Merge branch 'master' into release-v0.8.x

source/CMakeLists.txt

@@ -34,7 +34,8 @@ add_executable(UnitTests
         tests/UnitTests.cpp
         tests/SequenceUtilsTest.cpp
         tests/PurityScoreTest.cpp
-        tests/GenomicRegionTest.cpp)
+        tests/GenomicRegionTest.cpp
+        tests/IrrFinderTest.cpp)
 target_link_libraries(UnitTests common reads region)
 target_include_directories(UnitTests PUBLIC ${CMAKE_SOURCE_DIR})
 

source/app/ExpansionHunterDenovo.cpp

@@ -128,9 +128,9 @@ int runProfileWorkflow(int argc, char** argv)
 
     spdlog::info("Starting {} profile workflow", kProgramVersion);
 
+    Interval motifSizeRange(shortestUnitToConsider, longestUnitToConsider);
     ProfileWorkflowParameters params(
-        outputPrefix, pathToReads, pathToReference, shortestUnitToConsider, longestUnitToConsider, minMapqOfAnchorRead,
-        maxMapqOfInrepeatRead);
+        outputPrefix, pathToReads, pathToReference, motifSizeRange, minMapqOfAnchorRead, maxMapqOfInrepeatRead);
     return runProfileWorkflow(params);
 }
 

source/app/Version.hh

@@ -24,4 +24,5 @@
 
 #include <string>
 
-const std::string kProgramVersion = "ExpansionHunter Denovo v0.8.1";
+const std::string kProgramVersion = "ExpansionHunter Denovo v0.8.6";
+

source/common/CMakeLists.txt

@@ -1,6 +1,6 @@
 add_library(common STATIC
         Parameters.hh
-        SequenceUtils.hh SequenceUtils.cpp)
+        SequenceUtils.hh SequenceUtils.cpp Interval.cpp Interval.hh)
 
 target_include_directories(common PUBLIC ${CMAKE_SOURCE_DIR})
 target_link_libraries(common Boost::boost)

source/purity/unit_tests/purity_test.cc → source/common/Interval.cpp

@@ -20,11 +20,4 @@
 //
 //
 
-#include "purity/purity.h"
-#include "gmock/gmock.h"
-
-#include <string>
-#include <vector>
-
-using std::string;
-using std::vector;
+#include "common/Interval.hh"

source/common/Interval.hh

@@ -0,0 +1,49 @@
+//
+// ExpansionHunter Denovo
+// Copyright 2016-2019 Illumina, Inc.
+// All rights reserved.
+//
+// Author: Egor Dolzhenko <[email protected]>,
+//         Michael Eberle <[email protected]>
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//      http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+//
+
+#pragma once
+
+#include <stdexcept>
+#include <string>
+
+class Interval
+{
+public:
+    Interval(int start, int end)
+        : start_(start)
+        , end_(end)
+    {
+        if (start_ > end_)
+        {
+            const auto interval = "(" + std::to_string(start_) + ", " + std::to_string(end_) + ")";
+            throw std::runtime_error("Invalid interval endpoints " + interval);
+        }
+    }
+
+    int start() const { return start_; }
+    int end() const { return end_; }
+    bool contains(int value) const { return start_ <= value && value <= end_; }
+
+private:
+    int start_;
+    int end_;
+};