Merge pull request #8 from mklarqvist/yon_block

Release 0.6.0

.gitignore

@@ -37,5 +37,6 @@ bin/
 openssl/
 zstd/
 
-# Binary
+# Binary and library
 tachyon
+lib*.so.*

.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="-939566099868401782" 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="-353402777504187126" 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>
@@ -17,7 +17,7 @@
 			<provider copy-of="extension" id="org.eclipse.cdt.ui.UserLanguageSettingsProvider"/>
 			<provider-reference id="org.eclipse.cdt.core.ReferencedProjectsLanguageSettingsProvider" ref="shared-provider"/>
 			<provider copy-of="extension" id="org.eclipse.cdt.managedbuilder.core.GCCBuildCommandParser"/>
-			<provider class="org.eclipse.cdt.internal.build.crossgcc.CrossGCCBuiltinSpecsDetector" console="false" env-hash="-939566099868401782" 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="-353402777504187126" 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>

.travis.yml

@@ -209,7 +209,8 @@ before_install:
   - git clone https://github.com/facebook/zstd
   - cd zstd && make -j4 && sudo make install && cd ..
   - git clone https://github.com/samtools/htslib
-  - cd htslib && autoheader && autoconf && ./configure && make -j 4 && sudo make install && cd ..
+  - cd htslib && git checkout 1832d3a1b75133e55fb6abffc3f50f8a6ed5ceae
+  - autoheader && autoconf && ./configure && make -j 4 && sudo make install && cd ..
 
 script:
   - git submodule update --recursive

README.md

@@ -1,5 +1,5 @@
 [![Build Status](https://travis-ci.org/mklarqvist/tachyon.svg?branch=master)](https://travis-ci.org/mklarqvist/tachyon)
-[![Release](https://img.shields.io/badge/Release-beta_0.5.0-blue.svg)](https://github.com/mklarqvist/Tachyon/releases)
+[![Release](https://img.shields.io/badge/Release-beta_0.6.0-blue.svg)](https://github.com/mklarqvist/Tachyon/releases)
 [![License](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE)
 
 <div align="center">
@@ -66,7 +66,6 @@ When installing locally the required dependencies are downloaded and built in th
 * Overview.
 * [Building and installing](docs/building.md)
 * [Getting started](docs/getting_started.md)
-* [Summary of example programs](docs/example_programs.md).
 * [Performance benchmarks](docs/benchmarks.md)
 
 ### Contributing
@@ -77,7 +76,7 @@ Interested in contributing? Fork and submit a pull request and it will be review
 We are actively developing Tachyon and are always interested in improving its quality. If you run into an issue, please report the problem on our Issue tracker. Be sure to add enough detail to your report that we can reproduce the problem and address it. We have not reached version 1.0 and as such the specification and/or the API interfaces may change.
 
 ### Version
-This is Tachyon 0.5.0. Tachyon follows [semantic versioning](https://semver.org/).
+This is Tachyon 0.6.0. Tachyon follows [semantic versioning](https://semver.org/).
 
 ### History
 Tachyon grew out of the [Tomahawk][tomahawk] project for calculating genome-wide linkage-disequilibrium.

docs/building.md

@@ -12,10 +12,6 @@ git clone --recursive https://github.com/mklarqvist/tachyon
 cd tachyon
 make
 ```
-Tachyon comes bundled with several API-examples in the `lib_example` directory. They are built by default but should you want to rebuild them execute the command:
-```bash
-make examples
-```
 
 ## Installation
 For Ubuntu, Debian, and Mac systems, installation is easy: just run

docs/getting_started.md

@@ -7,7 +7,6 @@
     - [Field-slicing](#field-slicing)
     - [Searching for genomic regions](#searching-for-genomic-regions)
     - [Annotating meta-data](#annotating-meta-data)
-- [C++ API Examples](#c-api-examples)
 
 ---
 
@@ -132,7 +131,4 @@ tachyon view -i example_dataset.yon -GHX
 Output
 ```
 Contig110_arrow	672	.	A	T	525.07	basic_filtering	AC=10;AF=0.217;AN=46;BaseQRankSum=0.967;DP=72;ExcessHet=0.8113;FS=54.73;InbreedingCoeff=-0.0525;MLEAC=11;MLEAF=0.239;MQ=31.05;MQRankSum=1.38;QD=18.11;ReadPosRankSum=-0.431;SOR=5.889;FS_A=11.5091,0;NM=26;AC_FWD=21,2;AC_REV=15,8;HWE_P=0.25072;VT=SNP
-```
-
-## C++ API Examples
-We provide several API examples in the `lib_example` directory. Get started by `make examples`: this requires you to have compiled the shared library first.
+```

lib/io/basic_buffer.h → include/buffer.h

@@ -1,5 +1,27 @@
-#ifndef BASICBUFFER__H_
-#define BASICBUFFER__H_
+/*
+Copyright (C) 2017-current Genome Research Ltd.
+Author: Marcus D. R. Klarqvist <mk819@cam.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
+==============================================================================*/
+#ifndef TACHYON_BUFFER_H_
+#define TACHYON_BUFFER_H_
 
 #define __STDC_FORMAT_MACROS 1
 #include <inttypes.h>
@@ -9,15 +31,14 @@
 #include <stdint.h>
 #include <cassert>
 
-#include "support/helpers.h"
-#include "containers/components/generic_iterator.h"
+#include "utility.h"
+#include "generic_iterator.h"
 
 namespace tachyon {
-namespace io{
 
-struct BasicBuffer{
+struct yon_buffer_t {
 public:
-    typedef BasicBuffer       self_type;
+    typedef yon_buffer_t      self_type;
     typedef char              value_type;
     typedef value_type&       reference;
     typedef const value_type& const_reference;
@@ -30,14 +51,15 @@ struct BasicBuffer{
 	typedef yonRawIterator<const value_type> const_iterator;
 
 public:
-	BasicBuffer();
-	BasicBuffer(const uint64_t size);
-	BasicBuffer(char* target, const size_t length);
-	BasicBuffer(const uint64_t size, char* target);
-	BasicBuffer(const self_type& other);
-	virtual ~BasicBuffer();
+	yon_buffer_t();
+	yon_buffer_t(const uint64_t size);
+	yon_buffer_t(char* target, const size_t length);
+	yon_buffer_t(const uint64_t size, char* target);
+	yon_buffer_t(const self_type& other);
+	yon_buffer_t(self_type&& other) noexcept;
 	self_type& operator=(const self_type& other);
 	self_type& operator=(self_type&& other) noexcept;
+	~yon_buffer_t();
 
 	inline reference back(void){ return(this->buffer_[this->n_chars_-1]); }
 	inline reference front(void){ return(this->buffer_[0]); }
@@ -52,26 +74,9 @@ struct BasicBuffer{
 	inline const_iterator cbegin() const{ return const_iterator(&this->buffer_[0]); }
 	inline const_iterator cend()   const{ return const_iterator(&this->buffer_[this->n_chars_]); }
 
-	inline void set(const size_t size){
-		this->n_chars_ = 0;
-		this->width_ = size;
-		if(this->buffer_ != nullptr)
-			delete [] this->buffer_;
-
-		this->buffer_ = new char[size];
-	}
-
-	inline void set(const size_t size, char* target){
-		this->n_chars_ = 0;
-		this->width_ = size;
-		this->buffer_ = target;
-	}
-
-	inline void set(char* target){
-		this->n_chars_ = 0;
-		this->width_ = 0;
-		this->buffer_ = target;
-	}
+	inline void set(const size_t size);
+	inline void set(const size_t size, char* target);
+	inline void set(char* target);
 
 	inline void reset(){ this->n_chars_ = 0; this->iterator_position_ = 0; }
 	inline void resetIterator(){ this->iterator_position_ = 0; }
@@ -86,6 +91,7 @@ struct BasicBuffer{
 	void AddReadble(const int8_t& value);
 	void AddReadble(const int16_t& value);
 	void AddReadble(const int32_t& value);
+	void AddReadble(const int64_t& value);
 	void AddReadble(const uint8_t& value);
 	void AddReadble(const uint16_t& value);
 	void AddReadble(const uint32_t& value);
@@ -120,91 +126,46 @@ struct BasicBuffer{
 	}
 
 private:
-	friend self_type& operator>>(self_type& data, uint8_t& target){
-		target = *reinterpret_cast<uint8_t*>(&data.buffer_[data.iterator_position_++]);
-		return(data);
-	}
-
-	friend self_type& operator>>(self_type& data, uint16_t& target){
-		target = *reinterpret_cast<uint16_t*>(&data.buffer_[data.iterator_position_]);
-		data.iterator_position_ += sizeof(uint16_t);
-		return(data);
-	}
-
-	friend self_type& operator>>(self_type& data, uint32_t& target){
-		target = *reinterpret_cast<uint32_t*>(&data.buffer_[data.iterator_position_]);
-		data.iterator_position_ += sizeof(uint32_t);
-		return(data);
-	}
-
-	friend self_type& operator>>(self_type& data, uint64_t& target){
-		target = *reinterpret_cast<uint64_t*>(&data.buffer_[data.iterator_position_]);
-		data.iterator_position_ += sizeof(uint64_t);
-		return(data);
-	}
-
-	friend self_type& operator>>(self_type& data, int8_t& target){
-		target = *reinterpret_cast<int8_t*>(&data.buffer_[data.iterator_position_++]);
-		return(data);
-	}
-
-	friend self_type& operator>>(self_type& data, int16_t& target){
-		target = *reinterpret_cast<int16_t*>(&data.buffer_[data.iterator_position_]);
-		data.iterator_position_ += sizeof(int16_t);
-		return(data);
-	}
-
-	friend self_type& operator>>(self_type& data, int32_t& target){
-		target = *reinterpret_cast<int32_t*>(&data.buffer_[data.iterator_position_]);
-		data.iterator_position_ += sizeof(int32_t);
-		return(data);
-	}
-
-	friend self_type& operator>>(self_type& data, int64_t& target){
-		target = *reinterpret_cast<int64_t*>(&data.buffer_[data.iterator_position_]);
-		data.iterator_position_ += sizeof(int64_t);
-		return(data);
-	}
-
-	friend self_type& operator>>(self_type& data, float& target){
-		target = *reinterpret_cast<float*>(&data.buffer_[data.iterator_position_]);
-		data.iterator_position_ += sizeof(float);
-		return(data);
-	}
-
-	friend self_type& operator>>(self_type& data, double& target){
-		target = *reinterpret_cast<double*>(&data.buffer_[data.iterator_position_]);
-		data.iterator_position_ += sizeof(double);
-		return(data);
-	}
-
-	friend std::ostream& operator<<(std::ostream& out, const self_type& data){
-		out.write(data.data(), data.size());
-		return(out);
-	}
+	friend self_type& operator>>(self_type& data, uint8_t& target);
+	friend self_type& operator>>(self_type& data, uint16_t& target);
+	friend self_type& operator>>(self_type& data, uint32_t& target);
+	friend self_type& operator>>(self_type& data, uint64_t& target);
+	friend self_type& operator>>(self_type& data, int8_t& target);
+	friend self_type& operator>>(self_type& data, int16_t& target);
+	friend self_type& operator>>(self_type& data, int32_t& target);
+	friend self_type& operator>>(self_type& data, int64_t& target);
+	friend self_type& operator>>(self_type& data, float& target);
+	friend self_type& operator>>(self_type& data, double& target);
+
+	friend std::ostream& operator<<(std::ostream& out, const self_type& data);
 
 public:
-	bool         owns_data_;
-	uint64_t     n_chars_;
-	uint64_t     width_;
-	uint64_t     iterator_position_;
-	pointer      buffer_;
+	bool     owns_data_;
+	uint64_t n_chars_;
+	uint64_t width_;
+	uint64_t iterator_position_;
+	pointer  buffer_;
 };
 
-void SerializeString(const std::string& string, io::BasicBuffer& buffer);
-void DeserializeString(std::string& string, io::BasicBuffer& buffer);
+/**<
+ * Supportive functions for serializing/deserialize data to/from a byte
+ * stream.
+ * @param value  Src value.
+ * @param buffer Dst buffer reference.
+ */
+void SerializeString(const std::string& string, yon_buffer_t& buffer);
+void DeserializeString(std::string& string, yon_buffer_t& buffer);
 
 template <class T>
-static void SerializePrimitive(const T& value, io::BasicBuffer& buffer){
+static void SerializePrimitive(const T& value, yon_buffer_t& buffer){
 	buffer += value;
 }
 
 template <class T>
-static void DeserializePrimitive(T& value, io::BasicBuffer& buffer){
+static void DeserializePrimitive(T& value, yon_buffer_t& buffer){
 	buffer >> value;
 }
 
-} /* namespace IO */
-} /* namespace Tomahawk */
+}
 
-#endif /* BASICBUFFER__H_ */
+#endif