Merge pull request #106 from Illumina/update-to-version-4

Update to version 4
Illumina · Oct 6, 2020 · a656b27 · a656b27
2 parents c4f88fc + e199e4d
commit a656b27
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Showing 360 changed files with 37,808 additions and 17,472 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -12,17 +12,17 @@ include(ExternalProject)
 # Download and unpack googletest at configure time
 configure_file(cmake/google_test.cmake googletest-download/CMakeLists.txt)
 execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
-        RESULT_VARIABLE result
-        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/googletest-download)
-if (result)
-    message(FATAL_ERROR "CMake step for googletest failed: ${result}")
-endif ()
+		RESULT_VARIABLE result
+		WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/googletest-download )
+if(result)
+	message(FATAL_ERROR "CMake step for googletest failed: ${result}")
+endif()
 execute_process(COMMAND ${CMAKE_COMMAND} --build .
-        RESULT_VARIABLE result
-        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/googletest-download)
-if (result)
-    message(FATAL_ERROR "Build step for googletest failed: ${result}")
-endif ()
+		RESULT_VARIABLE result
+		WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/googletest-download )
+if(result)
+	message(FATAL_ERROR "Build step for googletest failed: ${result}")
+endif()
 
 # Add googletest directly to our build. This defines
 # the gtest and gtest_main targets.
@@ -32,30 +32,31 @@ add_subdirectory(${CMAKE_BINARY_DIR}/googletest-src
 
 
 ExternalProject_Add(zlib
-        PREFIX ${CMAKE_BINARY_DIR}/thirdparty/zlib
-        GIT_REPOSITORY "https://github.com/madler/zlib.git"
-        GIT_TAG "v1.2.8"
-        UPDATE_COMMAND ""
-        BUILD_IN_SOURCE 1
-        CONFIGURE_COMMAND ${CMAKE_BINARY_DIR}/thirdparty/zlib/src/zlib/configure --prefix=${CMAKE_BINARY_DIR}/thirdparty/zlib --static
-        INSTALL_DIR ${CMAKE_BINARY_DIR}/thirdparty/zlib
-        LOG_DOWNLOAD 1
-        LOG_INSTALL 1
-        )
+	PREFIX ${CMAKE_BINARY_DIR}/thirdparty/zlib
+	GIT_REPOSITORY "https://github.com/madler/zlib.git"
+	GIT_TAG "v1.2.8"
+	UPDATE_COMMAND ""
+	BUILD_IN_SOURCE 1
+	CONFIGURE_COMMAND ${CMAKE_BINARY_DIR}/thirdparty/zlib/src/zlib/configure --prefix=${CMAKE_BINARY_DIR}/thirdparty/zlib --static
+	INSTALL_DIR ${CMAKE_BINARY_DIR}/thirdparty/zlib
+	LOG_DOWNLOAD 1
+	LOG_INSTALL 1
+)
 
 ExternalProject_Add(htslib
-        PREFIX ${CMAKE_BINARY_DIR}/thirdparty/htslib
+	PREFIX ${CMAKE_BINARY_DIR}/thirdparty/htslib
         GIT_REPOSITORY "https://github.com/samtools/htslib.git"
-        GIT_TAG "1.3.1"
+	GIT_TAG "1.3.1"
         UPDATE_COMMAND ""
-        BUILD_IN_SOURCE 1
+	BUILD_IN_SOURCE 1
         CONFIGURE_COMMAND ""
-        BUILD_COMMAND make
-        INSTALL_COMMAND make install prefix=${CMAKE_BINARY_DIR}/thirdparty/htslib
-        LOG_DOWNLOAD 1
-        )
-
+	BUILD_COMMAND make
+	INSTALL_COMMAND make install prefix=${CMAKE_BINARY_DIR}/thirdparty/htslib
+	LOG_DOWNLOAD 1
+)
 
+include_directories(${CMAKE_BINARY_DIR}/thirdparty/zlib/include)
+include_directories(${CMAKE_SOURCE_DIR}/thirdparty/spdlog/include)
 set(zlib_static ${CMAKE_BINARY_DIR}/thirdparty/zlib/lib/libz.a)
 set(htslib_static ${CMAKE_BINARY_DIR}/thirdparty/htslib/lib/libhts.a)
 
@@ -67,7 +68,7 @@ find_package(Boost 1.4 REQUIRED COMPONENTS program_options filesystem regex date
 
 include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 include_directories(SYSTEM ${Boost_INCLUDE_DIR})
-
+include_directories(${CMAKE_BINARY_DIR}/thirdparty/htslib/include)
 
 add_subdirectory(thirdparty/graph-tools-master)
 
@@ -78,23 +79,19 @@ add_subdirectory(genotyping)
 add_subdirectory(reads)
 add_subdirectory(classification)
 add_subdirectory(region_spec)
+add_subdirectory(region_analysis)
 add_subdirectory(sample_analysis)
 add_subdirectory(input)
 add_subdirectory(output)
 add_subdirectory(alignment)
 add_subdirectory(stats)
 add_subdirectory(filtering)
-add_subdirectory(graph_components)
-add_subdirectory(workflow)
-
 
-add_executable(ExpansionHunter src/Version.hh src/ExpansionHunter.cpp)
+file(GLOB SOURCES "src/*.cpp")
+add_executable(ExpansionHunter ${SOURCES})
 target_compile_features(ExpansionHunter PRIVATE cxx_range_for)
-target_link_libraries(ExpansionHunter graphtools common workflow genotyping region_spec sample_analysis input output
-        alignment filtering stats classification graph_components pthread ${Boost_LIBRARIES})
-install(TARGETS ExpansionHunter DESTINATION bin)
+target_link_libraries(ExpansionHunter graphtools common genotyping region_analysis region_spec sample_analysis input output alignment filtering stats pthread ${Boost_LIBRARIES})
+install (TARGETS ExpansionHunter DESTINATION bin)
 
 add_dependencies(htslib zlib)
 add_dependencies(common htslib)
-target_include_directories(common PUBLIC ${CMAKE_BINARY_DIR}/thirdparty/zlib/include)
-target_include_directories(common PUBLIC ${CMAKE_BINARY_DIR}/thirdparty/htslib/include)
diff --git a/COPYRIGHT.txt b/COPYRIGHT.txt
@@ -258,37 +258,4 @@ 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.
-
-******************************************************************
-
-The Netlib repository
-
-Copyright © 1996 California Institute of Technology, Pasadena, California. 
-ALL RIGHTS RESERVED. Based on Government Sponsored Research NAS7-03001. 
-Redistribution and use in source and binary forms, with or without modification, 
-are permitted provided that the following conditions are met: Redistributions 
-of source code must retain this copyright notice, this list of conditions and 
-the following disclaimer. Redistributions in binary form must reproduce the 
-above copyright notice, this list of conditions and the following disclaimer 
-in the documentation and/or other materials provided with the distribution. 
-Neither the name of the California Institute of Technology (Caltech) nor the 
-names of its contributors may be used to endorse or promote products derived 
-from this software without specific prior written permission. 
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
-ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
-LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
-CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
-SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF 
-THE POSSIBILITY OF SUCH DAMAGE.
-
-******************************************************************
-
-MurmurHash3 was written by Austin Appleby, and is placed in the public
-domain. The author hereby disclaims copyright to this source code.
+THE SOFTWARE.
diff --git a/README.md b/README.md
@@ -33,11 +33,10 @@ contained in the [docs folder](docs/01_Introduction.md).
 
 The method is described in the following papers:
 
-- Dolzhenko and others, [Detection of long repeat expansions from PCR-free
-whole-genome sequence data](http://genome.cshlp.org/content/27/11/1895), Genome
-Research 2017
+- Egor Dolzhenko, Joke van Vugt, Richard Shaw, Mitch Bekritsky, and others,
+  [Detection of long repeat expansions from PCR-free whole-genome sequence data](http://genome.cshlp.org/content/27/11/1895),
+  Genome Research 2017
 
-- Dolzhenko and others,
-[ExpansionHunter: A sequence-graph based tool to analyze variation in short
-tandem repeat regions](https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btz431/5499079),
+- Egor Dolzhenko, Viraj Deshpande, Felix Schlesinger, Peter Krusche, Roman Petrovski, and others,
+[ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions](https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btz431/5499079),
 Bioinformatics 2019
diff --git a/alignment/AlignmentFilters.cpp b/alignment/AlignmentFilters.cpp
@@ -21,7 +21,6 @@
 
 #include "alignment/AlignmentFilters.hh"
 
-#include <algorithm>
 #include <list>
 #include <vector>
 
@@ -44,26 +43,26 @@ using std::vector;
 namespace ehunter
 {
 
-bool checkIfComesFromGraphLocus(
-    const list<GraphAlignment>& readAlignments, const list<GraphAlignment>& mateAlignments,
+bool checkIfLocallyPlacedReadPair(
+    boost::optional<GraphAlignment> readAlignment, boost::optional<GraphAlignment> mateAlignment,
     int kMinNonRepeatAlignmentScore)
 {
-    int maxReadScore = 0;
-    for (const auto& alignment : readAlignments)
+    int nonRepeatAlignmentScore = 0;
+
+    if (readAlignment)
     {
-        maxReadScore = std::max(maxReadScore, scoreAlignmentToNonloopNodes(alignment));
+        nonRepeatAlignmentScore += scoreAlignmentToNonloopNodes(*readAlignment);
     }
 
-    int maxMateScore = 0;
-    for (const auto& alignment : mateAlignments)
+    if (mateAlignment)
     {
-        maxMateScore = std::max(maxMateScore, scoreAlignmentToNonloopNodes(alignment));
+        nonRepeatAlignmentScore += scoreAlignmentToNonloopNodes(*mateAlignment);
     }
 
-    return maxReadScore + maxMateScore >= kMinNonRepeatAlignmentScore;
+    return nonRepeatAlignmentScore >= kMinNonRepeatAlignmentScore;
 }
 
-bool checkIfUpstreamAlignmentIsGood(NodeId nodeId, const GraphAlignment& alignment)
+bool checkIfUpstreamAlignmentIsGood(NodeId nodeId, GraphAlignment alignment)
 {
     const list<int> repeatNodeIndexes = alignment.getIndexesOfNode(nodeId);
 
@@ -86,7 +85,7 @@ bool checkIfUpstreamAlignmentIsGood(NodeId nodeId, const GraphAlignment& alignme
     return score >= kScoreCutoff;
 }
 
-bool checkIfDownstreamAlignmentIsGood(NodeId nodeId, const GraphAlignment& alignment)
+bool checkIfDownstreamAlignmentIsGood(NodeId nodeId, GraphAlignment alignment)
 {
     const list<int> repeatNodeIndexes = alignment.getIndexesOfNode(nodeId);
 
@@ -123,7 +122,14 @@ bool checkIfPassesAlignmentFilters(const GraphAlignment& alignment)
     const int percentQueryMatches = (100 * alignment.numMatches()) / clippedQueryLength;
     const int percentReferenceMatches = (100 * alignment.numMatches()) / referenceLength;
 
-    return percentQueryMatches >= 80 && percentReferenceMatches >= 80;
+    if (percentQueryMatches >= 80 && percentReferenceMatches >= 80)
+    {
+        return true;
+    }
+    else
+    {
+        return false;
+    }
 }
 
 }
diff --git a/alignment/AlignmentFilters.hh b/alignment/AlignmentFilters.hh
@@ -21,33 +21,35 @@
 
 #pragma once
 
-#include <list>
 #include <string>
 
+#include <boost/optional.hpp>
+
 #include "graphalign/GraphAlignment.hh"
 
 namespace ehunter
 {
 
 /**
- * Checks if a read pair originated in the locus defined by the graph
+ * Checks if a read pair is likely to have originated in the alignment region
  *
- * Verifies that there is a pair of read/mate alignments with a sufficiently high combined score to non-repeat nodes
+ * The check is performed by verifying that the alignment score to non-repeat nodes (combined for both mates) is
+ * sufficiently high.
  *
- * @param readAlignments: Alignments of a read
- * @param mateAlignments: Alignments of read's mate
- * @param kMinNonRepeatAlignmentScore: Positive score threshold
- * @return true if read/mate alignment with above properties exists
+ * @param readAlignment: Alignment of a read
+ * @param mateAlignment: Alignment of read's mate
+ * @param kMinNonRepeatAlignmentScore: Score threshold
+ * @return true if the alignment score to non-repeat nodes exceeds the threshold
  */
-bool checkIfComesFromGraphLocus(
-    const std::list<graphtools::GraphAlignment>& readAlignments,
-    const std::list<graphtools::GraphAlignment>& mateAlignments, int kMinNonRepeatAlignmentScore);
+bool checkIfLocallyPlacedReadPair(
+    boost::optional<graphtools::GraphAlignment> readAlignment,
+    boost::optional<graphtools::GraphAlignment> mateAlignment, int kMinNonRepeatAlignmentScore);
 
 // Checks if alignment upstream of a given node is high quality
-bool checkIfUpstreamAlignmentIsGood(graphtools::NodeId nodeId, const graphtools::GraphAlignment& alignment);
+bool checkIfUpstreamAlignmentIsGood(graphtools::NodeId nodeId, graphtools::GraphAlignment alignment);
 
 // Checks if alignment downstream of a given node is high quality
-bool checkIfDownstreamAlignmentIsGood(graphtools::NodeId nodeId, const graphtools::GraphAlignment& alignment);
+bool checkIfDownstreamAlignmentIsGood(graphtools::NodeId nodeId, graphtools::GraphAlignment alignment);
 
 bool checkIfPassesAlignmentFilters(const graphtools::GraphAlignment& alignment);