src/test/api/BamIndex/BamIndexFactoryTest.h

   1 #ifndef BAMINDEX_FACTORYTEST_H
   2 #define BAMINDEX_FACTORYTEST_H
   3
   4 #include "api/BamIndex.h"
   5 #include "api/internal/index/BamIndexFactory_p.h"
   6 #include "api/internal/index/BamStandardIndex_p.h"
   7 #include "api/internal/index/BamToolsIndex_p.h"
   8
   9 #include <gtest/gtest.h>
  10 #include <iostream>
  11 #include <string>
  12
  13 TEST(BamIndex_FactoryTest, CreateIndexFilename) {
  14
  15     const std::string bamFilename      = "dummy.bam";
  16     const std::string baiIndexFilename = BamTools::Internal::BamIndexFactory::CreateIndexFilename(bamFilename, BamTools::BamIndex::STANDARD);
  17     const std::string btiIndexFilename = BamTools::Internal::BamIndexFactory::CreateIndexFilename(bamFilename, BamTools::BamIndex::BAMTOOLS);
  18
  19     EXPECT_EQ("dummy.bam.bai", baiIndexFilename);
  20     EXPECT_EQ("dummy.bam.bti", btiIndexFilename);
  21 }
  22
  23 TEST(BamIndex_FactoryTest, FileExtension) {
  24
  25     const std::string bamFilename      = "dummy.bam";
  26     const std::string baiIndexFilename = "dummy.bam.bai";
  27     const std::string btiIndexFilename = "path/to/dummy.bam.bti";
  28
  29     const std::string bamExtension = BamTools::Internal::BamIndexFactory::FileExtension(bamFilename);
  30     const std::string baiExtension = BamTools::Internal::BamIndexFactory::FileExtension(baiIndexFilename);
  31     const std::string btiExtension = BamTools::Internal::BamIndexFactory::FileExtension(btiIndexFilename);
  32
  33     EXPECT_EQ(".bam", bamExtension);
  34     EXPECT_EQ(".bai", baiExtension);
  35     EXPECT_EQ(".bti", btiExtension);
  36
  37     // TODO: try some invalid values, just to make sure this is robust/safe enough
  38 }
  39
  40 TEST(BamIndex_FactoryTest, CreateIndexFromFilename) {
  41
  42     const std::string baiIndexFilename = "../data/ex1.bam.bai";
  43     const std::string btiIndexFilename = "../data/ex1.bam.bti";
  44
  45     BamTools::BamIndex* bai = BamTools::Internal::BamIndexFactory::CreateIndexFromFilename(baiIndexFilename, 0);
  46     BamTools::BamIndex* bti = BamTools::Internal::BamIndexFactory::CreateIndexFromFilename(btiIndexFilename, 0);
  47
  48     ASSERT_TRUE(bai != NULL);
  49     ASSERT_TRUE(bti != NULL);
  50
  51     EXPECT_EQ(BamTools::BamIndex::STANDARD, bai->Type());
  52     EXPECT_EQ(BamTools::BamIndex::BAMTOOLS, bti->Type());
  53
  54     delete bai;
  55     delete bti;
  56
  57     std::cerr << "TestMessage 4" << std::endl;
  58 }
  59
  60 TEST(BamIndex_FactoryTest, CreateIndexOfType) {
  61
  62     BamTools::BamIndex* bai = BamTools::Internal::BamIndexFactory::CreateIndexOfType(BamTools::BamIndex::STANDARD, 0);
  63     BamTools::BamIndex* bti = BamTools::Internal::BamIndexFactory::CreateIndexOfType(BamTools::BamIndex::BAMTOOLS, 0);
  64
  65     EXPECT_EQ(BamTools::BamIndex::STANDARD, bai->Type());
  66     EXPECT_EQ(BamTools::BamIndex::BAMTOOLS, bti->Type());
  67
  68     delete bai;
  69     delete bti;
  70 }
  71
  72 TEST(BamIndex_FactoryTest, FindIndexFilename) {
  73
  74     // Both BAI & BTI are available
  75     const std::string bamFilename = "../data/ex1.bam";
  76     const std::string baiIndexFilename = BamTools::Internal::BamIndexFactory::FindIndexFilename(bamFilename, BamTools::BamIndex::STANDARD);
  77     const std::string btiIndexFilename = BamTools::Internal::BamIndexFactory::FindIndexFilename(bamFilename, BamTools::BamIndex::BAMTOOLS);
  78     EXPECT_EQ("../data/ex1.bam.bai", baiIndexFilename);
  79     EXPECT_EQ("../data/ex1.bam.bti", btiIndexFilename);
  80
  81     // No BTI index available, both requests should fall back to BAI
  82     const std::string bamFilename2 = "../data/BCM.ceph.chr20.bam";
  83     const std::string baiIndexFilename2 = BamTools::Internal::BamIndexFactory::FindIndexFilename(bamFilename2, BamTools::BamIndex::STANDARD);
  84     const std::string btiIndexFilename2 = BamTools::Internal::BamIndexFactory::FindIndexFilename(bamFilename2, BamTools::BamIndex::BAMTOOLS);
  85     EXPECT_EQ("../data/BCM.ceph.chr20.bam.bai", baiIndexFilename2);
  86     EXPECT_EQ("../data/BCM.ceph.chr20.bam.bai", btiIndexFilename2);
  87 }
  88
  89 #endif // BAMINDEX_FACTORYTEST_H