git rev-parse --abbrev-ref HEAD)
@@ -55,7 +55,7 @@ all: tomahawk
 tomahawk: $(OBJS) $(USER_OBJS)
 	g++ -pthread -o "tomahawk" $(OBJS) $(USER_OBJS) $(LIBS)
 	@echo 'Constructing shared library...'
-	g++ $(LD_LIB_FLAGS) -pthread -o ltomahawk.so.$(LIBVER_SCRIPT) $(OBJS) $(USER_OBJS) $(LIBS)
+	g++ $(LD_LIB_FLAGS) -pthread -o ltomahawk.so.$(LIBVER) $(OBJS) $(USER_OBJS) $(LIBS)
 	@echo 'Symlinking library...'
 	ln -sf ltomahawk.so.$(LIBVER) ltomahawk.so
 

diff --git a/README.md b/README.md
@@ -325,9 +325,9 @@ Department of Genetics, University of Cambridge
 Wellcome Trust Sanger Institute
 
 ### Acknowledgements 
-[Professor John A Todd](https://www.ndm.ox.ac.uk/principal-investigators/researcher/john-todd), Nuffield Department of Medicine, University of Oxford  
+[John A Todd](https://www.ndm.ox.ac.uk/principal-investigators/researcher/john-todd), Nuffield Department of Medicine, University of Oxford  
 [Chris Wallace](https://github.com/chr1swallace), MRC Biostatistics Unit, University of Cambridge  
-[Professor Richard Durbin](https://github.com/richarddurbin), Wellcome Trust Sanger Institute, and Department of Genetics, University of Cambridge  
+[Richard Durbin](https://github.com/richarddurbin), Wellcome Trust Sanger Institute, and Department of Genetics, University of Cambridge  
 
 ### License
 [MIT](LICENSE)
diff --git a/RELEASE.md b/RELEASE.md
@@ -1,3 +1,24 @@
+# Release 0.5.2
+
+## Minor Features And Improvements
+* Now correctly filters `two` files
+
+# Release 0.5.1
+
+## Minor Features And Improvements
+* Meta index for faster queries of `two` files now builds correctly
+* Interval slicing for sorted `two` files now outputs filtering hits for the from positions only
+* Haplotype counts in binary `two` files are now stored as `double` instead of `float` 
+
+# Release 0.5.0
+
+## Breaking Changes
+* All changes are breaking because of structural rechanges. No files generated prior to this release are supported.
+
+## Minor Features And Improvements
+* Build process now smoother
+* Shared C++ library is now built by default
+
 # Release 0.4.0
 
 ## Breaking Changes

diff --git a/src/algorithm/load_balancer_block.h b/src/algorithm/load_balancer_block.h
@@ -23,6 +23,14 @@ struct LoadBalancerBlock{
 		staggered(false)
 	{}
 
+	LoadBalancerBlock(const U32 fromRow, const U32 toRow, const U32 fromColumn, const U32 toColumn, bool staggered) :
+		fromRow(fromRow),
+		toRow(toRow),
+		fromColumn(fromColumn),
+		toColumn(toColumn),
+		staggered(staggered)
+	{}
+
 	~LoadBalancerBlock(){}
 
 	inline U32 getRows(void) const{ return(this->toRow - this->fromRow); }
@@ -47,15 +55,13 @@ struct LoadBalancerBlock{
 	}
 
 	friend std::ostream& operator<<(std::ostream& os, const LoadBalancerBlock& block){
-		os << block.fromRow << '-' << block.toRow << '\t' << block.fromColumn << '-' << block.toColumn << (int)block.staggered;
+		os << "[" << block.fromRow << '-' << block.toRow << ", " << block.fromColumn << '-' << block.toColumn << "] staggered: " << (int)block.staggered;
 		return(os);
 	}
 
 	// Relative order
-	U32 fromRow;
-	U32 toRow;
-	U32 fromColumn;
-	U32 toColumn;
+	U32 fromRow, toRow;
+	U32 fromColumn, toColumn;
 	bool staggered;
 };