MANTA-1361 Create unit test utility library

Take existing unit test support code to create an IndelBuffer,
already shared between multiple tests, and use this to seed a
new unit test utility library following the same pattern as
for manta.

src/c++/lib/CMakeLists.txt

@@ -42,6 +42,17 @@ macro(buildLibraries library_dirs library_targets)
 endmacro()
 
 
+#
+# Build libraries needed for unit testing separately
+#
+# This is logic required for unit-testing, but not deployed production code. This must be run before the
+# primary loop below, so that PROJECT_TEST_LIBRARY_TARGETS is populated prior to configuring the unit test
+# directories.
+#
+set (PROJECT_TEST_LIBRARY_DIRS test)
+buildLibraries("${PROJECT_TEST_LIBRARY_DIRS}" PROJECT_TEST_LIBRARY_TARGETS)
+
+
 #
 # Build all primary libraries for the project
 #

src/c++/lib/README.md

@@ -0,0 +1,43 @@
+# Libraries
+
+- alignment
+  - sequence alignment utilities
+
+- applications/X:
+  - code specific to command-line application X
+
+- appstats
+  - shared performance tracking code between applications
+
+- assembly
+  - local sequence assembly utilities
+
+- blt\_common
+  - shared snv-calling logic (from old 'blt' snp-caller)
+
+- blt\_util
+  - general utility functions from manta/starling/strelka/gvcftools
+
+- calibration
+  - empirical variant scoring logic
+
+- common
+  - general utility functions from CASAVA/Grouper/Isaac
+
+- errorAnalysis
+  - shared libraries for utilities that estimate sequence artifact rates from data, used for various forms of model parameter estimation
+
+- htsapi
+  - various c++ wrapper objects built on top of samtools/htslib and other utilities for standard genomic indexed file formats like bam/cram,bed,vcf, etc...
+
+- options
+  - command-line options objects which are shared between applications
+
+- starling\_common
+  - shared small variant calling logic
+
+- strelka\_common
+  - shared comparitive small variant calling logic
+
+- test
+  - Logic used only for unit testing other libraries. These are linked into the unit tests but not production binaries

src/c++/lib/starling_common/test/ActiveRegionPloidyTest.cpp

@@ -20,9 +20,13 @@
 /// \file
 /// \author Sangtae Kim
 ///
-#include "TestIndelBuffer.hh"
+
 #include "boost/test/unit_test.hpp"
 
+#include "starling_common/ActiveRegionDetector.hh"
+#include "starling_common/CandidateSnvBuffer.hh"
+#include "test/testIndelBuffer.hh"
+
 
 /// Test whether ActiveRegionDetector correctly handles ploidy
 static int ploidyTest(const unsigned ploidy)

src/c++/lib/starling_common/test/ActiveRegionTest.cpp

@@ -22,9 +22,12 @@
 ///
 
 
-#include "TestIndelBuffer.hh"
 #include "boost/test/unit_test.hpp"
 
+#include "starling_common/ActiveRegionDetector.hh"
+#include "starling_common/CandidateSnvBuffer.hh"
+#include "test/testIndelBuffer.hh"
+
 const unsigned maxIndelSize = 49;
 
 

src/c++/lib/starling_common/test/starling_read_align_test.cpp

@@ -22,9 +22,9 @@
 #include "starling_read_align.cpp"
 
 // required to mock-up a read segment:
-#include "starling_base_options_test.hh"
 #include "htsapi/align_path_bam_util.hh"
-#include "starling_read.hh"
+#include "starling_common/starling_read.hh"
+#include "test/starling_base_options_test.hh"
 
 
 

src/c++/lib/test/CMakeLists.txt

@@ -0,0 +1,20 @@
+#
+# Manta - Structural Variant and Indel Caller
+# Copyright (c) 2013-2018 Illumina, Inc.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+#
+
+include(${THIS_CXX_LIBRARY_CMAKE})

src/c++/lib/starling_common/test/starling_base_options_test.hh → src/c++/lib/test/starling_base_options_test.hh

@@ -19,7 +19,8 @@
 
 #pragma once
 
-#include "starling_base_shared.hh"
+#include "options/AlignmentFileOptions.hh"
+#include "starling_common/starling_base_shared.hh"
 
 
 /// \brief This version of starling_base_options provides null implementations of required virtuals

src/c++/lib/test/testIndelBuffer.cpp

@@ -0,0 +1,37 @@
+//
+// Strelka - Small Variant Caller
+// Copyright (c) 2009-2018 Illumina, Inc.
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program.  If not, see <http://www.gnu.org/licenses/>.
+//
+//
+
+#include "testIndelBuffer.hh"
+
+
+
+TestIndelBuffer::
+TestIndelBuffer(
+    const reference_contig_segment& ref)
+{
+    _opt.is_candidate_indel_signal_test = false;
+
+    const double maxDepth = 100.0;
+    _doptPtr.reset(new starling_base_deriv_options(_opt));
+
+    _IndelBufferPtr.reset(new IndelBuffer(_opt, *_doptPtr, ref));
+
+    _IndelBufferPtr->registerSample(depth_buffer(), depth_buffer(), maxDepth);
+    _IndelBufferPtr->finalizeSamples();
+}

src/c++/lib/starling_common/test/TestIndelBuffer.hh → src/c++/lib/test/testIndelBuffer.hh

@@ -20,24 +20,20 @@
 #pragma once
 
 #include "starling_base_options_test.hh"
-#include "starling_common/ActiveRegionDetector.hh"
+#include "blt_util/reference_contig_segment.hh"
+#include "starling_common/IndelBuffer.hh"
 
+#include <memory>
+
+
+/// Manages a mock indel buffer approriate for unit testing
+///
+// TODO Refactor this to a factory function returning a unique_ptr to an IndelBuffer instead
 struct TestIndelBuffer
 {
     explicit
     TestIndelBuffer(
-        const reference_contig_segment& ref)
-    {
-        _opt.is_candidate_indel_signal_test = false;
-
-        const double maxDepth = 100.0;
-        _doptPtr.reset(new starling_base_deriv_options(_opt));
-
-        _IndelBufferPtr.reset(new IndelBuffer(_opt, *_doptPtr, ref));
-
-        _IndelBufferPtr->registerSample(depth_buffer(), depth_buffer(), maxDepth);
-        _IndelBufferPtr->finalizeSamples();
-    }
+        const reference_contig_segment& ref);
 
     IndelBuffer&
     getIndelBuffer()