Rolled back test suite code from master until it's ready for full merge

diff --git a/CMakeLists.txt b/CMakeLists.txt
index f4f23bdce12166fd37c77ff14c9181e95f98b5f2..8deded9166da085bb94a1726d2732a3dfaaa204d 100644 (file)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -11,9 +11,6 @@ project( BamTools )
 # Cmake requirements
 cmake_minimum_required( VERSION 2.6.4 )
 
-# init CTest
-enable_testing()
-
 # Force the build directory to be different from source directory
 macro( ENSURE_OUT_OF_SOURCE_BUILD MSG )
     string( COMPARE EQUAL "${CMAKE_SOURCE_DIR}" "${CMAKE_BINARY_DIR}" insource )
@@ -34,8 +31,8 @@ ensure_out_of_source_build( "
 
 # set BamTools version information
 set( BamTools_VERSION_MAJOR 2 )
-set( BamTools_VERSION_MINOR 0 )
-set( BamTools_VERSION_BUILD 5 )
+set( BamTools_VERSION_MINOR 1 )
+set( BamTools_VERSION_BUILD 0 )
 
 # set our library and executable destination dirs
 set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin" )

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 9513abb6adeae2572484e9fadf64e3933c872270..e35969556f51cac245b3da70ee7b7929bf953795 100644 (file)
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -6,7 +6,6 @@
 # ==========================
 
 add_subdirectory( api )
-add_subdirectory( test )
 add_subdirectory( third_party )
 add_subdirectory( toolkit )
 add_subdirectory( utils )

diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt
index d559c45e084180f796291513ddb9b0847d851468..cdfc10bdd634c1d5cce1500baf0ed01c07795b58 100644 (file)
--- a/src/api/CMakeLists.txt
+++ b/src/api/CMakeLists.txt
@@ -34,7 +34,7 @@ set( BamToolsAPISources
 # create main BamTools API shared library
 add_library( BamTools SHARED ${BamToolsAPISources} )
 set_target_properties( BamTools PROPERTIES
-                       SOVERSION "2.0.5"
+                       SOVERSION "2.1.0"
                        OUTPUT_NAME "bamtools" )
 
 # create main BamTools API static library

diff --git a/src/test/CMakeLists.txt b/src/test/CMakeLists.txt
deleted file mode 100644 (file)
index 2026958..0000000
--- a/src/test/CMakeLists.txt
+++ /dev/null
@@ -1,28 +0,0 @@
-# ==========================
-# BamTools CMakeLists.txt
-# (c) 2010 Derek Barnett
-#
-# src/test
-# ==========================
-
-# specify source include directories
-include_directories( ${BamTools_SOURCE_DIR}/src/api
-                     ${BamTools_SOURCE_DIR}/src/test
-                     ${BamTools_SOURCE_DIR}/src/third_party
-                     ${BamTools_SOURCE_DIR}/src/third_party/gtest-1.6.0/include
-                     ${BamTools_SOURCE_DIR}/src/utils
-                   )
-
-# create our test app 'test_bamtools'
-add_executable( BamTools-test EXCLUDE_FROM_ALL
-                TestMain.cpp
-              )
-set_target_properties( BamTools-test PROPERTIES
-                       OUTPUT_NAME "test_bamtools" )
-target_link_libraries( BamTools-test BamTools BamTools-utils jsoncpp gtest )
-
-# add test - running 'make check' will ensure build & run
-add_test( BamToolsTest BamTools-test )
-add_custom_target( check COMMAND ${EXECUTABLE_OUTPUT_PATH}/test_bamtools
-                         DEPENDS BamTools-test gtest )
-

diff --git a/src/test/TestMain.cpp b/src/test/TestMain.cpp
deleted file mode 100755 (executable)
index 8d2d861..0000000
--- a/src/test/TestMain.cpp
+++ /dev/null
@@ -1,13 +0,0 @@
-
-// GoogleTest
-#include <gtest/gtest.h>
-
-// BamTools unit tests
-#include "test/api/BamToolsApiTest.h"
-#include "test/toolkit/BamToolsToolkitTest.h"
-#include "test/utils/BamToolsUtilsTest.h"
-
-int main(int argc, char* argv[]) {
-    ::testing::InitGoogleTest(&argc, argv);
-    return RUN_ALL_TESTS();
-}

diff --git a/src/test/api/BamAlignmentDefaultTest.h b/src/test/api/BamAlignmentDefaultTest.h
deleted file mode 100755 (executable)
index 6187342..0000000
--- a/src/test/api/BamAlignmentDefaultTest.h
+++ /dev/null
@@ -1,20 +0,0 @@
-#ifndef BAMALIGNMENT_DEFAULTTEST_H
-#define BAMALIGNMENT_DEFAULTTEST_H
-
-#include "api/BamAlignment.h"
-#include <gtest/gtest.h>
-
-class BamAlignment_DefaultTest : public ::testing::Test {
-    protected:
-        BamTools::BamAlignment al;
-};
-
-TEST_F(BamAlignment_DefaultTest, DefaultValues) {
-    EXPECT_EQ(-1, al.RefID);
-    EXPECT_EQ(-1, al.Position);
-    EXPECT_EQ(-1, al.MateRefID);
-    EXPECT_EQ(-1, al.MatePosition);
-    EXPECT_EQ(0,  al.InsertSize);
-}
-
-#endif // BAMALIGNMENT_DEFAULTTEST_H

diff --git a/src/test/api/BamAlignmentFlagTest.h b/src/test/api/BamAlignmentFlagTest.h
deleted file mode 100755 (executable)
index 5f92557..0000000
--- a/src/test/api/BamAlignmentFlagTest.h
+++ /dev/null
@@ -1,89 +0,0 @@
-#ifndef BAMALIGNMENT_FLAGTEST_H
-#define BAMALIGNMENT_FLAGTEST_H
-
-#include "api/BamAlignment.h"
-#include <gtest/gtest.h>
-
-class BamAlignment_FlagTest : public ::testing::Test {
-    protected:
-        BamTools::BamAlignment al;
-};
-        
-TEST_F(BamAlignment_FlagTest, IsDuplicate) {
-    al.SetIsDuplicate(true);
-    EXPECT_TRUE(al.IsDuplicate());
-    al.SetIsDuplicate(false);
-    EXPECT_FALSE(al.IsDuplicate());
-}
-
-TEST_F(BamAlignment_FlagTest, IsFailedQC) {
-    al.SetIsFailedQC(true);
-    EXPECT_TRUE(al.IsFailedQC());
-    al.SetIsFailedQC(false);
-    EXPECT_FALSE(al.IsFailedQC());
-}
-
-TEST_F(BamAlignment_FlagTest, IsFirstMate) {
-    al.SetIsFirstMate(true);
-    EXPECT_TRUE(al.IsFirstMate());
-    al.SetIsFirstMate(false);
-    EXPECT_FALSE(al.IsFirstMate());
-}
-
-TEST_F(BamAlignment_FlagTest, IsMapped) {
-    al.SetIsMapped(true);
-    EXPECT_TRUE(al.IsMapped());
-    al.SetIsMapped(false);
-    EXPECT_FALSE(al.IsMapped());
-}
-
-TEST_F(BamAlignment_FlagTest, IsMateMapped) {
-    al.SetIsMateMapped(true);
-    EXPECT_TRUE(al.IsMateMapped());
-    al.SetIsMateMapped(false);
-    EXPECT_FALSE(al.IsMateMapped());
-}
-
-TEST_F(BamAlignment_FlagTest, IsMateReverseStrand) {
-    al.SetIsMateReverseStrand(true);
-    EXPECT_TRUE(al.IsMateReverseStrand());
-    al.SetIsMateReverseStrand(false);
-    EXPECT_FALSE(al.IsMateReverseStrand());
-}
-
-TEST_F(BamAlignment_FlagTest, IsPaired) {
-    al.SetIsPaired(true);
-    EXPECT_TRUE(al.IsPaired());
-    al.SetIsPaired(false);
-    EXPECT_FALSE(al.IsPaired());
-}
-
-TEST_F(BamAlignment_FlagTest, IsPrimaryAlignment) {
-    al.SetIsPrimaryAlignment(true);
-    EXPECT_TRUE(al.IsPrimaryAlignment());
-    al.SetIsPrimaryAlignment(false);
-    EXPECT_FALSE(al.IsPrimaryAlignment());
-}
-
-TEST_F(BamAlignment_FlagTest, IsProperPair) {
-    al.SetIsProperPair(true);
-    EXPECT_TRUE(al.IsProperPair());
-    al.SetIsProperPair(false);
-    EXPECT_FALSE(al.IsProperPair());
-}
-
-TEST_F(BamAlignment_FlagTest, IsReverseStrand) {
-    al.SetIsReverseStrand(true);
-    EXPECT_TRUE(al.IsReverseStrand());
-    al.SetIsReverseStrand(false);
-    EXPECT_FALSE(al.IsReverseStrand());
-}
-
-TEST_F(BamAlignment_FlagTest, IsSecondMate) {
-    al.SetIsSecondMate(true);
-    EXPECT_TRUE(al.IsSecondMate());
-    al.SetIsSecondMate(false);
-    EXPECT_FALSE(al.IsSecondMate());
-}  
-
-#endif // BAMALIGNMENT_FLAGTEST_H

diff --git a/src/test/api/BamMultiReaderFileOpsTest.h b/src/test/api/BamMultiReaderFileOpsTest.h
deleted file mode 100644 (file)
index aba2b7c..0000000
--- a/src/test/api/BamMultiReaderFileOpsTest.h
+++ /dev/null
@@ -1,58 +0,0 @@
-#ifndef BAMMULTIREADER_FILEOPSTEST_H
-#define BAMMULTIREADER_FILEOPSTEST_H
-
-#include "api/BamMultiReader.h"
-#include <gtest/gtest.h>
-
-#include <iostream>
-#include <string>
-#include <vector>
-
-TEST(BamMultiReaderFileOpsTest, Defaults) {
-
-    BamTools::BamMultiReader reader;
-
-    EXPECT_FALSE(reader.HasOpenReaders());
-    EXPECT_FALSE(reader.HasIndexes());
-    std::vector<std::string> filenames = reader.Filenames();
-    EXPECT_EQ(0, (int)filenames.size());
-    EXPECT_EQ("", reader.GetHeaderText());
-    EXPECT_EQ(0, reader.GetReferenceCount());
-}
-
-TEST(BamMultiReaderFileOpsTest, NonExistentFiles) {
-
-    std::vector<std::string> inputFiles;
-    inputFiles.push_back("../data/fake.bam");
-    inputFiles.push_back("../data/fake2.bam");
-
-    BamTools::BamMultiReader reader;
-    EXPECT_FALSE(reader.Open(inputFiles));
-
-    EXPECT_FALSE(reader.HasOpenReaders());
-    EXPECT_FALSE(reader.HasIndexes());
-    std::vector<std::string> filenames = reader.Filenames();
-    EXPECT_EQ(0, (int)filenames.size());
-    EXPECT_EQ("", reader.GetHeaderText());
-    EXPECT_EQ(0, reader.GetReferenceCount());
-}
-
-TEST(BamMultiReaderFileOpsTest, EmptyFiles) {
-
-    std::vector<std::string> inputFiles;
-    inputFiles.push_back("../data/empty.bam");
-    inputFiles.push_back("../data/empty1.bam");
-    inputFiles.push_back("../data/empty2.bam");
-
-    BamTools::BamMultiReader reader;
-    EXPECT_FALSE(reader.Open(inputFiles));
-
-    EXPECT_FALSE(reader.HasOpenReaders());
-    EXPECT_FALSE(reader.HasIndexes());
-    std::vector<std::string> filenames = reader.Filenames();
-    EXPECT_EQ(0, (int)filenames.size());
-    EXPECT_EQ("", reader.GetHeaderText());
-    EXPECT_EQ(0, reader.GetReferenceCount());
-}
-
-#endif // BAMMULTIREADER_FILEOPSTEST_H

diff --git a/src/test/api/BamReaderFileOpsTest.h b/src/test/api/BamReaderFileOpsTest.h
deleted file mode 100644 (file)
index 8c574e2..0000000
--- a/src/test/api/BamReaderFileOpsTest.h
+++ /dev/null
@@ -1,73 +0,0 @@
-#ifndef BAMREADER_FILEOPSTEST_H
-#define BAMREADER_FILEOPSTEST_H
-
-#include "api/BamReader.h"
-#include <gtest/gtest.h>
-
-TEST(BamReaderFileOpsTest, Defaults) {
-
-    BamTools::BamReader reader;
-    EXPECT_FALSE(reader.IsOpen());
-    EXPECT_FALSE(reader.HasIndex());
-    EXPECT_EQ("", reader.GetFilename());
-    EXPECT_EQ("", reader.GetHeaderText());
-    EXPECT_EQ(0,  reader.GetReferenceCount());
-}
-
-TEST(BamReaderFileOpsTest, NonExistentFile) {
-
-    BamTools::BamReader reader;
-    EXPECT_FALSE(reader.Open("../data/fake.bam"));
-
-    EXPECT_FALSE(reader.IsOpen());
-    EXPECT_FALSE(reader.HasIndex());
-    EXPECT_EQ("", reader.GetFilename());
-    EXPECT_EQ("", reader.GetHeaderText());
-    EXPECT_EQ(0,  reader.GetReferenceCount());
-}
-
-TEST(BamReaderFileOpsTest, EmptyFile) {
-
-    BamTools::BamReader reader;
-    EXPECT_FALSE(reader.Open("../data/empty.bam"));
-
-    EXPECT_FALSE(reader.IsOpen());
-    EXPECT_FALSE(reader.HasIndex());
-    EXPECT_EQ("", reader.GetFilename());
-    EXPECT_EQ("", reader.GetHeaderText());
-    EXPECT_EQ(0,  reader.GetReferenceCount());
-}
-
-TEST(BamReaderFileOpsTest, NormalFile_NoIndexNoHeader) {
-
-    BamTools::BamReader reader;
-    EXPECT_TRUE(reader.Open("../data/ex1.bam"));
-
-    EXPECT_TRUE(reader.IsOpen());
-    EXPECT_FALSE(reader.HasIndex());
-    EXPECT_EQ("../data/ex1.bam", reader.GetFilename());
-    EXPECT_EQ("", reader.GetHeaderText());
-    EXPECT_EQ(2,  reader.GetReferenceCount());
-}
-
-TEST(BamReaderFileOpsTest, NormalFile_ExplicitIndexFilename) {
-
-    BamTools::BamReader reader;
-    EXPECT_TRUE(reader.Open("../data/ex1.bam"));
-
-    EXPECT_TRUE(reader.IsOpen());
-    EXPECT_FALSE(reader.HasIndex());
-    EXPECT_EQ("../data/ex1.bam", reader.GetFilename());
-    EXPECT_EQ("", reader.GetHeaderText());
-    EXPECT_EQ(2,  reader.GetReferenceCount());
-
-    EXPECT_TRUE(reader.OpenIndex("../data/ex1.bam.bai"));
-
-    EXPECT_TRUE(reader.IsOpen());
-    EXPECT_TRUE(reader.HasIndex());
-    EXPECT_EQ("../data/ex1.bam", reader.GetFilename());
-    EXPECT_EQ("", reader.GetHeaderText());
-    EXPECT_EQ(2,  reader.GetReferenceCount());
-}
-
-#endif // BAMREADER_FILEOPSTEST_H

diff --git a/src/test/api/BamRegionTest.h b/src/test/api/BamRegionTest.h
deleted file mode 100644 (file)
index 5b6009e..0000000
--- a/src/test/api/BamRegionTest.h
+++ /dev/null
@@ -1,49 +0,0 @@
-#ifndef BAMAUX_BAMREGIONTEST_H
-#define BAMAUX_BAMREGIONTEST_H
-
-#include "api/BamAux.h"
-#include <gtest/gtest.h>
-
-TEST(BamAux_BamRegionTest, DefaultValues) {
-    BamTools::BamRegion region;
-    EXPECT_EQ(-1, region.LeftRefID);
-    EXPECT_EQ(-1, region.LeftPosition);
-    EXPECT_EQ(-1, region.RightRefID);
-    EXPECT_EQ(-1, region.RightPosition);
-}
-
-TEST(BamAux_BamRegionTest, IsNull) {
-    
-    BamTools::BamRegion empty;
-    EXPECT_TRUE(empty.isNull());
-
-    BamTools::BamRegion normal(1,100,2,200);
-    EXPECT_FALSE(normal.isNull());
-}
-
-TEST(BamAux_BamRegionTest, Clear) {
-
-    BamTools::BamRegion region(1,100);
-    EXPECT_FALSE(region.isNull());
-    region.clear();
-    EXPECT_TRUE(region.isNull());
-}
-
-TEST(BamAux_BamRegionTest, IsLeftBoundSpecified) {
-
-    // no left bound
-    BamTools::BamRegion empty;
-    EXPECT_FALSE(empty.isLeftBoundSpecified());
-
-    // regular left bound
-    BamTools::BamRegion region(1, 100);
-    EXPECT_TRUE(region.isLeftBoundSpecified());
-
-    // invalid left bound
-    BamTools::BamRegion invalidID(-2);
-    EXPECT_FALSE(invalidID.isLeftBoundSpecified());
-    BamTools::BamRegion invalidPosition(1, -200);
-    EXPECT_FALSE(invalidPosition.isLeftBoundSpecified());
-}
-
-#endif // BAMAUX_BAMREGIONTEST_H

diff --git a/src/test/api/BamToolsApiTest.h b/src/test/api/BamToolsApiTest.h
deleted file mode 100644 (file)
index a7ba5ae..0000000
--- a/src/test/api/BamToolsApiTest.h
+++ /dev/null
@@ -1,28 +0,0 @@
-#ifndef BAMTOOLS_TEST_API_H
-#define BAMTOOLS_TEST_API_H
-
-// general API behavior
-#include "BamAlignmentDefaultTest.h"
-#include "BamAlignmentFlagTest.h"
-#include "BamMultiReaderFileOpsTest.h"
-#include "BamReaderFileOpsTest.h"
-#include "BamRegionTest.h"
-#include "SamHeaderValidationTest.h"
-#include "SamReadGroupDictionaryTest.h"
-#include "SamSequenceDictionaryTest.h"
-
-// internal BAM behavior
-
-// internal indexing behavior
-#include "internal/index/BamIndexFactoryTest.h"
-#include "internal/index/BamStandardIndexTest.h"
-#include "internal/index/BamToolsIndexTest.h"
-
-// internal I/O behavior
-
-// internal SAM behavior
-
-// internal utils behavior
-
-#endif // BAMTOOLS_TEST_API_H
-

diff --git a/src/test/api/SamHeaderValidationTest.h b/src/test/api/SamHeaderValidationTest.h
deleted file mode 100644 (file)
index 4b59505..0000000
--- a/src/test/api/SamHeaderValidationTest.h
+++ /dev/null
@@ -1,292 +0,0 @@
-#ifndef SAMHEADER_VALIDATIONTEST_H
-#define SAMHEADER_VALIDATIONTEST_H
-
-#include "api/SamHeader.h"
-#include <gtest/gtest.h>
-#include <iostream>
-#include <string>
-
-TEST(SamHeader_ValidationTest, EmptyHeader) {
-
-    BamTools::SamHeader header("");
-    std::string headerText = header.ToString();
-    ASSERT_TRUE(headerText.empty());
-    EXPECT_TRUE(header.IsValid());
-}
-
-TEST(SamHeader_ValidationTest, Version) {
-
-    BamTools::SamHeader header("");
-
-    // empty - VALID HEADER
-    header.Version = "";
-    EXPECT_TRUE(header.IsValid());
-
-    // normal - VALID HEADER
-    header.Version = "1.1";
-    EXPECT_TRUE(header.IsValid());
-    header.Version = "11.1";
-    EXPECT_TRUE(header.IsValid());
-    header.Version = "1.11";
-
-    // no period - INVALID HEADER
-    header.Version = "11";
-    EXPECT_FALSE(header.IsValid());
-
-    // no major - INVALID HEADER
-    header.Version = ".1";
-    EXPECT_FALSE(header.IsValid());
-
-    // invalid major - INVALID HEADER
-    header.Version = "a.1";
-    EXPECT_FALSE(header.IsValid());
-
-    // no minor - INVALID HEADER
-    header.Version = "1.";
-    EXPECT_FALSE(header.IsValid());
-
-    // invalid minor - INVALID HEADER
-    header.Version = "1.a";
-    EXPECT_FALSE(header.IsValid());
-}
-
-TEST(SamHeader_ValidationTest, GroupOrder) {
-
-    BamTools::SamHeader header("");
-
-    // empty - VALID HEADER
-    header.GroupOrder = "";
-    EXPECT_TRUE(header.IsValid());
-
-    // normal group order- VALID HEADER
-    header.GroupOrder = "none";
-    EXPECT_TRUE(header.IsValid());
-    header.GroupOrder = "query";
-    EXPECT_TRUE(header.IsValid());
-    header.GroupOrder = "reference";
-    EXPECT_TRUE(header.IsValid());
-
-    // invalid group order - INVALID HEADER
-    header.GroupOrder = "fake";
-    EXPECT_FALSE(header.IsValid());
-}
-
-TEST(SamHeader_ValidationTest, SortOrder) {
-
-    BamTools::SamHeader header("");
-
-    // empty - VALID HEADER
-    header.SortOrder = "";
-    EXPECT_TRUE(header.IsValid());
-
-    // normal sort order- VALID HEADER
-    header.SortOrder = "coordinate";
-    EXPECT_TRUE(header.IsValid());
-    header.SortOrder = "queryname";
-    EXPECT_TRUE(header.IsValid());
-    header.SortOrder = "unsorted";
-    EXPECT_TRUE(header.IsValid());
-
-    // invalid sort order - INVALID HEADER
-    header.SortOrder = "fake";
-    EXPECT_FALSE(header.IsValid());
-}
-
-TEST(SamHeader_ValidationTest, SequenceDictionary) {
-
-    BamTools::SamHeader header("");
-    BamTools::SamSequence sequence;
-
-    // --------------------------------
-    // empty - VALID HEADER
-
-    header.Sequences.Clear();
-    EXPECT_TRUE(header.IsValid());
-
-    // --------------------------------
-    // normal - VALID HEADER
-
-    sequence.Name   = "MT";
-    sequence.Length = "1000";
-    header.Sequences.Add(sequence);
-    EXPECT_TRUE(header.IsValid());
-
-    // normal ( length == MIN )
-    sequence.Name   = "MT";
-    sequence.Length = "1";
-    header.Sequences.Clear();
-    header.Sequences.Add(sequence);
-    EXPECT_TRUE(header.IsValid());
-
-    // normal ( length == MAX )
-    sequence.Name = "MT";
-    sequence.Length = "536870911";
-    header.Sequences.Clear();
-    header.Sequences.Add(sequence);
-    EXPECT_TRUE(header.IsValid());
-
-    // ---------------------------------
-    // missing required info - INVALID HEADER
-
-    // missing ID
-    sequence.Name = "";
-    sequence.Length = "1000";
-    header.Sequences.Clear();
-    header.Sequences.Add(sequence);
-    EXPECT_FALSE(header.IsValid());
-
-    // missing length
-    sequence.Name = "MT";
-    sequence.Length = "";
-    header.Sequences.Clear();
-    header.Sequences.Add(sequence);
-    EXPECT_FALSE(header.IsValid());
-
-    // -------------------------------------
-    // improper SN format - INVALID HEADER
-
-    // starts with *
-    sequence.Name = "*MT";
-    sequence.Length = "1000";
-    header.Sequences.Clear();
-    header.Sequences.Add(sequence);
-    EXPECT_FALSE(header.IsValid());
-
-    // starts with =
-    sequence.Name = "=MT";
-    sequence.Length = "1000";
-    header.Sequences.Clear();
-    header.Sequences.Add(sequence);
-    EXPECT_FALSE(header.IsValid());
-
-    // -----------------------------------------
-    // nonunique ID - INVALID HEADER
-
-    // this behavior is blocked by SamSequenceDictionary
-    // see SamSequenceDictionaryTest::AddDuplicateOk
-
-    // --------------------------------------------
-    // invalid length  - INVALID HEADER
-
-    // length = 0 (MIN == 1)
-    sequence.Name = "MT";
-    sequence.Length = "0";
-    header.Sequences.Clear();
-    header.Sequences.Add(sequence);
-    EXPECT_FALSE(header.IsValid());
-
-    // length = -1
-    sequence.Name = "MT";
-    sequence.Length = "-1";
-    header.Sequences.Clear();
-    header.Sequences.Add(sequence);
-    EXPECT_FALSE(header.IsValid());
-
-    // length = MAX + 1
-    sequence.Name ="MT";
-    sequence.Length = "536870912";
-    header.Sequences.Clear();
-    header.Sequences.Add(sequence);
-    EXPECT_FALSE(header.IsValid());
-}
-
-TEST(SamHeader_ValidationTest, ReadGroupDictionary) {
-
-    BamTools::SamHeader header("");
-    BamTools::SamReadGroup readGroup;
-
-    // ---------------------------------
-    // empty - VALID HEADER
-
-    header.ReadGroups.Clear();
-    EXPECT_TRUE(header.IsValid());
-
-    // ---------------------------------
-    // normal - VALID HEADER
-
-    readGroup.ID = "Group123";
-    readGroup.PlatformUnit = "PU001";
-
-    // technology: none
-    header.ReadGroups.Clear();
-    header.ReadGroups.Add(readGroup);
-    EXPECT_TRUE(header.IsValid());
-
-    // technology: capillary
-    readGroup.SequencingTechnology = "CAPILLARY";
-    header.ReadGroups.Clear();
-    header.ReadGroups.Add(readGroup);
-    EXPECT_TRUE(header.IsValid());
-
-    // technology: Helicos
-    readGroup.SequencingTechnology = "HELICOS";
-    header.ReadGroups.Clear();
-    header.ReadGroups.Add(readGroup);
-    EXPECT_TRUE(header.IsValid());
-
-    // technology: Illumina
-    readGroup.SequencingTechnology = "ILLUMINA";
-    header.ReadGroups.Clear();
-    header.ReadGroups.Add(readGroup);
-    EXPECT_TRUE(header.IsValid());
-
-    // technology: IonTorrent
-    readGroup.SequencingTechnology = "IONTORRENT";
-    header.ReadGroups.Clear();
-    header.ReadGroups.Add(readGroup);
-    EXPECT_TRUE(header.IsValid());
-
-    // technology: 454
-    readGroup.SequencingTechnology = "LS454";
-    header.ReadGroups.Clear();
-    header.ReadGroups.Add(readGroup);
-    EXPECT_TRUE(header.IsValid());
-
-    // technology: Pacific Bio
-    readGroup.SequencingTechnology = "PACBIO";
-    header.ReadGroups.Clear();
-    header.ReadGroups.Add(readGroup);
-    EXPECT_TRUE(header.IsValid());
-
-    // technology: Solid
-    readGroup.SequencingTechnology = "SOLID";
-    header.ReadGroups.Clear();
-    header.ReadGroups.Add(readGroup);
-    EXPECT_TRUE(header.IsValid());
-
-    // ---------------------------------
-    // missing ID - INVALID HEADER
-
-    readGroup.ID = "";
-    header.ReadGroups.Clear();
-    header.ReadGroups.Add(readGroup);
-    EXPECT_FALSE(header.IsValid());
-
-    // -----------------------------------------
-    // nonunique ID - INVALID HEADER
-
-    // this behavior is blocked by SamReadGroupDictionary
-    // see SamReadGroupDictionaryTest::AddDuplicateOk
-
-    // ------------------------------------------
-    // nonunique platform unit - INVALID HEADER
-
-    BamTools::SamReadGroup dupPU("Group1");
-    BamTools::SamReadGroup dupPU2("Group2");
-    dupPU.PlatformUnit = "PU001";
-    dupPU2.PlatformUnit = "PU001";
-    header.ReadGroups.Clear();
-    header.ReadGroups.Add(dupPU);
-    header.ReadGroups.Add(dupPU2);
-    EXPECT_FALSE(header.IsValid());
-
-    // ------------------------------------------------
-    // invalid sequencing technology - INVALID HEADER
-
-    readGroup.SequencingTechnology = "fake";
-    header.ReadGroups.Clear();
-    header.ReadGroups.Add(readGroup);
-    EXPECT_FALSE(header.IsValid());
-}
-
-#endif // SAMHEADER_VALIDATIONTEST_H

diff --git a/src/test/api/SamReadGroupDictionaryTest.h b/src/test/api/SamReadGroupDictionaryTest.h
deleted file mode 100644 (file)
index ccf8d89..0000000
--- a/src/test/api/SamReadGroupDictionaryTest.h
+++ /dev/null
@@ -1,68 +0,0 @@
-#ifndef SAMREADGROUPDICTIONARY_TEST_H
-#define SAMREADGROUPDICTIONARY_TEST_H
-
-#include "api/SamReadGroupDictionary.h"
-#include <gtest/gtest.h>
-#include <vector>
-
-TEST(SamReadGroupDictionaryTest, Empty) {
-    BamTools::SamReadGroupDictionary readGroups;
-    EXPECT_TRUE(readGroups.IsEmpty());
-    EXPECT_EQ(0, readGroups.Size());
-}
-
-TEST(SamReadGroupDictionaryTest, AddOne) {
-
-    BamTools::SamReadGroupDictionary readGroups;
-    readGroups.Add(BamTools::SamReadGroup());
-    EXPECT_FALSE(readGroups.IsEmpty());
-    EXPECT_EQ(1, readGroups.Size());
-}
-
-TEST(SamReadGroupDictionaryTest, AddMulti) {
-
-    std::vector<BamTools::SamReadGroup> groups;
-    groups.push_back(BamTools::SamReadGroup("1"));
-    groups.push_back(BamTools::SamReadGroup("2"));
-
-    BamTools::SamReadGroupDictionary readGroups;
-    readGroups.Add(groups);
-    EXPECT_FALSE(readGroups.IsEmpty());
-    EXPECT_EQ(2, readGroups.Size());
-}
-
-TEST(SamReadGroupDictionaryTest, AddDuplicate) {
-
-    std::vector<BamTools::SamReadGroup> groups;
-    groups.push_back(BamTools::SamReadGroup("1"));
-    groups.push_back(BamTools::SamReadGroup("1"));
-
-    // add duplicates through Add()
-    BamTools::SamReadGroupDictionary readGroups;
-    readGroups.Add(groups);
-    EXPECT_FALSE(readGroups.IsEmpty());
-    EXPECT_EQ(1, readGroups.Size());    // duplicate should not get added
-
-    // add duplicates through operator[]
-    readGroups.Clear();
-    readGroups["1"] = groups.at(0);
-    readGroups["1"] = groups.at(0);
-    EXPECT_FALSE(readGroups.IsEmpty());
-    EXPECT_EQ(1, readGroups.Size());     // duplicate should not get added
-}
-
-TEST(SamReadGroupDictionaryTest, Clear) {
-
-    // add a read group
-    BamTools::SamReadGroupDictionary readGroups;
-    readGroups.Add(BamTools::SamReadGroup());
-    EXPECT_FALSE(readGroups.IsEmpty());
-    EXPECT_EQ(1, readGroups.Size());;
-
-    // test clear
-    readGroups.Clear();
-    EXPECT_TRUE(readGroups.IsEmpty());
-    EXPECT_EQ(0, readGroups.Size());
-}
-
-#endif // SAMREADGROUPDICTIONARY_TEST_H

diff --git a/src/test/api/SamSequenceDictionaryTest.h b/src/test/api/SamSequenceDictionaryTest.h
deleted file mode 100644 (file)
index bd75e1e..0000000
--- a/src/test/api/SamSequenceDictionaryTest.h
+++ /dev/null
@@ -1,69 +0,0 @@
-#ifndef SAMSEQUENCEDICTIONARY_TEST_H
-#define SAMSEQUENCEDICTIONARY_TEST_H
-
-#include "api/SamSequenceDictionary.h"
-#include <gtest/gtest.h>
-#include <vector>
-
-TEST(SamSequenceDictionaryTest, Empty) {
-
-    BamTools::SamSequenceDictionary sequences;
-    EXPECT_TRUE(sequences.IsEmpty());
-    EXPECT_EQ(0, sequences.Size());
-}
-
-TEST(SamSequenceDictionaryTest, AddOne) {
-
-    BamTools::SamSequenceDictionary sequences;
-    sequences.Add(BamTools::SamSequence());
-    EXPECT_FALSE(sequences.IsEmpty());
-    EXPECT_EQ(1, sequences.Size());
-}
-
-TEST(SamSequenceDictionaryTest, AddMulti) {
-
-    std::vector<BamTools::SamSequence> groups;
-    groups.push_back(BamTools::SamSequence("1", 100));
-    groups.push_back(BamTools::SamSequence("2", 100));
-
-    BamTools::SamSequenceDictionary sequences;
-    sequences.Add(groups);
-    EXPECT_FALSE(sequences.IsEmpty());
-    EXPECT_EQ(2, sequences.Size());
-}
-
-TEST(SamSequenceDictionaryTest, AddDuplicate) {
-
-    std::vector<BamTools::SamSequence> groups;
-    groups.push_back(BamTools::SamSequence("1", 100));
-    groups.push_back(BamTools::SamSequence("1", 100));
-
-    // add duplicates through Add()
-    BamTools::SamSequenceDictionary sequences;
-    sequences.Add(groups);
-    EXPECT_FALSE(sequences.IsEmpty());
-    EXPECT_EQ(1, sequences.Size());     // duplicate should not get added
-
-    // add duplicates through operator[]
-    sequences.Clear();
-    sequences["1"] = groups.at(0);
-    sequences["1"] = groups.at(0);
-    EXPECT_FALSE(sequences.IsEmpty());
-    EXPECT_EQ(1, sequences.Size());     // duplicate should not get added
-}
-
-TEST(SamSequenceDictionaryTest, Clear) {
-
-    // add a sequence
-    BamTools::SamSequenceDictionary sequences;
-    sequences.Add(BamTools::SamSequence());
-    EXPECT_FALSE(sequences.IsEmpty());
-    EXPECT_EQ(1, sequences.Size());;
-
-    // test clear
-    sequences.Clear();
-    EXPECT_TRUE(sequences.IsEmpty());
-    EXPECT_EQ(0, sequences.Size());
-}
-
-#endif // SAMSEQUENCEDICTIONARY_TEST_H

diff --git a/src/test/api/internal/index/BamIndexFactoryTest.h b/src/test/api/internal/index/BamIndexFactoryTest.h
deleted file mode 100644 (file)
index f6755df..0000000
--- a/src/test/api/internal/index/BamIndexFactoryTest.h
+++ /dev/null
@@ -1,89 +0,0 @@
-#ifndef BAMINDEX_FACTORYTEST_H
-#define BAMINDEX_FACTORYTEST_H
-
-#include "api/BamIndex.h"
-#include "api/internal/index/BamIndexFactory_p.h"
-#include "api/internal/index/BamStandardIndex_p.h"
-#include "api/internal/index/BamToolsIndex_p.h"
-
-#include <gtest/gtest.h>
-#include <iostream>
-#include <string>
-
-TEST(BamIndex_FactoryTest, CreateIndexFilename) {
-
-    const std::string bamFilename      = "dummy.bam";
-    const std::string baiIndexFilename = BamTools::Internal::BamIndexFactory::CreateIndexFilename(bamFilename, BamTools::BamIndex::STANDARD);
-    const std::string btiIndexFilename = BamTools::Internal::BamIndexFactory::CreateIndexFilename(bamFilename, BamTools::BamIndex::BAMTOOLS);
-
-    EXPECT_EQ("dummy.bam.bai", baiIndexFilename);
-    EXPECT_EQ("dummy.bam.bti", btiIndexFilename);
-}
-
-TEST(BamIndex_FactoryTest, FileExtension) {
-
-    const std::string bamFilename      = "dummy.bam";
-    const std::string baiIndexFilename = "dummy.bam.bai";
-    const std::string btiIndexFilename = "path/to/dummy.bam.bti";
-
-    const std::string bamExtension = BamTools::Internal::BamIndexFactory::FileExtension(bamFilename);
-    const std::string baiExtension = BamTools::Internal::BamIndexFactory::FileExtension(baiIndexFilename);
-    const std::string btiExtension = BamTools::Internal::BamIndexFactory::FileExtension(btiIndexFilename);
-
-    EXPECT_EQ(".bam", bamExtension);
-    EXPECT_EQ(".bai", baiExtension);
-    EXPECT_EQ(".bti", btiExtension);
-
-    // TODO: try some invalid values, just to make sure this is robust/safe enough
-}
-
-TEST(BamIndex_FactoryTest, CreateIndexFromFilename) {
-
-    const std::string baiIndexFilename = "../data/ex1.bam.bai";
-    const std::string btiIndexFilename = "../data/ex1.bam.bti";
-
-    BamTools::BamIndex* bai = BamTools::Internal::BamIndexFactory::CreateIndexFromFilename(baiIndexFilename, 0);
-    BamTools::BamIndex* bti = BamTools::Internal::BamIndexFactory::CreateIndexFromFilename(btiIndexFilename, 0);
-
-    ASSERT_TRUE(bai != NULL);
-    ASSERT_TRUE(bti != NULL);
-
-    EXPECT_EQ(BamTools::BamIndex::STANDARD, bai->Type());
-    EXPECT_EQ(BamTools::BamIndex::BAMTOOLS, bti->Type());
-
-    delete bai;
-    delete bti;
-
-    std::cerr << "TestMessage 4" << std::endl;
-}
-
-TEST(BamIndex_FactoryTest, CreateIndexOfType) {
-
-    BamTools::BamIndex* bai = BamTools::Internal::BamIndexFactory::CreateIndexOfType(BamTools::BamIndex::STANDARD, 0);
-    BamTools::BamIndex* bti = BamTools::Internal::BamIndexFactory::CreateIndexOfType(BamTools::BamIndex::BAMTOOLS, 0);
-
-    EXPECT_EQ(BamTools::BamIndex::STANDARD, bai->Type());
-    EXPECT_EQ(BamTools::BamIndex::BAMTOOLS, bti->Type());
-
-    delete bai;
-    delete bti;
-}
-
-TEST(BamIndex_FactoryTest, FindIndexFilename) {
-
-    // Both BAI & BTI are available
-    const std::string bamFilename = "../data/ex1.bam";
-    const std::string baiIndexFilename = BamTools::Internal::BamIndexFactory::FindIndexFilename(bamFilename, BamTools::BamIndex::STANDARD);
-    const std::string btiIndexFilename = BamTools::Internal::BamIndexFactory::FindIndexFilename(bamFilename, BamTools::BamIndex::BAMTOOLS);
-    EXPECT_EQ("../data/ex1.bam.bai", baiIndexFilename);
-    EXPECT_EQ("../data/ex1.bam.bti", btiIndexFilename);
-
-    // No BTI index available, both requests should fall back to BAI
-    const std::string bamFilename2 = "../data/BCM.ceph.chr20.bam";
-    const std::string baiIndexFilename2 = BamTools::Internal::BamIndexFactory::FindIndexFilename(bamFilename2, BamTools::BamIndex::STANDARD);
-    const std::string btiIndexFilename2 = BamTools::Internal::BamIndexFactory::FindIndexFilename(bamFilename2, BamTools::BamIndex::BAMTOOLS);
-    EXPECT_EQ("../data/BCM.ceph.chr20.bam.bai", baiIndexFilename2);
-    EXPECT_EQ("../data/BCM.ceph.chr20.bam.bai", btiIndexFilename2);
-}
-
-#endif // BAMINDEX_FACTORYTEST_H

diff --git a/src/test/api/internal/index/BamStandardIndexTest.h b/src/test/api/internal/index/BamStandardIndexTest.h
deleted file mode 100644 (file)
index ca1aadd..0000000
--- a/src/test/api/internal/index/BamStandardIndexTest.h
+++ /dev/null
@@ -1,13 +0,0 @@
-#ifndef BAMSTANDARDINDEX_TEST_H
-#define BAMSTANDARDINDEX_TEST_H
-
-#include <gtest/gtest.h>
-#include "api/internal/index/BamStandardIndex_p.h"
-
-TEST(BamStandardIndexTest, Open) {
-
-
-
-}
-
-#endif // BAMSTANDARDINDEX_TEST_H

diff --git a/src/test/api/internal/index/BamToolsIndexTest.h b/src/test/api/internal/index/BamToolsIndexTest.h
deleted file mode 100644 (file)
index e1b6cd4..0000000
--- a/src/test/api/internal/index/BamToolsIndexTest.h
+++ /dev/null
@@ -1,13 +0,0 @@
-#ifndef BAMTOOLSINDEX_TEST_H
-#define BAMTOOLSINDEX_TEST_H
-
-#include <gtest/gtest.h>
-#include "api/internal/index/BamToolsIndex_p.h"
-
-TEST(BamToolsIndexTest, Open) {
-
-
-
-}
-
-#endif // BAMTOOLSINDEX_TEST_H

diff --git a/src/test/toolkit/BamToolsToolkitTest.h b/src/test/toolkit/BamToolsToolkitTest.h
deleted file mode 100644 (file)
index 2655cdd..0000000
--- a/src/test/toolkit/BamToolsToolkitTest.h
+++ /dev/null
@@ -1,6 +0,0 @@
-#ifndef BAMTOOLS_TEST_TOOLKIT_H
-#define BAMTOOLS_TEST_TOOLKIT_H
-
-
-#endif // BAMTOOLS_TEST_TOOLKIT_H
-

diff --git a/src/test/utils/BamToolsUtilsTest.h b/src/test/utils/BamToolsUtilsTest.h
deleted file mode 100644 (file)
index 6e7b060..0000000
--- a/src/test/utils/BamToolsUtilsTest.h
+++ /dev/null
@@ -1,6 +0,0 @@
-#ifndef BAMTOOLS_TEST_UTILS_H
-#define BAMTOOLS_TEST_UTILS_H
-
-
-#endif // BAMTOOLS_TEST_UTILS_H
-

diff --git a/src/third_party/CMakeLists.txt b/src/third_party/CMakeLists.txt
index 653e39148bfe0b8bbd4cb65a953b712da40e88a6..ec965bea879da9b466541a343b7b6e1ecd4508f2 100644 (file)
--- a/src/third_party/CMakeLists.txt
+++ b/src/third_party/CMakeLists.txt
@@ -6,5 +6,4 @@
 # ==========================
 
 # list third-party subdirectories to build in
-add_subdirectory( gtest-1.6.0 )
 add_subdirectory( jsoncpp )

diff --git a/src/toolkit/CMakeLists.txt b/src/toolkit/CMakeLists.txt
index 2f0bf87c560c718155d2a9d703a1230e0edba983..58f3697ed780ee82a62130f82490411da0eb36c6 100644 (file)
--- a/src/toolkit/CMakeLists.txt
+++ b/src/toolkit/CMakeLists.txt
@@ -31,7 +31,7 @@ add_executable( bamtools_cmd
 
 # set BamTools application properties
 set_target_properties( bamtools_cmd PROPERTIES
-                       VERSION  2.0.0
+                       VERSION  2.1.0
                        OUTPUT_NAME "bamtools"
                      )
 # make version info available in application

diff --git a/src/utils/CMakeLists.txt b/src/utils/CMakeLists.txt
index 6e37cca13a5e406ec4c8b5502bcb4fea7c494d31..e810eb36d548bac965d09ee815db5204786283e8 100644 (file)
--- a/src/utils/CMakeLists.txt
+++ b/src/utils/CMakeLists.txt
@@ -25,6 +25,6 @@ target_link_libraries( BamTools-utils BamTools )
 
 # set BamTools library properties
 set_target_properties( BamTools-utils PROPERTIES
-                       SOVERSION   2.0.0
+                       SOVERSION   2.1.0
                        OUTPUT_NAME bamtools-utils
                      )