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Fixed signed-unsigned comparison errors in tests
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@kgururaj
kgururaj committed Sep 20, 2014
1 parent 372cab8 commit 0eb3445
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Showing 8 changed files with 68 additions and 68 deletions.
12 changes: 6 additions & 6 deletions test/indexed_sam_reader_test.cpp
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Expand Up @@ -16,18 +16,18 @@ 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);

const auto interval_read_counts = vector<int>{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<string>{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]);
Expand All @@ -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);
Expand All @@ -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);
Expand All @@ -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);
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18 changes: 9 additions & 9 deletions test/sam_builder_test.cpp
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Expand Up @@ -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 ) {
Expand Down Expand Up @@ -365,19 +365,19 @@ 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();

BOOST_CHECK_EQUAL(second_read.name(), "foo");
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();
Expand Down
8 changes: 4 additions & 4 deletions test/sam_header_test.cpp
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Expand Up @@ -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! */
Expand Down
2 changes: 1 addition & 1 deletion test/sam_reader_test.cpp
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Expand Up @@ -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);
Expand Down
8 changes: 4 additions & 4 deletions test/sam_test.cpp
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Expand Up @@ -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<uint8_t> 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};
Expand Down Expand Up @@ -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);
}
8 changes: 4 additions & 4 deletions test/select_if_test.cpp
View file
Expand Up @@ -33,8 +33,8 @@ BOOST_AUTO_TEST_CASE( select_if_individual_fields ) {
const auto hom_ref = [](const IndividualFieldValue<int32_t>& 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);
Expand All @@ -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<int>{1,1,1,1,1};
const auto truth_af_counts = std::vector<int>{0,0,0,0,1};
const auto truth_an_counts = std::vector<uint32_t>{1,1,1,1,1};
const auto truth_af_counts = std::vector<uint32_t>{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");
Expand Down
4 changes: 2 additions & 2 deletions test/variant_header_test.cpp
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Expand Up @@ -18,9 +18,9 @@ const auto samples = vector<string>{"S1", "S292", "S30034"};
const auto chromosomes = vector<string>{"chr1", "chr2", "chr3", "chr4"};
const auto filters = vector<string>{"LOW_QUAL", "PASS", "VQSR_FAILED"};
const auto shareds = vector<string>{"DP", "MQ", "RankSum"};
const auto shareds_indices = vector<uint32_t>{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<int32_t>{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<string>{"GQ", "PL", "DP"};
const auto individuals_indices = vector<uint32_t>{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<int32_t>{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);
Expand Down

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