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Fix for signed/unsigned comparisons (by Karthik)
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@jmthibault79
jmthibault79 committed Nov 17, 2014
1 parent da97926 commit 6526c90
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Showing 2 changed files with 47 additions and 47 deletions.
36 changes: 18 additions & 18 deletions test/short_value_optimized_storage_test.cpp
View file
Expand Up @@ -10,8 +10,8 @@ void test_short_value_storage( const uint32_t capacity, const uint32_t short_val
auto storage = ShortValueOptimizedStorage<int32_t>{capacity, short_value_upper_bound};

BOOST_CHECK_EQUAL(storage.capacity(), capacity);
BOOST_CHECK_EQUAL(storage.num_values(), 0);
BOOST_CHECK_EQUAL(storage.max_value_length(), 0);
BOOST_CHECK_EQUAL(storage.num_values(), 0u);
BOOST_CHECK_EQUAL(storage.max_value_length(), 0u);

auto max_length = 0u;
for ( auto i = 0u; i < storage.capacity(); ++i ) {
Expand Down Expand Up @@ -40,8 +40,8 @@ void test_short_value_storage( const uint32_t capacity, const uint32_t short_val

storage.clear();
BOOST_CHECK_EQUAL(storage.capacity(), capacity);
BOOST_CHECK_EQUAL(storage.num_values(), 0);
BOOST_CHECK_EQUAL(storage.max_value_length(), 0);
BOOST_CHECK_EQUAL(storage.num_values(), 0u);
BOOST_CHECK_EQUAL(storage.max_value_length(), 0u);
}

BOOST_AUTO_TEST_CASE( test_all_short_values ) {
Expand Down Expand Up @@ -72,18 +72,18 @@ BOOST_AUTO_TEST_CASE( test_set_by_vector ) {
auto storage = ShortValueOptimizedStorage<int32_t>{5, 3}; // capacity of 5 arrays, short value defined as <= length 3
auto mixed_values = vector<vector<int32_t>>{ {1, 2}, {3, 4, 5, 6, 7}, {8}, {9, 10}, {11, 12, 13, 14, 15, 16} };

BOOST_CHECK_EQUAL(storage.capacity(), 5);
BOOST_CHECK_EQUAL(storage.num_values(), 0);
BOOST_CHECK_EQUAL(storage.max_value_length(), 0);
BOOST_CHECK_EQUAL(storage.capacity(), 5u);
BOOST_CHECK_EQUAL(storage.num_values(), 0u);
BOOST_CHECK_EQUAL(storage.max_value_length(), 0u);

for ( auto i = 0u; i < storage.capacity(); ++i ) {
BOOST_CHECK(! storage.is_set(i));
storage.set(i, mixed_values[i]); // set by vector instead of by pointer
BOOST_CHECK(storage.is_set(i));
BOOST_CHECK_EQUAL(storage.capacity(), 5); // make sure capacity stays constant as we insert items
BOOST_CHECK_EQUAL(storage.capacity(), 5u); // make sure capacity stays constant as we insert items
BOOST_CHECK_EQUAL(storage.num_values(), i + 1);
BOOST_CHECK_EQUAL(storage.value_length(i), mixed_values[i].size());
BOOST_CHECK_EQUAL(storage.max_value_length(), i < 1 ? 2 : (i < 4 ? 5 : 6));
BOOST_CHECK_EQUAL(storage.max_value_length(), i < 1 ? 2u : (i < 4 ? 5u : 6u));
}

for ( auto i = 0u; i < storage.capacity(); ++i ) {
Expand All @@ -96,18 +96,18 @@ BOOST_AUTO_TEST_CASE( test_set_by_vector ) {
}

storage.clear();
BOOST_CHECK_EQUAL(storage.capacity(), 5);
BOOST_CHECK_EQUAL(storage.num_values(), 0);
BOOST_CHECK_EQUAL(storage.max_value_length(), 0);
BOOST_CHECK_EQUAL(storage.capacity(), 5u);
BOOST_CHECK_EQUAL(storage.num_values(), 0u);
BOOST_CHECK_EQUAL(storage.max_value_length(), 0u);
}

BOOST_AUTO_TEST_CASE( test_set_empty_values ) {
auto storage = ShortValueOptimizedStorage<int32_t>{4, 5}; // capacity of 4 arrays, short value defined as <= length 5
auto values = vector<vector<int32_t>>{ {1}, {} };

BOOST_CHECK_EQUAL(storage.capacity(), 4);
BOOST_CHECK_EQUAL(storage.num_values(), 0);
BOOST_CHECK_EQUAL(storage.max_value_length(), 0);
BOOST_CHECK_EQUAL(storage.capacity(), 4u);
BOOST_CHECK_EQUAL(storage.num_values(), 0u);
BOOST_CHECK_EQUAL(storage.max_value_length(), 0u);

// Attempting to set empty values should have no effect on the state of the storage
storage.set(0, nullptr, 1); // null pointer
Expand All @@ -117,13 +117,13 @@ BOOST_AUTO_TEST_CASE( test_set_empty_values ) {
storage.set(2, values[1]); // empty vector
BOOST_CHECK(! storage.is_set(2));

BOOST_CHECK_EQUAL(storage.num_values(), 0); // num values should be unchanged
BOOST_CHECK_EQUAL(storage.max_value_length(), 0);
BOOST_CHECK_EQUAL(storage.num_values(), 0u); // num values should be unchanged
BOOST_CHECK_EQUAL(storage.max_value_length(), 0u);

for ( auto i = 0u; i < storage.capacity(); ++i ) {
auto val = storage.get(i);
BOOST_CHECK(val.first == nullptr);
BOOST_CHECK_EQUAL(val.second, 0);
BOOST_CHECK_EQUAL(val.second, 0u);
}
}

Expand Down
58 changes: 29 additions & 29 deletions test/variant_builder_test.cpp
View file
Expand Up @@ -21,29 +21,29 @@ BOOST_AUTO_TEST_CASE( set_required_fields_only ) {

// chromosome by string, one-base ref allele
auto variant = builder.set_chromosome("20").set_alignment_start(5).set_ref_allele("A").build();
BOOST_CHECK_EQUAL(variant.chromosome(), 1);
BOOST_CHECK_EQUAL(variant.alignment_start(), 5);
BOOST_CHECK_EQUAL(variant.chromosome(), 1u);
BOOST_CHECK_EQUAL(variant.alignment_start(), 5u);
BOOST_CHECK_EQUAL(variant.ref(), "A");
BOOST_CHECK_EQUAL(variant.alignment_stop(), 5); // making sure rlen was set to length of ref allele here (1)
BOOST_CHECK_EQUAL(variant.alignment_stop(), 5u); // making sure rlen was set to length of ref allele here (1)

BOOST_CHECK(missing(variant.qual()));
BOOST_CHECK(missing(variant.id()));
BOOST_CHECK(missing(variant.alt()));
BOOST_CHECK_EQUAL(variant.filters().size(), 0);
BOOST_CHECK_EQUAL(variant.filters().size(), 0u);
BOOST_CHECK(missing(variant.genotypes()));

// chromosome by index, multi-base ref allele
builder.clear();
variant = builder.set_ref_allele("CA").set_chromosome(2).set_alignment_start(3).build();
BOOST_CHECK_EQUAL(variant.ref(), "CA");
BOOST_CHECK_EQUAL(variant.chromosome(), 2);
BOOST_CHECK_EQUAL(variant.alignment_start(), 3);
BOOST_CHECK_EQUAL(variant.alignment_stop(), 4); // making sure rlen was set to length of ref allele here (2)
BOOST_CHECK_EQUAL(variant.chromosome(), 2u);
BOOST_CHECK_EQUAL(variant.alignment_start(), 3u);
BOOST_CHECK_EQUAL(variant.alignment_stop(), 4u); // making sure rlen was set to length of ref allele here (2)

BOOST_CHECK(missing(variant.qual()));
BOOST_CHECK(missing(variant.id()));
BOOST_CHECK(missing(variant.alt()));
BOOST_CHECK_EQUAL(variant.filters().size(), 0);
BOOST_CHECK_EQUAL(variant.filters().size(), 0u);
BOOST_CHECK(missing(variant.genotypes()));

// long ref allele
Expand Down Expand Up @@ -85,19 +85,19 @@ BOOST_AUTO_TEST_CASE( set_alignment_stop ) {
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("ACG");

// when not explicitly set, alignment stop should be based on ref allele length
BOOST_CHECK_EQUAL(builder.build().alignment_stop(), 7);
BOOST_CHECK_EQUAL(builder.build().alignment_stop(), 7u);

// alignment stop == alignment start
auto variant = builder.set_alignment_stop(5).build();
BOOST_CHECK_EQUAL(variant.alignment_stop(), 5);
BOOST_CHECK_EQUAL(variant.alignment_stop(), 5u);

// alignment stop == alignment start + 1
variant = builder.set_alignment_stop(6).build();
BOOST_CHECK_EQUAL(variant.alignment_stop(), 6);
BOOST_CHECK_EQUAL(variant.alignment_stop(), 6u);

// alignment stop > alignment start by more than 1
variant = builder.set_alignment_stop(10).build();
BOOST_CHECK_EQUAL(variant.alignment_stop(), 10);
BOOST_CHECK_EQUAL(variant.alignment_stop(), 10u);

// alignment stop < alignment start is an error
BOOST_CHECK_THROW(builder.set_alignment_stop(4).build(), logic_error);
Expand Down Expand Up @@ -138,9 +138,9 @@ BOOST_AUTO_TEST_CASE( remove_core_fields ) {

// Clearing alignment stop via remove_alignment_stop() after setting it
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("AC").set_alignment_stop(10);
BOOST_CHECK_EQUAL(builder.build().alignment_stop(), 10);
BOOST_CHECK_EQUAL(builder.build().alignment_stop(), 10u);
builder.remove_alignment_stop();
BOOST_CHECK_EQUAL(builder.build().alignment_stop(), 6); // once cleared, should be based on ref allele length
BOOST_CHECK_EQUAL(builder.build().alignment_stop(), 6u); // once cleared, should be based on ref allele length

// Clearing qual via remove_qual() after setting it to non-missing
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A").set_qual(1.5);
Expand Down Expand Up @@ -202,34 +202,34 @@ BOOST_AUTO_TEST_CASE( set_alt_alleles ) {
// One alt allele, using the string setter
auto variant = builder.set_alt_allele("C").build();
auto alts = variant.alt();
BOOST_CHECK_EQUAL(alts.size(), 1);
BOOST_CHECK_EQUAL(alts.size(), 1u);
BOOST_CHECK_EQUAL(alts[0], "C");

// One alt allele, using the vector setter
variant = builder.set_alt_alleles({"C"}).build();
alts = variant.alt();
BOOST_CHECK_EQUAL(alts.size(), 1);
BOOST_CHECK_EQUAL(alts.size(), 1u);
BOOST_CHECK_EQUAL(alts[0], "C");

// Two alt alleles
variant = builder.set_alt_alleles({"C", "ATG"}).build();
alts = variant.alt();
BOOST_CHECK_EQUAL(alts.size(), 2);
BOOST_CHECK_EQUAL(alts.size(), 2u);
BOOST_CHECK_EQUAL(alts[0], "C");
BOOST_CHECK_EQUAL(alts[1], "ATG");

// Three alt alleles
variant = builder.set_alt_alleles({"C", "ATG", "T"}).build();
alts = variant.alt();
BOOST_CHECK_EQUAL(alts.size(), 3);
BOOST_CHECK_EQUAL(alts.size(), 3u);
BOOST_CHECK_EQUAL(alts[0], "C");
BOOST_CHECK_EQUAL(alts[1], "ATG");
BOOST_CHECK_EQUAL(alts[2], "T");

// Long alt alleles
variant = builder.set_alt_alleles({"CTGACTGACTGACTGACTGACTGACTGACTGATCGATCGATCGATCGCTAGCTAGCTCGATC", "TGCATGCTAGCTGATCGATCGGGGGATTCGAGGGCTTTAGGGCTA"}).build();
alts = variant.alt();
BOOST_CHECK_EQUAL(alts.size(), 2);
BOOST_CHECK_EQUAL(alts.size(), 2u);
BOOST_CHECK_EQUAL(alts[0], "CTGACTGACTGACTGACTGACTGACTGACTGATCGATCGATCGATCGCTAGCTAGCTCGATC");
BOOST_CHECK_EQUAL(alts[1], "TGCATGCTAGCTGATCGATCGGGGGATTCGAGGGCTTTAGGGCTA");

Expand Down Expand Up @@ -263,23 +263,23 @@ BOOST_AUTO_TEST_CASE( set_filters ) {

// Set one filter by name
auto filters = builder.set_filters(vector<string>{"PASS"}).build().filters();
BOOST_CHECK_EQUAL(filters.size(), 1);
BOOST_CHECK_EQUAL(filters.size(), 1u);
BOOST_CHECK_EQUAL(filters[0], "PASS");

// Set one filter by index
filters = builder.set_filters(vector<int32_t>{0}).build().filters();
BOOST_CHECK_EQUAL(filters.size(), 1);
BOOST_CHECK_EQUAL(filters.size(), 1u);
BOOST_CHECK_EQUAL(filters[0], "PASS");

// Set multiple filters by name
filters = builder.set_filters(vector<string>{"LOW_QUAL", "MISSED"}).build().filters();
BOOST_CHECK_EQUAL(filters.size(), 2);
BOOST_CHECK_EQUAL(filters.size(), 2u);
BOOST_CHECK_EQUAL(filters[0], "LOW_QUAL");
BOOST_CHECK_EQUAL(filters[1], "MISSED");

// Set multiple filters by index
filters = builder.set_filters(vector<int32_t>{header.field_index("LOW_QUAL"), header.field_index("MISSED")}).build().filters();
BOOST_CHECK_EQUAL(filters.size(), 2);
BOOST_CHECK_EQUAL(filters.size(), 2u);
BOOST_CHECK_EQUAL(filters[0], "LOW_QUAL");
BOOST_CHECK_EQUAL(filters[1], "MISSED");

Expand Down Expand Up @@ -493,28 +493,28 @@ BOOST_AUTO_TEST_CASE( set_string_shared_fields ) {
// Normal string value by field name
auto variant = builder.set_string_shared_field("DESC", "helloworld").build();
auto field = variant.string_shared_field("DESC");
BOOST_CHECK_EQUAL(field.size(), 1);
BOOST_CHECK_EQUAL(field.size(), 1u);
BOOST_CHECK_EQUAL(field[0], "helloworld");

// Normal string value by field index
variant = builder.set_string_shared_field(header.field_index("DESC"), "helloworld").build();
field = variant.string_shared_field("DESC");
BOOST_CHECK_EQUAL(field.size(), 1);
BOOST_CHECK_EQUAL(field.size(), 1u);
BOOST_CHECK_EQUAL(field[0], "helloworld");

// Long string value
variant = builder.set_string_shared_field("DESC", "very long string that definitely absolutely positively will require tons and tons of memory").build();
field = variant.string_shared_field("DESC");
BOOST_CHECK_EQUAL(field.size(), 1);
BOOST_CHECK_EQUAL(field.size(), 1u);
BOOST_CHECK_EQUAL(field[0], "very long string that definitely absolutely positively will require tons and tons of memory");

// Multiple string fields
variant = builder.set_string_shared_field("DESC", "helloworld").set_string_shared_field("ZS", "bjarne").build();
auto desc_field = variant.string_shared_field("DESC");
auto zs_field = variant.string_shared_field("ZS");
BOOST_CHECK_EQUAL(desc_field.size(), 1);
BOOST_CHECK_EQUAL(desc_field.size(), 1u);
BOOST_CHECK_EQUAL(desc_field[0], "helloworld");
BOOST_CHECK_EQUAL(zs_field.size(), 1);
BOOST_CHECK_EQUAL(zs_field.size(), 1u);
BOOST_CHECK_EQUAL(zs_field[0], "bjarne");

// Set string field to a missing value without having previously set it
Expand Down Expand Up @@ -1217,7 +1217,7 @@ BOOST_AUTO_TEST_CASE( bulk_set_individual_fields_wrong_number_of_values ) {
auto builder = VariantBuilder{header};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");

BOOST_CHECK_EQUAL(header.n_samples(), 3); // Make sure samples haven't been added to the test file,
BOOST_CHECK_EQUAL(header.n_samples(), 3u); // Make sure samples haven't been added to the test file,
// as the tests below will be invalidated if they have

// int field: less than num_samples values in flat vector
Expand Down

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