KMC 3.0.0

algbio · Jan 28, 2017 · e3156f3 · e3156f3
1 parent 0a7059b
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diff --git a/API.pdf b/API.pdf
diff --git a/README.md b/README.md
@@ -12,6 +12,7 @@ If your system needs other binary formats, you should put the following librarie
 * asmlib - for fast memcpy operation (http://www.agner.org/optimize/asmlib-instructions.pdf)
 * libbzip2 - for support for bzip2-compressed input FASTQ/FASTA files (http://www.bzip.org/)
 * zlib - for support for gzip-compressed input FASTQ/FASTA files (http://www.zlib.net/)
+* vcl (C++ vector class library) - for detection of processor extensions (SSE, AVX, etc.)
 
 Note: asmlib is free only for non commercial purposes. If needed, you can contact the author of asmlib or compile KMC without asmlib.
 
@@ -72,6 +73,8 @@ License
 Note: for commercial usage of asmlib follow the instructions in 'License conditions' (http://www.agner.org/optimize/asmlib-instructions.pdf) or compile KMC without asmlib.
 In case of doubt, please consult the original documentations.
 
+* vcl is under the licence GNU GPL 3 or higher 
+Node: for commercial usage of vcl follow the instructions in 'License' section (http://www.agner.org/optimize/vectorclass.pdf)
 
 Warranty
 =

diff --git a/kmc_api/kmc_file.cpp b/kmc_api/kmc_file.cpp
@@ -4,8 +4,8 @@
 
   Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot
 
-  Version: 2.3.0
-  Date   : 2015-08-21
+  Version: 3.0.0
+  Date   : 2017-01-28
 */
 
 #include "stdafx.h"

diff --git a/kmc_api/kmc_file.h b/kmc_api/kmc_file.h
@@ -4,8 +4,8 @@
 
   Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot
 
-  Version: 2.3.0
-  Date   : 2015-08-21
+  Version: 3.0.0
+  Date   : 2017-01-28
  */
 
 #ifndef _KMC_FILE_H

diff --git a/kmc_api/kmer_api.cpp b/kmc_api/kmer_api.cpp
@@ -4,8 +4,8 @@
 
   Authors: Sebastian Deorowicz and Agnieszka Debudaj-Grabysz
 
-  Version: 2.3.0
-  Date   : 2015-08-21
+  Version: 3.0.0
+  Date   : 2017-01-28
 */
 
 

diff --git a/kmc_api/kmer_api.h b/kmc_api/kmer_api.h
@@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc
 
 Authors: Sebastian Deorowicz and Agnieszka Debudaj-Grabysz
 
-Version: 2.3.0
-Date   : 2015-08-21
+Version: 3.0.0
+Date   : 2017-01-28
 */
 
 #ifndef _KMER_API_H

diff --git a/kmc_api/kmer_defs.h b/kmc_api/kmer_defs.h
@@ -4,16 +4,16 @@
 
   Authors: Sebastian Deorowicz and Agnieszka Debudaj-Grabysz
 
-  Version: 2.3.0
-  Date   : 2015-08-21
+  Version: 3.0.0
+  Date   : 2017-01-28
 */
 
 
 #ifndef _KMER_DEFS_H
 #define _KMER_DEFS_H
 
-#define KMC_VER		"2.3.0"
-#define KMC_DATE	"2015-08-21"
+#define KMC_VER		"3.0.0"
+#define KMC_DATE	"2017-01-28"
 
 #define MIN(x,y)	((x) < (y) ? (x) : (y))
 

diff --git a/kmc_api/mmer.cpp b/kmc_api/mmer.cpp
@@ -5,8 +5,8 @@
   
   Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot
   
-  Version: 2.3.0
-  Date   : 2015-08-21
+  Version: 3.0.0
+  Date   : 2017-01-28
 */
 
 #include "../kmc_api/mmer.h"
@@ -16,6 +16,9 @@ uint32 CMmer::norm5[];
 uint32 CMmer::norm6[];
 uint32 CMmer::norm7[];
 uint32 CMmer::norm8[];
+uint32 CMmer::norm9[];
+uint32 CMmer::norm10[];
+uint32 CMmer::norm11[];
 
 CMmer::_si CMmer::_init;
 
@@ -37,6 +40,15 @@ CMmer::CMmer(uint32 _len)
 	case 8:
 		norm = norm8;
 		break;
+	case 9:
+		norm = norm9;
+		break;
+	case 10:
+		norm = norm10;
+		break;
+	case 11:
+		norm = norm11;
+		break;
 	default:
 		break;
 	}

diff --git a/kmc_api/mmer.h b/kmc_api/mmer.h
@@ -4,8 +4,8 @@
   
   Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot
   
-  Version: 2.3.0
-  Date   : 2015-08-21
+  Version: 3.0.0
+  Date   : 2017-01-28
 */
 
 #ifndef _MMER_H
@@ -27,6 +27,9 @@ class CMmer
 	static uint32 norm6[1 << 12];
 	static uint32 norm7[1 << 14];	
 	static uint32 norm8[1 << 16];
+	static uint32 norm9[1 << 18];
+	static uint32 norm10[1 << 20];
+	static uint32 norm11[1 << 22];
 
 	static bool is_allowed(uint32 mmer, uint32 len)
 	{
@@ -89,6 +92,9 @@ class CMmer
 			init_norm(norm6, 6);
 			init_norm(norm7, 7);
 			init_norm(norm8, 8);
+			init_norm(norm9, 9);
+			init_norm(norm10, 10);
+			init_norm(norm11, 11);
 		}
 
 	}static _init;
@@ -171,6 +177,15 @@ inline void CMmer::insert(const char* seq)
 	case 8:
 		str = (seq[0] << 14) + (seq[1] << 12) + (seq[2] << 10) + (seq[3] << 8) + (seq[4] << 6) + (seq[5] << 4) + (seq[6] << 2) + (seq[7]);
 		break;
+	case 9:
+		str = (seq[0] << 16) + (seq[1] << 14) + (seq[2] << 12) + (seq[3] << 10) + (seq[4] << 8) + (seq[5] << 6) + (seq[6] << 4) + (seq[7] << 2) + (seq[8]);
+		break;
+	case 10:
+		str = (seq[0] << 18) + (seq[1] << 16) + (seq[2] << 14) + (seq[3] << 12) + (seq[4] << 10) + (seq[5] << 8) + (seq[6] << 6) + (seq[7] << 4) + (seq[8] << 2) + (seq[9]);
+		break;
+	case 11:
+		str = (seq[0] << 20) + (seq[1] << 18) + (seq[2] << 16) + (seq[3] << 14) + (seq[4] << 12) + (seq[5] << 10) + (seq[6] << 8) + (seq[7] << 6) + (seq[8] << 4) + (seq[9] << 2) + (seq[10]);
+		break;
 	default:
 		break;
 	}

diff --git a/kmc_dump/kmc_dump.cpp b/kmc_dump/kmc_dump.cpp
@@ -7,8 +7,8 @@
 
   Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot
 
-  Version: 2.3.0
-  Date   : 2015-08-21
+  Version: 3.0.0
+  Date   : 2017-01-28
 */
 
 #include "stdafx.h"

diff --git a/kmc_dump/kmc_dump.vcxproj b/kmc_dump/kmc_dump.vcxproj
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="12.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+<Project DefaultTargets="Build" ToolsVersion="14.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
   <ItemGroup Label="ProjectConfigurations">
     <ProjectConfiguration Include="Debug|Win32">
       <Configuration>Debug</Configuration>
@@ -27,27 +27,27 @@
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
-    <PlatformToolset>v120</PlatformToolset>
+    <PlatformToolset>v140</PlatformToolset>
     <CharacterSet>NotSet</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
-    <PlatformToolset>v120</PlatformToolset>
+    <PlatformToolset>v140</PlatformToolset>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
-    <PlatformToolset>v120</PlatformToolset>
+    <PlatformToolset>v140</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>NotSet</CharacterSet>
     <UseOfMfc>Static</UseOfMfc>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
-    <PlatformToolset>v120</PlatformToolset>
+    <PlatformToolset>v140</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>NotSet</CharacterSet>
     <UseOfMfc>Static</UseOfMfc>

diff --git a/kmc_dump/nc_utils.cpp b/kmc_dump/nc_utils.cpp
@@ -7,8 +7,8 @@
 
   Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot
 
-  Version: 2.3.0
-  Date   : 2015-08-21
+  Version: 3.0.0
+  Date   : 2017-01-28
 */
 
 #include "stdafx.h"

diff --git a/kmc_dump/nc_utils.h b/kmc_dump/nc_utils.h
@@ -7,8 +7,8 @@
 
   Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot
 
-  Version: 2.3.0
-  Date   : 2015-08-21
+  Version: 3.0.0
+  Date   : 2017-01-28
 */
 
 #include <string>

diff --git a/kmc_dump_sample/kmc_dump_sample.cpp b/kmc_dump_sample/kmc_dump_sample.cpp
@@ -7,8 +7,8 @@
 
   Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot
 
-  Version: 2.3.0
-  Date   : 2015-08-21
+  Version: 3.0.0
+  Date   : 2017-01-28
 */
 
 #include "stdafx.h"

diff --git a/kmc_dump_sample/kmc_dump_sample.vcxproj b/kmc_dump_sample/kmc_dump_sample.vcxproj
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="12.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+<Project DefaultTargets="Build" ToolsVersion="14.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
   <ItemGroup Label="ProjectConfigurations">
     <ProjectConfiguration Include="Debug|Win32">
       <Configuration>Debug</Configuration>
@@ -27,27 +27,27 @@
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
-    <PlatformToolset>v120</PlatformToolset>
+    <PlatformToolset>v140</PlatformToolset>
     <CharacterSet>NotSet</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
-    <PlatformToolset>v120</PlatformToolset>
+    <PlatformToolset>v140</PlatformToolset>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
-    <PlatformToolset>v120</PlatformToolset>
+    <PlatformToolset>v140</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>NotSet</CharacterSet>
     <UseOfMfc>Static</UseOfMfc>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
-    <PlatformToolset>v120</PlatformToolset>
+    <PlatformToolset>v140</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>NotSet</CharacterSet>
     <UseOfMfc>Static</UseOfMfc>

diff --git a/kmc_tools.pdf b/kmc_tools.pdf
diff --git a/kmc_tools/asmlib_wrapper.h b/kmc_tools/asmlib_wrapper.h
@@ -4,8 +4,8 @@
   
   Authors: Marek Kokot
   
-  Version: 2.3.0
-  Date   : 2015-08-21
+  Version: 3.0.0
+  Date   : 2017-01-28
 */