From 0eb3445597eb2ebc272226d44cabdab3cf983e21 Mon Sep 17 00:00:00 2001 From: Karthik Gururaj Date: Fri, 19 Sep 2014 14:49:08 -0700 Subject: [PATCH] Fixed signed-unsigned comparison errors in tests --- test/indexed_sam_reader_test.cpp | 12 ++--- test/sam_builder_test.cpp | 18 ++++---- test/sam_header_test.cpp | 8 ++-- test/sam_reader_test.cpp | 2 +- test/sam_test.cpp | 8 ++-- test/select_if_test.cpp | 8 ++-- test/variant_header_test.cpp | 4 +- test/variant_reader_test.cpp | 76 ++++++++++++++++---------------- 8 files changed, 68 insertions(+), 68 deletions(-) diff --git a/test/indexed_sam_reader_test.cpp b/test/indexed_sam_reader_test.cpp index 0708a9866..12e627585 100644 --- a/test/indexed_sam_reader_test.cpp +++ b/test/indexed_sam_reader_test.cpp @@ -16,7 +16,7 @@ BOOST_AUTO_TEST_CASE( indexed_single_readers_intervals ) for (const auto& sam : IndexedSingleSamReader{filename, interval_list}) { BOOST_CHECK_EQUAL(sam.name().substr(0, 15), "30PPJAAXX090125"); - BOOST_CHECK_EQUAL(sam.chromosome(), 0); + BOOST_CHECK_EQUAL(sam.chromosome(), 0u); ++read_counter; } BOOST_CHECK_EQUAL(read_counter, 15u); @@ -24,10 +24,10 @@ BOOST_AUTO_TEST_CASE( indexed_single_readers_intervals ) const auto interval_read_counts = vector{3, 4, 4, 4}; auto interval_number = 0u; for (const auto& interval : interval_list) { - auto interval_read_counter = 0u; + auto interval_read_counter = 0; for (const auto& sam : IndexedSingleSamReader{filename, vector{interval}}) { BOOST_CHECK_EQUAL(sam.name().substr(0, 15), "30PPJAAXX090125"); - BOOST_CHECK_EQUAL(sam.chromosome(), 0); + BOOST_CHECK_EQUAL(sam.chromosome(), 0u); ++interval_read_counter; } BOOST_CHECK_EQUAL(interval_read_counter, interval_read_counts[interval_number]); @@ -43,7 +43,7 @@ BOOST_AUTO_TEST_CASE( indexed_single_readers_entire_file ) auto read_counter = 0u; for (const auto& sam : IndexedSingleSamReader{filename, entire_file}) { BOOST_CHECK_EQUAL(sam.name().substr(0, 15), "30PPJAAXX090125"); - BOOST_CHECK_EQUAL(sam.chromosome(), 0); + BOOST_CHECK_EQUAL(sam.chromosome(), 0u); ++read_counter; } BOOST_CHECK_EQUAL(read_counter, 33u); @@ -57,7 +57,7 @@ BOOST_AUTO_TEST_CASE( indexed_single_readers_unmapped ) auto read_counter = 0u; for (const auto& sam : IndexedSingleSamReader{filename, unmapped_reads}) { BOOST_CHECK_EQUAL(sam.name().substr(0, 15), "30PPJAAXX090125"); - BOOST_CHECK_EQUAL(sam.chromosome(), 0); + BOOST_CHECK_EQUAL(sam.chromosome(), 0u); ++read_counter; } BOOST_CHECK_EQUAL(read_counter, 0u); @@ -71,7 +71,7 @@ BOOST_AUTO_TEST_CASE( indexed_single_readers_empty ) auto read_counter = 0u; for (const auto& sam : IndexedSingleSamReader{filename, empty_list}) { BOOST_CHECK_EQUAL(sam.name().substr(0, 15), "30PPJAAXX090125"); - BOOST_CHECK_EQUAL(sam.chromosome(), 0); + BOOST_CHECK_EQUAL(sam.chromosome(), 0u); ++read_counter; } BOOST_CHECK_EQUAL(read_counter, 0u); diff --git a/test/sam_builder_test.cpp b/test/sam_builder_test.cpp index e68f61ec8..8b61efcc1 100644 --- a/test/sam_builder_test.cpp +++ b/test/sam_builder_test.cpp @@ -305,9 +305,9 @@ BOOST_AUTO_TEST_CASE( set_multiple_data_fields_from_scratch ) { BOOST_CHECK_EQUAL(constructed_read.cigar().to_string(), "1M1I1M"); BOOST_CHECK_EQUAL(constructed_read.bases().to_string(), "ACT"); BOOST_CHECK_EQUAL(constructed_read.base_quals().to_string(), "1 2 3"); - BOOST_CHECK_EQUAL(constructed_read.chromosome(), 1); - BOOST_CHECK_EQUAL(constructed_read.alignment_start(), 142); - BOOST_CHECK_EQUAL(constructed_read.mate_alignment_start(), 199); + BOOST_CHECK_EQUAL(constructed_read.chromosome(), 1u); + BOOST_CHECK_EQUAL(constructed_read.alignment_start(), 142u); + BOOST_CHECK_EQUAL(constructed_read.mate_alignment_start(), 199u); } BOOST_AUTO_TEST_CASE( reconstruct_complete_read ) { @@ -365,9 +365,9 @@ BOOST_AUTO_TEST_CASE( build_multiple_reads ) { BOOST_CHECK_EQUAL(constructed_read.cigar().to_string(), "1M1I1M"); BOOST_CHECK_EQUAL(constructed_read.bases().to_string(), "ACT"); BOOST_CHECK_EQUAL(constructed_read.base_quals().to_string(), "1 2 3"); - BOOST_CHECK_EQUAL(constructed_read.chromosome(), 1); - BOOST_CHECK_EQUAL(constructed_read.alignment_start(), 142); - BOOST_CHECK_EQUAL(constructed_read.mate_alignment_start(), 199); + BOOST_CHECK_EQUAL(constructed_read.chromosome(), 1u); + BOOST_CHECK_EQUAL(constructed_read.alignment_start(), 142u); + BOOST_CHECK_EQUAL(constructed_read.mate_alignment_start(), 199u); auto second_read = builder.set_chromosome(2).set_cigar("2M1I").set_bases("GGA").build(); @@ -375,9 +375,9 @@ BOOST_AUTO_TEST_CASE( build_multiple_reads ) { BOOST_CHECK_EQUAL(second_read.cigar().to_string(), "2M1I"); BOOST_CHECK_EQUAL(second_read.bases().to_string(), "GGA"); BOOST_CHECK_EQUAL(second_read.base_quals().to_string(), "1 2 3"); - BOOST_CHECK_EQUAL(second_read.chromosome(), 2); - BOOST_CHECK_EQUAL(second_read.alignment_start(), 142); - BOOST_CHECK_EQUAL(second_read.mate_alignment_start(), 199); + BOOST_CHECK_EQUAL(second_read.chromosome(), 2u); + BOOST_CHECK_EQUAL(second_read.alignment_start(), 142u); + BOOST_CHECK_EQUAL(second_read.mate_alignment_start(), 199u); } BOOST_AUTO_TEST_CASE( set_illegal_base_quals ) { auto header = SingleSamReader{"testdata/test_simple.bam"}.header(); diff --git a/test/sam_header_test.cpp b/test/sam_header_test.cpp index 209f6a525..4c1fb297a 100644 --- a/test/sam_header_test.cpp +++ b/test/sam_header_test.cpp @@ -10,10 +10,10 @@ BOOST_AUTO_TEST_CASE( sam_header ) { auto reader = SingleSamReader{"testdata/test_simple.bam"}; auto header = reader.header(); BOOST_CHECK_EQUAL("chr1", header.sequence_name(0)); - BOOST_CHECK_EQUAL(100000, header.sequence_length("chr1")); - BOOST_CHECK_EQUAL(100000, header.sequence_length(0)); - BOOST_CHECK_EQUAL(0, header.sequence_length("foo")); - BOOST_CHECK_EQUAL(1, header.n_sequences()); + BOOST_CHECK_EQUAL(100000u, header.sequence_length("chr1")); + BOOST_CHECK_EQUAL(100000u, header.sequence_length(0)); + BOOST_CHECK_EQUAL(0u, header.sequence_length("foo")); + BOOST_CHECK_EQUAL(1u, header.n_sequences()); } /** @todo Need a way to modify the header in between these copies/moves to make sure these are working properly! */ diff --git a/test/sam_reader_test.cpp b/test/sam_reader_test.cpp index c76ad3352..f4c07984f 100644 --- a/test/sam_reader_test.cpp +++ b/test/sam_reader_test.cpp @@ -13,7 +13,7 @@ BOOST_AUTO_TEST_CASE( single_readers ) auto read_counter = 0u; for (const auto& sam : SingleSamReader{filename}) { BOOST_CHECK_EQUAL(sam.name().substr(0, 15), "30PPJAAXX090125"); - BOOST_CHECK_EQUAL(sam.chromosome(), 0); + BOOST_CHECK_EQUAL(sam.chromosome(), 0u); ++read_counter; } BOOST_CHECK_EQUAL(read_counter, 33u); diff --git a/test/sam_test.cpp b/test/sam_test.cpp index 24fd1b7bd..8f7fa85f0 100644 --- a/test/sam_test.cpp +++ b/test/sam_test.cpp @@ -17,8 +17,8 @@ void check_first_read(Sam& record) { const auto chr = 5u; const auto aln = 1000u; const auto expected_cigar = "76M"; - const auto expected_cigar_size = 1; - const auto expected_cigar_element_length = 76; + const auto expected_cigar_size = 1u; + const auto expected_cigar_element_length = 76u; const auto expected_cigar_element_operator = CigarOperator::M; const auto expected_bases = "ACCCTAACCCTAACCCTAACCCTAACCATAACCCTAAGACTAACCCTAAACCTAACCCTCATAATCGAAATACAAC"; const vector expected_quals = {33, 33, 33, 33, 34, 31, 34, 30, 32, 32, 33, 34, 33, 33, 27, 21, 18, 29, 28, 33, 31, 29, 10, 33, 24, 12, 24, 10, 8, 17, 33, 23, 11, 10, 31, 18, 17, 22, 33, 20, 32, 29, 24, 15, 7, 7, 29, 12, 10, 6, 6, 18, 30, 7, 14, 6, 6, 6, 32, 8, 7, 6, 6, 16, 24, 7, 6, 22, 13, 11, 9, 9, 4, 8, 18, 25}; @@ -425,6 +425,6 @@ BOOST_AUTO_TEST_CASE( sam_off_by_one_uber_test ) { const auto header = SingleSamReader{"testdata/test_simple.bam"}.header(); auto builder = SamBuilder{header}; const auto record = builder.set_name("TEST").set_bases("A").set_cigar("1M").set_base_quals({20}).set_alignment_start(1).build(); - BOOST_CHECK_EQUAL(record.alignment_start(), 1); - BOOST_CHECK_EQUAL(record.alignment_stop(), 1); + BOOST_CHECK_EQUAL(record.alignment_start(), 1u); + BOOST_CHECK_EQUAL(record.alignment_stop(), 1u); } diff --git a/test/select_if_test.cpp b/test/select_if_test.cpp index 49b9bfb0b..93ea54573 100644 --- a/test/select_if_test.cpp +++ b/test/select_if_test.cpp @@ -33,8 +33,8 @@ BOOST_AUTO_TEST_CASE( select_if_individual_fields ) { const auto hom_ref = [](const IndividualFieldValue& x) { return x[0] == 0; }; const auto comput_gq_select = Variant::select_if(g_quals.begin(), g_quals.end(), high_gq); const auto comput_pl_select = Variant::select_if(p_likes.begin(), p_likes.end(), hom_ref); - BOOST_CHECK_EQUAL(comput_gq_select.size(), 3); - BOOST_CHECK_EQUAL(comput_pl_select.size(), 3); + BOOST_CHECK_EQUAL(comput_gq_select.size(), 3u); + BOOST_CHECK_EQUAL(comput_pl_select.size(), 3u); const auto actual_gq_select = actual_gq_selects[record_idx]; const auto actual_pl_select = actual_pl_selects[record_idx]; BOOST_CHECK(comput_pl_select == actual_pl_select); @@ -45,8 +45,8 @@ BOOST_AUTO_TEST_CASE( select_if_individual_fields ) { } BOOST_AUTO_TEST_CASE( select_if_shared_field ) { - const auto truth_an_counts = std::vector{1,1,1,1,1}; - const auto truth_af_counts = std::vector{0,0,0,0,1}; + const auto truth_an_counts = std::vector{1,1,1,1,1}; + const auto truth_af_counts = std::vector{0,0,0,0,1}; auto truth_index = 0u; for (const auto& record : SingleVariantReader{"testdata/test_variants.vcf"}) { const auto an = record.integer_shared_field("AN"); diff --git a/test/variant_header_test.cpp b/test/variant_header_test.cpp index 356035d27..9f9239a25 100644 --- a/test/variant_header_test.cpp +++ b/test/variant_header_test.cpp @@ -18,9 +18,9 @@ const auto samples = vector{"S1", "S292", "S30034"}; const auto chromosomes = vector{"chr1", "chr2", "chr3", "chr4"}; const auto filters = vector{"LOW_QUAL", "PASS", "VQSR_FAILED"}; const auto shareds = vector{"DP", "MQ", "RankSum"}; -const auto shareds_indices = vector{3,4,5}; // looks arbitrary but these are the indices of the shared fields because the filters get 0, 1 and 2. +const auto shareds_indices = vector{3,4,5}; // looks arbitrary but these are the indices of the shared fields because the filters get 0, 1 and 2. const auto individuals = vector{"GQ", "PL", "DP"}; -const auto individuals_indices = vector{6,7,3}; // the last index gets the same number as the info index. Weird, but that's how htslib deals with this. +const auto individuals_indices = vector{6,7,3}; // the last index gets the same number as the info index. Weird, but that's how htslib deals with this. void variant_header_builder_checks(const VariantHeader& vh) { check_fields(vh.chromosomes(), chromosomes); diff --git a/test/variant_reader_test.cpp b/test/variant_reader_test.cpp index 99332fb1f..9954b7c1c 100644 --- a/test/variant_reader_test.cpp +++ b/test/variant_reader_test.cpp @@ -32,9 +32,9 @@ const auto truth_shared_af = vector>{{0.5}, {0.5}, {0.5}, const auto truth_shared_an = vector>{{6}, {6}, {6}, {6}, {6}}; const auto truth_shared_desc = vector>{{"Test1,Test2"}, {}, {}, {}, {}}; const auto truth_shared_validated = vector{true, false, true, false, false}; -const auto truth_gq = vector>{{25,12,650}, {35,35,35}, {35,35,35}, {35,35,35}, {35,35,35}}; +const auto truth_gq = vector>{{25,12,650}, {35,35,35}, {35,35,35}, {35,35,35}, {35,35,35}}; const auto truth_af = vector { 3.1,2.2 }; -const auto truth_pl = vector>>{ +const auto truth_pl = vector>>{ {{10,0,100 }, {0,10,1000 }, {10,100,0} }, {{10,0,100 }, {0,10,100 }, {10,100,0} }, {{10,0,100 }, {0,10,2000000000}, {10,100,0} }, @@ -66,7 +66,7 @@ void check_variant_basic_api(const Variant& record, const uint32_t truth_index) BOOST_CHECK_EQUAL(record.alignment_start(), truth_alignment_starts[truth_index]); BOOST_CHECK_EQUAL(record.alignment_stop(), truth_alignment_stops[truth_index]); BOOST_CHECK_EQUAL(record.n_alleles(), truth_n_alleles[truth_index]); - BOOST_CHECK_EQUAL(record.n_samples(), 3); + BOOST_CHECK_EQUAL(record.n_samples(), 3u); BOOST_CHECK_EQUAL(record.id(), truth_id[truth_index]); } @@ -356,7 +356,7 @@ void check_genotype_api(const Variant& record, const uint32_t truth_index) { BOOST_CHECK(gt_for_all_samples[0].het()); BOOST_CHECK(gt_for_all_samples[2].hom_var()); for (const auto& gt_for_single_sample: gt_for_all_samples) { - BOOST_CHECK_EQUAL(gt_for_single_sample.size(), 2); + BOOST_CHECK_EQUAL(gt_for_single_sample.size(), 2u); const auto alleles = gt_for_single_sample.allele_strings(); const auto allele_keys = gt_for_single_sample.allele_keys(); BOOST_CHECK_EQUAL(gt_for_single_sample.allele_string(0), alleles[0]); @@ -366,7 +366,7 @@ void check_genotype_api(const Variant& record, const uint32_t truth_index) { BOOST_CHECK_EQUAL(gt_for_single_sample[0], allele_keys[0]); BOOST_CHECK_EQUAL(gt_for_single_sample[1], allele_keys[1]); BOOST_CHECK(!missing(gt_for_single_sample)); - BOOST_CHECK_EQUAL(gt_for_single_sample.size(), 2); + BOOST_CHECK_EQUAL(gt_for_single_sample.size(), 2u); if (gt_for_single_sample.het()) { BOOST_CHECK(!gt_for_single_sample.hom_ref()); BOOST_CHECK(!gt_for_single_sample.hom_var()); @@ -379,7 +379,7 @@ void check_genotype_api(const Variant& record, const uint32_t truth_index) { BOOST_CHECK_EQUAL(allele_keys[1], 1); BOOST_CHECK_EQUAL(alleles[0], truth_ref[truth_index]); BOOST_CHECK_EQUAL(alleles[1], truth_alt[truth_index][0]); - BOOST_CHECK_EQUAL(gt_for_single_sample.fast_diploid_key_generation(), 0x00000001); + BOOST_CHECK_EQUAL(gt_for_single_sample.fast_diploid_key_generation(), 0x00000001u); } else { BOOST_CHECK(gt_for_single_sample.non_ref_het()); BOOST_CHECK_EQUAL(allele_keys[0], 1); @@ -387,7 +387,7 @@ void check_genotype_api(const Variant& record, const uint32_t truth_index) { BOOST_CHECK_NE(alleles[0], alleles[1]); BOOST_CHECK_EQUAL(alleles[0], truth_alt[truth_index][0]); BOOST_CHECK_EQUAL(alleles[1], truth_alt[truth_index][1]); - BOOST_CHECK_EQUAL(gt_for_single_sample.fast_diploid_key_generation(), 0x00010002); + BOOST_CHECK_EQUAL(gt_for_single_sample.fast_diploid_key_generation(), 0x00010002u); } } if (gt_for_single_sample.hom_ref()) { @@ -400,7 +400,7 @@ void check_genotype_api(const Variant& record, const uint32_t truth_index) { BOOST_CHECK_EQUAL(allele_keys[1], 0); BOOST_CHECK_EQUAL(alleles[0], truth_ref[truth_index]); BOOST_CHECK_EQUAL(alleles[1], truth_ref[truth_index]); - BOOST_CHECK_EQUAL(gt_for_single_sample.fast_diploid_key_generation(), 0x00000000); + BOOST_CHECK_EQUAL(gt_for_single_sample.fast_diploid_key_generation(), 0x00000000u); } if (gt_for_single_sample.hom_var()) { BOOST_CHECK(!gt_for_single_sample.het()); @@ -412,7 +412,7 @@ void check_genotype_api(const Variant& record, const uint32_t truth_index) { BOOST_CHECK_EQUAL(allele_keys[1], 1); BOOST_CHECK_EQUAL(alleles[0], truth_alt[truth_index][0]); BOOST_CHECK_EQUAL(alleles[1], truth_alt[truth_index][0]); - BOOST_CHECK_EQUAL(gt_for_single_sample.fast_diploid_key_generation(), 0x00010001); + BOOST_CHECK_EQUAL(gt_for_single_sample.fast_diploid_key_generation(), 0x00010001u); } if (truth_index == 0) { BOOST_CHECK(gt_for_all_samples[0] == gt_for_all_samples[0]); @@ -473,7 +473,7 @@ BOOST_AUTO_TEST_CASE( missing_id_field ) void single_variant_reader_sample_test(const string filename, const vector samples, const bool include, const int desired_samples) { for (const auto& record : SingleVariantReader{filename, samples, include}) - BOOST_CHECK_EQUAL(record.n_samples(), desired_samples); + BOOST_CHECK_EQUAL(record.n_samples(), static_cast(desired_samples)); } BOOST_AUTO_TEST_CASE( single_variant_reader_sites_only ) @@ -504,11 +504,11 @@ BOOST_AUTO_TEST_CASE( single_variant_reader_missing_data ) single_variant_reader_sample_test("testdata/test_variants_missing_data.vcf", vector{"0007B", "0008A", "0009A", "0009B"}, false, 7); // exclude 4 samples for (const auto& record : SingleVariantReader{"testdata/test_variants_missing_data.vcf"}){ // include all 11 samples - BOOST_CHECK_EQUAL(record.n_samples(), 11); + BOOST_CHECK_EQUAL(record.n_samples(), 11u); const auto gt_for_all_samples = record.genotypes(); for (const auto& gt_for_single_sample: gt_for_all_samples) { BOOST_CHECK(missing(gt_for_single_sample)); - BOOST_CHECK_EQUAL(gt_for_single_sample.size(), 2); + BOOST_CHECK_EQUAL(gt_for_single_sample.size(), 2u); BOOST_CHECK(missing(gt_for_single_sample.allele_string(0))); BOOST_CHECK(missing(gt_for_single_sample.allele_string(1))); BOOST_CHECK(missing(gt_for_single_sample.allele_key(0))); @@ -522,13 +522,13 @@ BOOST_AUTO_TEST_CASE( single_variant_reader_missing_data ) BOOST_AUTO_TEST_CASE( single_variant_reader_vector ) { for (const auto& record : SingleVariantReader{vector{"testdata/test_variants.vcf"}}) - BOOST_CHECK_EQUAL(record.n_samples(), 3); + BOOST_CHECK_EQUAL(record.n_samples(), 3u); } BOOST_AUTO_TEST_CASE( single_variant_reader_vector_all_samples ) { for (const auto& record : SingleVariantReader{vector{"testdata/test_variants.vcf"}, vector{}, false}) // include all samples by setting include == false and passing an empty list - BOOST_CHECK_EQUAL(record.n_samples(), 3); + BOOST_CHECK_EQUAL(record.n_samples(), 3u); } BOOST_AUTO_TEST_CASE( single_variant_reader_vector_too_large ) @@ -604,7 +604,7 @@ BOOST_AUTO_TEST_CASE( multiple_variant_reader_difference_test ) { BOOST_CHECK_EQUAL(record.alignment_start(), multi_diff_truth_alignment_starts[truth_index]); BOOST_CHECK_EQUAL(record.ref(), multi_diff_truth_ref[truth_index]); BOOST_CHECK_EQUAL(record.n_alleles(), multi_diff_truth_n_alleles[truth_index]); - BOOST_CHECK_EQUAL(record.n_samples(), 3); + BOOST_CHECK_EQUAL(record.n_samples(), 3u); BOOST_CHECK_EQUAL(record.id(), multi_diff_truth_id[truth_index]); } ++truth_index; @@ -617,7 +617,7 @@ void multiple_variant_reader_sample_test(const vector samples, const boo for (const auto& vec : MultipleVariantReader{filenames, false, samples, include}) for (const auto& record : vec) - BOOST_CHECK_EQUAL(record.n_samples(), desired_samples); + BOOST_CHECK_EQUAL(record.n_samples(), static_cast(desired_samples)); } /* TODO: Issue #209 @@ -691,7 +691,7 @@ BOOST_AUTO_TEST_CASE( gvcf_test ) { BOOST_CHECK_EQUAL(record.alignment_start(), gvcf_truth_alignment_starts[truth_index]); BOOST_CHECK_EQUAL(record.alignment_stop(), gvcf_truth_alignment_stops[truth_index]); BOOST_CHECK_EQUAL(record.n_alleles(), gvcf_truth_n_alleles[truth_index]); - BOOST_CHECK_EQUAL(record.n_samples(), 3); + BOOST_CHECK_EQUAL(record.n_samples(), 3u); BOOST_CHECK_EQUAL(record.id(), gvcf_truth_id[truth_index]); ++truth_index; } @@ -707,7 +707,7 @@ BOOST_AUTO_TEST_CASE( gvcf_test_multiple ) { BOOST_CHECK_EQUAL(record.alignment_start(), gvcf_truth_alignment_starts[truth_index]); BOOST_CHECK_EQUAL(record.alignment_stop(), gvcf_truth_alignment_stops[truth_index]); BOOST_CHECK_EQUAL(record.n_alleles(), gvcf_truth_n_alleles[truth_index]); - BOOST_CHECK_EQUAL(record.n_samples(), 3); + BOOST_CHECK_EQUAL(record.n_samples(), 3u); BOOST_CHECK_EQUAL(record.id(), gvcf_truth_id[truth_index]); } ++truth_index; @@ -757,11 +757,11 @@ BOOST_AUTO_TEST_CASE( indexed_variant_reader_partial_test ) { const auto reader1 = IndexedVariantReader{filename, indexed_variant_chrom_partial}; for (const auto& record : reader1) { BOOST_CHECK_EQUAL(record.ref(), "T"); - BOOST_CHECK_EQUAL(record.chromosome(), 0); - BOOST_CHECK_EQUAL(record.alignment_start(), 10000000); - BOOST_CHECK_EQUAL(record.alignment_stop(), 10000000); - BOOST_CHECK_EQUAL(record.n_alleles(), 2); - BOOST_CHECK_EQUAL(record.n_samples(), 3); + BOOST_CHECK_EQUAL(record.chromosome(), 0u); + BOOST_CHECK_EQUAL(record.alignment_start(), 10000000u); + BOOST_CHECK_EQUAL(record.alignment_stop(), 10000000u); + BOOST_CHECK_EQUAL(record.n_alleles(), 2u); + BOOST_CHECK_EQUAL(record.n_samples(), 3u); BOOST_CHECK_EQUAL(record.id(), "db2342"); ++truth_index; } @@ -771,11 +771,11 @@ BOOST_AUTO_TEST_CASE( indexed_variant_reader_partial_test ) { const auto reader2 = IndexedVariantReader{filename, indexed_variant_bp_partial}; for (const auto& record : reader2) { BOOST_CHECK_EQUAL(record.ref(), "GG"); - BOOST_CHECK_EQUAL(record.chromosome(), 1); - BOOST_CHECK_EQUAL(record.alignment_start(), 10001000); - BOOST_CHECK_EQUAL(record.alignment_stop(), 10001001); - BOOST_CHECK_EQUAL(record.n_alleles(), 2); - BOOST_CHECK_EQUAL(record.n_samples(), 3); + BOOST_CHECK_EQUAL(record.chromosome(), 1u); + BOOST_CHECK_EQUAL(record.alignment_start(), 10001000u); + BOOST_CHECK_EQUAL(record.alignment_stop(), 10001001u); + BOOST_CHECK_EQUAL(record.n_alleles(), 2u); + BOOST_CHECK_EQUAL(record.n_samples(), 3u); BOOST_CHECK_EQUAL(record.id(), "rs837472"); ++truth_index; } @@ -845,11 +845,11 @@ BOOST_AUTO_TEST_CASE( synced_variant_reader_partial_test ) { for (const auto& vec : reader1) { for (const auto& record : vec) { BOOST_CHECK_EQUAL(record.ref(), "T"); - BOOST_CHECK_EQUAL(record.chromosome(), 0); - BOOST_CHECK_EQUAL(record.alignment_start(), 10000000); - BOOST_CHECK_EQUAL(record.alignment_stop(), 10000000); - BOOST_CHECK_EQUAL(record.n_alleles(), 2); - BOOST_CHECK_EQUAL(record.n_samples(), 3); + BOOST_CHECK_EQUAL(record.chromosome(), 0u); + BOOST_CHECK_EQUAL(record.alignment_start(), 10000000u); + BOOST_CHECK_EQUAL(record.alignment_stop(), 10000000u); + BOOST_CHECK_EQUAL(record.n_alleles(), 2u); + BOOST_CHECK_EQUAL(record.n_samples(), 3u); BOOST_CHECK_EQUAL(record.id(), "db2342"); } ++truth_index; @@ -864,11 +864,11 @@ BOOST_AUTO_TEST_CASE( synced_variant_reader_partial_test ) { for (const auto& vec : reader2) { for (const auto& record : vec) { BOOST_CHECK_EQUAL(record.ref(), "GG"); - BOOST_CHECK_EQUAL(record.chromosome(), 1); - BOOST_CHECK_EQUAL(record.alignment_start(), 10001000); - BOOST_CHECK_EQUAL(record.alignment_stop(), 10001001); - BOOST_CHECK_EQUAL(record.n_alleles(), 2); - BOOST_CHECK_EQUAL(record.n_samples(), 3); + BOOST_CHECK_EQUAL(record.chromosome(), 1u); + BOOST_CHECK_EQUAL(record.alignment_start(), 10001000u); + BOOST_CHECK_EQUAL(record.alignment_stop(), 10001001u); + BOOST_CHECK_EQUAL(record.n_alleles(), 2u); + BOOST_CHECK_EQUAL(record.n_samples(), 3u); BOOST_CHECK_EQUAL(record.id(), "rs837472"); } ++truth_index;