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variant_builder_test.cpp
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#include "variant/variant_builder.h"
#include "variant/variant_reader.h"
#include "missing.h"
#include "variant/genotype.h"
#include "htslib/vcf.h"
#include <boost/test/unit_test.hpp>
#include <stdexcept>
#include <algorithm>
using namespace std;
using namespace gamgee;
/******************************************************
* Core field tests (chromosome, alignment start, etc.)
******************************************************/
BOOST_AUTO_TEST_CASE( set_required_fields_only ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
// 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(), 1u);
BOOST_CHECK_EQUAL(variant.alignment_start(), 5u);
BOOST_CHECK_EQUAL(variant.ref(), "A");
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(), 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(), 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(), 0u);
BOOST_CHECK(missing(variant.genotypes()));
// long ref allele
variant = builder.clear().set_chromosome(2).set_alignment_start(3).set_ref_allele("ABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZ").build();
BOOST_CHECK_EQUAL(variant.ref(), "ABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZ");
}
BOOST_AUTO_TEST_CASE( fail_to_set_required_fields ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
// Failing to set one or more of chromosome, alignment start, or the ref allele is an error
BOOST_CHECK_THROW(builder.build(), logic_error);
builder.clear();
BOOST_CHECK_THROW(builder.set_chromosome(0).build(), logic_error);
builder.clear();
BOOST_CHECK_THROW(builder.set_alignment_start(1).build(), logic_error);
builder.clear();
BOOST_CHECK_THROW(builder.set_ref_allele("A").build(), logic_error);
builder.clear();
BOOST_CHECK_THROW(builder.set_chromosome(0).set_alignment_start(1).build(), logic_error);
builder.clear();
BOOST_CHECK_THROW(builder.set_chromosome(0).set_ref_allele("A").build(), logic_error);
builder.clear();
BOOST_CHECK_THROW(builder.set_alignment_start(1).set_ref_allele("A").build(), logic_error);
// Setting ref to a missing value should trigger an exception
// (note that chromosome and alignment start can't be set to missing values, since
// they take unsigned arguments)
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
BOOST_CHECK_THROW(builder.set_ref_allele(""), invalid_argument);
builder.set_ref_allele("A");
BOOST_CHECK_THROW(builder.set_ref_allele("."), invalid_argument);
}
BOOST_AUTO_TEST_CASE( set_alignment_stop ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
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(), 7u);
// alignment stop == alignment start
auto variant = builder.set_alignment_stop(5).build();
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(), 6u);
// alignment stop > alignment start by more than 1
variant = builder.set_alignment_stop(10).build();
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);
BOOST_CHECK_THROW(builder.set_alignment_stop(3).build(), logic_error);
BOOST_CHECK_THROW(builder.set_alignment_stop(0).build(), logic_error);
}
BOOST_AUTO_TEST_CASE( set_qual ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
// Qual should be missing if not explicitly set
BOOST_CHECK(missing(builder.build().qual()));
// Set qual to positive value
auto variant = builder.set_qual(1.5).build();
BOOST_CHECK_EQUAL(variant.qual(), 1.5);
// Set qual to 0.0 (should NOT be missing!)
variant = builder.set_qual(0.0).build();
BOOST_CHECK_EQUAL(variant.qual(), 0.0);
BOOST_CHECK(! missing(variant.qual()));
// Set qual to negative value
variant = builder.set_qual(-1.5).build();
BOOST_CHECK_EQUAL(variant.qual(), -1.5);
// Setting qual to missing should work
auto missing_val = 0.0f; bcf_float_set_missing(missing_val);
variant = builder.set_qual(missing_val).build();
BOOST_CHECK(missing(variant.qual()));
}
BOOST_AUTO_TEST_CASE( remove_core_fields ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
// 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(), 10u);
builder.remove_alignment_stop();
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);
BOOST_CHECK_EQUAL(builder.build().qual(), 1.5);
builder.remove_qual();
BOOST_CHECK(missing(builder.build().qual()));
}
BOOST_AUTO_TEST_CASE( set_bad_contig ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
// Set non-existent contig by name
builder.set_alignment_start(5).set_ref_allele("A");
BOOST_CHECK_THROW(builder.set_chromosome("FOO").build(), invalid_argument);
// Set non-existent contig by index
BOOST_CHECK_THROW(builder.set_chromosome(500).build(), invalid_argument);
}
/************************************************************
* Non-info shared field tests
* (other than ref, which is a required field tested above)
************************************************************/
BOOST_AUTO_TEST_CASE( set_id ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
// ID should be missing unless explicitly set
BOOST_CHECK(missing(builder.build().id()));
// setting ID to a non-missing value
auto variant = builder.set_id("ABC").build();
BOOST_CHECK_EQUAL(variant.id(), "ABC");
// setting ID to a long value
variant = builder.set_id("ABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZ").build();
BOOST_CHECK_EQUAL(variant.id(), "ABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZ");
// Setting ID to a missing value without having previously set it to anything
// (the case where it HAS been previously set is tested below in remove_non_info_shared_field)
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_id("");
BOOST_CHECK(missing(builder.build().id()));
builder.set_id(".");
BOOST_CHECK(missing(builder.build().id()));
}
BOOST_AUTO_TEST_CASE( set_alt_alleles ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
// Alt alleles should be missing unless explicitly set
BOOST_CHECK(missing(builder.build().alt()));
// One alt allele, using the string setter
auto variant = builder.set_alt_allele("C").build();
auto alts = variant.alt();
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(), 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(), 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(), 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(), 2u);
BOOST_CHECK_EQUAL(alts[0], "CTGACTGACTGACTGACTGACTGACTGACTGATCGATCGATCGATCGCTAGCTAGCTCGATC");
BOOST_CHECK_EQUAL(alts[1], "TGCATGCTAGCTGATCGATCGGGGGATTCGAGGGCTTTAGGGCTA");
// Setting alt to a missing value without having previously set it to anything
// (the case where it HAS been previously set is tested below in remove_non_info_shared_field)
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
variant = builder.set_alt_alleles({}).build();
BOOST_CHECK(missing(variant.alt()));
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
variant = builder.set_alt_allele("").build();
BOOST_CHECK(missing(variant.alt()));
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
variant = builder.set_alt_allele(".").build();
BOOST_CHECK(missing(variant.alt()));
// Setting a mix of non-missing and missing alts is an error
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
BOOST_CHECK_THROW(builder.set_alt_alleles({"C", "", "T"}), invalid_argument);
BOOST_CHECK_THROW(builder.set_alt_alleles({"C", ".", "T"}), invalid_argument);
}
BOOST_AUTO_TEST_CASE( set_filters ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
// Filters should be missing unless explicitly set
BOOST_CHECK(missing(builder.build().filters()));
// Set one filter by name
auto filters = builder.set_filters(vector<string>{"PASS"}).build().filters();
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(), 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(), 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(), 2u);
BOOST_CHECK_EQUAL(filters[0], "LOW_QUAL");
BOOST_CHECK_EQUAL(filters[1], "MISSED");
// Set non-existent filter by name
BOOST_CHECK_THROW(builder.set_filters(vector<string>{"FOO"}).build(), invalid_argument);
// Set non-existent filter by index
BOOST_CHECK_THROW(builder.set_filters(vector<int32_t>{1000}).build(), invalid_argument);
// Set mix of valid and non-existent filters
BOOST_CHECK_THROW(builder.set_filters(vector<string>{"PASS", "FOO", "LOW_QUAL"}), invalid_argument);
BOOST_CHECK_THROW(builder.set_filters(vector<int32_t>{header.field_index("PASS"), 1000, header.field_index("LOW_QUAL")}), invalid_argument);
// Set filters to missing without having previously set it
// (the case where they HAVE been previously set is tested below in remove_non_info_shared_field)
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
BOOST_CHECK(missing(builder.set_filters(vector<int32_t>{}).build().filters()));
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
BOOST_CHECK(missing(builder.set_filters(vector<string>{}).build().filters()));
}
BOOST_AUTO_TEST_CASE( remove_non_info_shared_field ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
// Remove pre-existing ID via remove_id()
builder.set_id("ABC");
builder.remove_id();
BOOST_CHECK(missing(builder.build().id()));
// Remove pre-existing ID by setting it to missing
builder.set_id("ABC");
builder.set_id("");
BOOST_CHECK(missing(builder.build().id()));
builder.set_id("ABC");
builder.set_id(".");
BOOST_CHECK(missing(builder.build().id()));
// Remove pre-existing alts via remove_alt_alleles()
builder.set_alt_alleles({"A", "CT"});
builder.remove_alt_alleles();
BOOST_CHECK(missing(builder.build().alt()));
// Remove pre-existing alts by setting them to missing values
builder.set_alt_alleles({"A", "CT"});
builder.set_alt_alleles({});
BOOST_CHECK(missing(builder.build().alt()));
builder.set_alt_alleles({"A", "CT"});
builder.set_alt_allele("");
BOOST_CHECK(missing(builder.build().alt()));
builder.set_alt_alleles({"A", "CT"});
builder.set_alt_allele(".");
BOOST_CHECK(missing(builder.build().alt()));
// Remove pre-existing filters via remove_filters()
builder.set_filters(vector<string>{"LOW_QUAL", "MISSED"});
builder.remove_filters();
BOOST_CHECK(missing(builder.build().filters()));
// Remove pre-existing filters by setting them to missing
builder.set_filters(vector<string>{"LOW_QUAL", "MISSED"});
builder.set_filters(vector<string>{});
BOOST_CHECK(missing(builder.build().filters()));
builder.set_filters(vector<string>{"LOW_QUAL", "MISSED"});
builder.set_filters(vector<int32_t>{});
BOOST_CHECK(missing(builder.build().filters()));
}
/**********************************************
* Helper functions for info/shared field tests
**********************************************/
void check_integer_shared_field(const Variant& variant, const string& field, const vector<int32_t>& expected) {
auto shared_field = variant.integer_shared_field(field);
BOOST_CHECK_EQUAL(shared_field.size(), expected.size());
for ( auto i = 0u; i < shared_field.size(); ++i ) {
BOOST_CHECK_EQUAL(shared_field[i], expected[i]);
}
}
void check_float_shared_field(const Variant& variant, const string& field, const vector<float>& expected) {
auto shared_field = variant.float_shared_field(field);
BOOST_CHECK_EQUAL(shared_field.size(), expected.size());
for ( auto i = 0u; i < shared_field.size(); ++i ) {
if ( bcf_float_is_missing(expected[i]) ) BOOST_CHECK(bcf_float_is_missing(shared_field[i]));
else if ( bcf_float_is_vector_end(expected[i]) ) BOOST_CHECK(bcf_float_is_vector_end(shared_field[i]));
else BOOST_CHECK_EQUAL(shared_field[i], expected[i]);
}
}
/*******************************************
* Info/Shared field tests
*******************************************/
BOOST_AUTO_TEST_CASE( set_integer_shared_fields ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
auto field_values = vector<int32_t>{};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
// Run each test below using both field indices and field names
for ( bool use_field_index : { true, false } ) {
// Single value, no vector
auto variant = use_field_index ? builder.set_integer_shared_field(header.field_index("AN"), 5).build() : builder.set_integer_shared_field("AN", 5).build();
check_integer_shared_field(variant, "AN", {5});
// Single-element vector
field_values = {5};
variant = use_field_index ? builder.set_integer_shared_field(header.field_index("AN"), field_values).build() : builder.set_integer_shared_field("AN", field_values).build();
check_integer_shared_field(variant, "AN", field_values);
// Two-element vector
field_values = {5, 10};
variant = use_field_index ? builder.set_integer_shared_field(header.field_index("ZI"), field_values).build() : builder.set_integer_shared_field("ZI", field_values).build();
check_integer_shared_field(variant, "ZI", field_values);
// Four-element vector
field_values = {5, 10, 15, 20};
variant = use_field_index ? builder.set_integer_shared_field(header.field_index("ZI"), field_values).build() : builder.set_integer_shared_field("ZI", field_values).build();
check_integer_shared_field(variant, "ZI", field_values);
// Large vector
field_values = {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20};
variant = use_field_index ? builder.set_integer_shared_field(header.field_index("ZI"), field_values).build() : builder.set_integer_shared_field("ZI", field_values).build();
check_integer_shared_field(variant, "ZI", field_values);
// Multiple integer fields
auto an_field_values = vector<int32_t>{3};
auto zi_field_values = vector<int32_t>{5, 10, 15, 20};
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
variant = use_field_index ? builder.set_integer_shared_field(header.field_index("AN"), an_field_values).set_integer_shared_field(header.field_index("ZI"), zi_field_values).build() :
builder.set_integer_shared_field("AN", an_field_values).set_integer_shared_field("ZI", zi_field_values).build();
check_integer_shared_field(variant, "AN", an_field_values);
check_integer_shared_field(variant, "ZI", zi_field_values);
}
// Set integer field to a missing value without having previously set it
// (the case where you HAVE previously set it is tested in remove_info_shared_fields below)
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_integer_shared_field("ZI", vector<int32_t>{});
BOOST_CHECK(missing(builder.build().integer_shared_field("ZI")));
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_integer_shared_field("ZI", missing_values::int32);
BOOST_CHECK(missing(builder.build().integer_shared_field("ZI")));
}
BOOST_AUTO_TEST_CASE( set_float_shared_fields ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
auto float_missing = 0.0f; bcf_float_set_missing(float_missing);
auto field_values = vector<float>{};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A").set_alt_allele("G");
// Run each test below using both field indices and field names
for ( bool use_field_index : { true, false } ) {
// Single value, no vector
auto variant = use_field_index ? builder.set_float_shared_field(header.field_index("AF"), 5.5).build() : builder.set_float_shared_field("AF", 5.5).build();
check_float_shared_field(variant, "AF", vector<float>{5.5});
// Single-element vector
field_values = {5.5};
variant = use_field_index ? builder.set_float_shared_field(header.field_index("AF"), field_values).build() : builder.set_float_shared_field("AF", field_values).build();
check_float_shared_field(variant, "AF", field_values);
// Two-element vector
field_values = {5.5, 10.5};
variant = use_field_index ? builder.set_float_shared_field(header.field_index("ZF"), field_values).build() : builder.set_float_shared_field("ZF", field_values).build();
check_float_shared_field(variant, "ZF", field_values);
// Four-element vector
field_values = {5.5, 10.5, 15.5, 20.5};
variant = use_field_index ? builder.set_float_shared_field(header.field_index("ZF"), field_values).build() : builder.set_float_shared_field("ZF", field_values).build();
check_float_shared_field(variant, "ZF", field_values);
// Large vector
field_values = {1.5, 2.5, 3.5, 4.5, 5.5, 6.5, 7.5, 8.5, 9.5, 10.5, 11.5, 12.5, 13.5, 14.5, 15.5, 16.5, 17.5, 18.5, 19.5, 20.5};
variant = use_field_index ? builder.set_float_shared_field(header.field_index("ZF"), field_values).build() : builder.set_float_shared_field("ZF", field_values).build();
check_float_shared_field(variant, "ZF", field_values);
// Multiple float fields
auto af_field_values = vector<float>{3.5};
auto zf_field_values = vector<float>{5.5, 10.5, 15.5, 20.5};
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
variant = use_field_index ? builder.set_float_shared_field(header.field_index("AF"), af_field_values).set_float_shared_field(header.field_index("ZF"), zf_field_values).build() :
builder.set_float_shared_field("AF", af_field_values).set_float_shared_field("ZF", zf_field_values).build();
check_float_shared_field(variant, "AF", af_field_values);
check_float_shared_field(variant, "ZF", zf_field_values);
}
// Set float field to a missing value without having previously set it
// (the case where you HAVE previously set it is tested in remove_info_shared_fields below)
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_float_shared_field("ZF", vector<float>{});
BOOST_CHECK(missing(builder.build().float_shared_field("ZF")));
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_float_shared_field("ZF", float_missing);
BOOST_CHECK(missing(builder.build().float_shared_field("ZF")));
}
BOOST_AUTO_TEST_CASE( set_string_shared_fields ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
// 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(), 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(), 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(), 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(), 1u);
BOOST_CHECK_EQUAL(desc_field[0], "helloworld");
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
// (the case where you HAVE previously set it is tested in remove_info_shared_fields below)
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_string_shared_field("ZS", "");
BOOST_CHECK(missing(builder.build().string_shared_field("ZS")));
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_string_shared_field("ZS", ".");
BOOST_CHECK(missing(builder.build().string_shared_field("ZS")));
}
BOOST_AUTO_TEST_CASE( set_boolean_shared_fields ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
// Set boolean field by field name
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
auto variant = builder.set_boolean_shared_field("VALIDATED").build();
BOOST_CHECK(variant.boolean_shared_field("VALIDATED"));
// Set boolean field by field index
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
variant = builder.set_boolean_shared_field(header.field_index("VALIDATED")).build();
BOOST_CHECK(variant.boolean_shared_field("VALIDATED"));
// Set multiple boolean fields
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
variant = builder.set_boolean_shared_field("VALIDATED").set_boolean_shared_field("ZFLG").build();
BOOST_CHECK(variant.boolean_shared_field("VALIDATED"));
BOOST_CHECK(variant.boolean_shared_field("ZFLG"));
}
BOOST_AUTO_TEST_CASE( set_nonexistent_shared_field ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
// Non-existent field by name
BOOST_CHECK_THROW(builder.set_integer_shared_field("FOOBAR", 1), invalid_argument);
BOOST_CHECK_THROW(builder.set_float_shared_field("FOOBAR", 1.0), invalid_argument);
BOOST_CHECK_THROW(builder.set_string_shared_field("FOOBAR", "hello"), invalid_argument);
BOOST_CHECK_THROW(builder.set_boolean_shared_field("FOOBAR"), invalid_argument);
// Non-existent field by index
BOOST_CHECK_THROW(builder.set_integer_shared_field(1000, 1), invalid_argument);
BOOST_CHECK_THROW(builder.set_float_shared_field(1000, 1.0), invalid_argument);
BOOST_CHECK_THROW(builder.set_string_shared_field(1000, "hello"), invalid_argument);
BOOST_CHECK_THROW(builder.set_boolean_shared_field(1000), invalid_argument);
}
BOOST_AUTO_TEST_CASE( set_shared_field_wrong_type ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
// Type mismatch by name
BOOST_CHECK_THROW(builder.set_integer_shared_field("AF", 1), invalid_argument);
BOOST_CHECK_THROW(builder.set_float_shared_field("AN", 1.5), invalid_argument);
BOOST_CHECK_THROW(builder.set_string_shared_field("AF", "hello"), invalid_argument);
BOOST_CHECK_THROW(builder.set_boolean_shared_field("AF"), invalid_argument);
// Type mismatch by index
BOOST_CHECK_THROW(builder.set_integer_shared_field(header.field_index("AF"), 1), invalid_argument);
BOOST_CHECK_THROW(builder.set_float_shared_field(header.field_index("AN"), 1.5), invalid_argument);
BOOST_CHECK_THROW(builder.set_string_shared_field(header.field_index("AF"), "hello"), invalid_argument);
BOOST_CHECK_THROW(builder.set_boolean_shared_field(header.field_index("AF")), invalid_argument);
}
BOOST_AUTO_TEST_CASE( remove_integer_info_shared_fields ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
// Remove integer shared field via remove_shared_field()
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_integer_shared_field("ZI", vector<int32_t>{1, 2, 3});
builder.remove_shared_field("ZI");
BOOST_CHECK(missing(builder.build().integer_shared_field("ZI")));
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_integer_shared_field("ZI", vector<int32_t>{1, 2, 3});
builder.remove_shared_field(header.field_index("ZI"));
BOOST_CHECK(missing(builder.build().integer_shared_field("ZI")));
// Remove multiple integer shared fields via remove_shared_fields()
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_integer_shared_field("AN", 1);
builder.set_integer_shared_field("ZI", vector<int32_t>{1, 2, 3});
builder.remove_shared_fields(vector<string>{"AN", "ZI"});
auto variant = builder.build();
BOOST_CHECK(missing(variant.integer_shared_field("AN")));
BOOST_CHECK(missing(variant.integer_shared_field("ZI")));
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_integer_shared_field("AN", 1);
builder.set_integer_shared_field("ZI", vector<int32_t>{1, 2, 3});
builder.remove_shared_fields(vector<uint32_t>{uint32_t(header.field_index("AN")), uint32_t(header.field_index("ZI"))});
variant = builder.build();
BOOST_CHECK(missing(variant.integer_shared_field("AN")));
BOOST_CHECK(missing(variant.integer_shared_field("ZI")));
// Remove integer shared field by setting it to a missing value
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_integer_shared_field("ZI", vector<int32_t>{1, 2, 3});
builder.set_integer_shared_field("ZI", vector<int32_t>{});
BOOST_CHECK(missing(builder.build().integer_shared_field("ZI")));
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_integer_shared_field("ZI", vector<int32_t>{1, 2, 3});
builder.set_integer_shared_field("ZI", missing_values::int32);
BOOST_CHECK(missing(builder.build().integer_shared_field("ZI")));
}
BOOST_AUTO_TEST_CASE( remove_float_info_shared_fields ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
auto float_missing = 0.0f; bcf_float_set_missing(float_missing);
// Remove float shared field via remove_shared_field()
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_float_shared_field("ZF", vector<float>{1.0, 2.0, 3.0});
builder.remove_shared_field("ZF");
BOOST_CHECK(missing(builder.build().float_shared_field("ZF")));
// Remove multiple float shared fields via remove_shared_fields()
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_float_shared_field("AF", 1.0);
builder.set_float_shared_field("ZF", vector<float>{1.0, 2.0, 3.0});
builder.remove_shared_fields(vector<string>{"AF", "ZF"});
auto variant = builder.build();
BOOST_CHECK(missing(variant.float_shared_field("AF")));
BOOST_CHECK(missing(variant.float_shared_field("ZF")));
// Remove float shared field by setting it to a missing value
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_float_shared_field("ZF", vector<float>{1.0, 2.0, 3.0});
builder.set_float_shared_field("ZF", vector<float>{});
BOOST_CHECK(missing(builder.build().float_shared_field("ZF")));
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_float_shared_field("ZF", vector<float>{1.0, 2.0, 3.0});
builder.set_float_shared_field("ZF", float_missing);
BOOST_CHECK(missing(builder.build().float_shared_field("ZF")));
}
BOOST_AUTO_TEST_CASE( remove_string_info_shared_fields ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
// Remove string shared field via remove_shared_field()
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_string_shared_field("ZS", "ABC");
builder.remove_shared_field("ZS");
BOOST_CHECK(missing(builder.build().string_shared_field("ZS")));
// Remove multiple string shared fields via remove_shared_fields()
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_string_shared_field("DESC", "ABC");
builder.set_string_shared_field("ZS", "FOO");
builder.remove_shared_fields(vector<string>{"DESC", "ZS"});
auto variant = builder.build();
BOOST_CHECK(missing(variant.string_shared_field("DESC")));
BOOST_CHECK(missing(variant.string_shared_field("ZS")));
// Remove string shared field by setting it to a missing value
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_string_shared_field("ZS", "ABC");
builder.set_string_shared_field("ZS", "");
BOOST_CHECK(missing(builder.build().string_shared_field("ZS")));
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_string_shared_field("ZS", "ABC");
builder.set_string_shared_field("ZS", ".");
BOOST_CHECK(missing(builder.build().string_shared_field("ZS")));
}
BOOST_AUTO_TEST_CASE( remove_boolean_info_shared_fields ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
// Remove boolean shared field via remove_shared_field()
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_boolean_shared_field("ZFLG");
builder.remove_shared_field("ZFLG");
BOOST_CHECK(missing(builder.build().boolean_shared_field("ZFLG")));
// Remove multiple boolean shared fields via remove_shared_fields()
builder.clear().set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
builder.set_boolean_shared_field("VALIDATED");
builder.set_boolean_shared_field("ZFLG");
builder.remove_shared_fields(vector<string>{"VALIDATED", "ZFLG"});
auto variant = builder.build();
BOOST_CHECK(missing(variant.boolean_shared_field("VALIDATED")));
BOOST_CHECK(missing(variant.boolean_shared_field("ZFLG")));
}
BOOST_AUTO_TEST_CASE( remove_subset_of_shared_fields ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
auto zi_values = vector<int32_t>{1, 2, 3};
auto zf_values = vector<float>{3.0, 4.5, 5.0};
builder.set_integer_shared_field("ZI", zi_values);
builder.set_float_shared_field("AF", 1.0);
builder.set_float_shared_field("ZF", zf_values);
builder.set_string_shared_field("ZS", "FOO");
builder.set_boolean_shared_field("ZFLG");
// Remove only a subset of the total shared fields set
builder.remove_shared_fields(vector<string>{"AF", "ZS"});
auto variant = builder.build();
// And make sure only those fields were removed
BOOST_CHECK(missing(variant.float_shared_field("AF")));
BOOST_CHECK(missing(variant.string_shared_field("ZS")));
check_integer_shared_field(variant, "ZI", zi_values);
check_float_shared_field(variant, "ZF", zf_values);
BOOST_CHECK(variant.boolean_shared_field("ZFLG"));
}
BOOST_AUTO_TEST_CASE( set_shared_field_after_removal ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
auto zi_final_values = vector<int32_t>{4, 5, 6, 7};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
// Need to make sure that the "removed" flag gets cleared when we re-set a field after removal
builder.set_integer_shared_field("ZI", {1, 2, 3});
builder.remove_shared_field("ZI");
builder.set_integer_shared_field("ZI", zi_final_values);
auto variant = builder.build();
BOOST_CHECK( ! missing(variant.integer_shared_field("ZI")) );
check_integer_shared_field(variant, "ZI", zi_final_values);
}
BOOST_AUTO_TEST_CASE( test_shared_field_memory_pool_compaction ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
auto zi_values = vector<int32_t>{1, 2, 3};
auto zf_values = vector<float>{3.0, 4.5, 5.0};
builder.set_string_shared_field("ZS", "FOO");
builder.set_integer_shared_field("ZI", zi_values);
builder.set_float_shared_field("ZF", zf_values);
// Repeatedly set ZS in order to fill the shared memory pool multiple times and trigger
// several rounds of memory compaction (VariantBuilderSharedRegion::compact_shared_buffer()).
//
// (Note that this is not going to be a very common occurrence -- typically users will clear()
// their builders between records instead of just setting repeatedly without clearing)
for ( auto i = 0u; i < 30000; ++i ) {
builder.set_string_shared_field("ZS", "BAR");
}
builder.set_string_shared_field("ZS", "BINGO");
auto variant = builder.build();
// Make sure the memory compaction process hasn't corrupted field values!
BOOST_CHECK( ! missing(variant.integer_shared_field("ZI")) );
BOOST_CHECK( ! missing(variant.float_shared_field("ZF")) );
BOOST_CHECK( ! missing(variant.string_shared_field("ZS")) );
check_integer_shared_field(variant, "ZI", zi_values);
check_float_shared_field(variant, "ZF", zf_values);
BOOST_CHECK_EQUAL(variant.string_shared_field("ZS")[0], "BINGO");
}
/*********************************************
* Helper functions for individual field tests
*********************************************/
VariantBuilderMultiSampleVector<int32_t> initialize_flat_multi_sample_integer_vector(const VariantBuilder& builder, const vector<vector<int32_t>>& sample_values) {
auto max_values_per_sample = 0u;
for ( auto& sample_vec : sample_values ) {
if ( sample_vec.size() > max_values_per_sample ) max_values_per_sample = sample_vec.size();
}
auto flat_vector = builder.get_integer_multi_sample_vector(sample_values.size(), max_values_per_sample);
for ( auto sample_index = 0u; sample_index < sample_values.size(); ++sample_index ) {
flat_vector.set_sample_values(sample_index, sample_values[sample_index]);
}
return flat_vector;
}
VariantBuilderMultiSampleVector<float> initialize_flat_multi_sample_float_vector(const VariantBuilder& builder, const vector<vector<float>>& sample_values) {
auto max_values_per_sample = 0u;
for ( auto& sample_vec : sample_values ) {
if ( sample_vec.size() > max_values_per_sample ) max_values_per_sample = sample_vec.size();
}
auto flat_vector = builder.get_float_multi_sample_vector(sample_values.size(), max_values_per_sample);
for ( auto sample_index = 0u; sample_index < sample_values.size(); ++sample_index ) {
flat_vector.set_sample_values(sample_index, sample_values[sample_index]);
}
return flat_vector;
}
VariantBuilderMultiSampleVector<int32_t> initialize_flat_multi_sample_genotypes_vector(const VariantBuilder& builder, const vector<vector<int32_t>>& sample_genotypes) {
auto max_values_per_sample = 0u;
for ( auto& sample_vec : sample_genotypes ) {
if ( sample_vec.size() > max_values_per_sample ) max_values_per_sample = sample_vec.size();
}
auto flat_vector = builder.get_genotype_multi_sample_vector(sample_genotypes.size(), max_values_per_sample);
for ( auto sample_index = 0u; sample_index < sample_genotypes.size(); ++sample_index ) {
flat_vector.set_sample_values(sample_index, sample_genotypes[sample_index]);
}
return flat_vector;
}
void check_integer_individual_field(const Variant& variant, const string& field, const vector<vector<int32_t>>& expected) {
auto sample_index = 0u;
for ( const auto& sample_values : variant.integer_individual_field(field) ) {
BOOST_CHECK_EQUAL(sample_values.size(), expected[sample_index].size());
for ( auto value_index = 0u; value_index < sample_values.size(); ++value_index ) {
BOOST_CHECK_EQUAL(sample_values[value_index], expected[sample_index][value_index]);
}
++sample_index;
}
}
void check_float_individual_field(const Variant& variant, const string& field, const vector<vector<float>>& expected) {
auto sample_index = 0u;
for ( const auto& sample_values : variant.float_individual_field(field) ) {
BOOST_CHECK_EQUAL(sample_values.size(), expected[sample_index].size());
for ( auto value_index = 0u; value_index < sample_values.size(); ++value_index ) {
if ( bcf_float_is_missing(expected[sample_index][value_index]) ) BOOST_CHECK(bcf_float_is_missing(sample_values[value_index]));
else if ( bcf_float_is_vector_end(expected[sample_index][value_index]) ) BOOST_CHECK(bcf_float_is_vector_end(sample_values[value_index]));
else BOOST_CHECK_EQUAL(expected[sample_index][value_index], sample_values[value_index]);
}
++sample_index;
}
}
void check_string_individual_field(const Variant& variant, const string& field, const vector<string>& expected) {
auto expected_max_length = 0u;
for_each(expected.begin(), expected.end(), [&expected_max_length] (const string& str) { if ( str.length() > expected_max_length ) expected_max_length = str.length(); });
auto sample_index = 0u;
for ( const auto& sample_values : variant.string_individual_field(field) ) {
BOOST_CHECK_EQUAL(sample_values.size(), expected_max_length);
BOOST_CHECK_EQUAL(sample_values[0], expected[sample_index].empty() ? "." : expected[sample_index]);
++sample_index;
}
}
void check_genotype_field(const Variant& variant, const vector<vector<int32_t>>& expected) {
auto sample_index = 0u;
for ( const auto& genotype : variant.genotypes() ) {
BOOST_CHECK_EQUAL(genotype.size(), expected[sample_index].size());
for ( auto allele = 0u; allele < genotype.size(); ++allele ) {
BOOST_CHECK_EQUAL(genotype[allele], expected[sample_index][allele]);
}
++sample_index;
}
}
void init_integer_individual_field_by_sample(VariantBuilder& builder, const string& field, const vector<string>& samples,
const vector<vector<int32_t>>& values, bool use_indices) {
auto header = builder.header();
auto sample_idx = 0;
for ( const auto& sample : samples ) {
// Don't set values for samples with no data
if ( ! values[sample_idx].empty() ) {
use_indices ? builder.set_integer_individual_field(header.field_index(field), sample_idx, values[sample_idx]) :
builder.set_integer_individual_field(field, sample, values[sample_idx]);
}
++sample_idx;
}
}
void init_integer_individual_field_by_sample(VariantBuilder& builder, const string& field, const vector<string>& samples,
const vector<int32_t>& values, bool use_indices) {
auto header = builder.header();
auto sample_idx = 0;
for ( const auto& sample : samples ) {
use_indices ? builder.set_integer_individual_field(header.field_index(field), sample_idx, values[sample_idx]) :
builder.set_integer_individual_field(field, sample, values[sample_idx]);
++sample_idx;
}
}
void init_float_individual_field_by_sample(VariantBuilder& builder, const string& field, const vector<string>& samples,
const vector<vector<float>>& values, bool use_indices) {
auto header = builder.header();
auto sample_idx = 0;
for ( const auto& sample : samples ) {
// Don't set values for samples with no data
if ( ! values[sample_idx].empty() ) {
use_indices ? builder.set_float_individual_field(header.field_index(field), sample_idx, values[sample_idx]) :
builder.set_float_individual_field(field, sample, values[sample_idx]);
}
++sample_idx;
}
}
void init_float_individual_field_by_sample(VariantBuilder& builder, const string& field, const vector<string>& samples,
const vector<float>& values, bool use_indices) {
auto header = builder.header();
auto sample_idx = 0;
for ( const auto& sample : samples ) {
use_indices ? builder.set_float_individual_field(header.field_index(field), sample_idx, values[sample_idx]) :
builder.set_float_individual_field(field, sample, values[sample_idx]);
++sample_idx;
}
}
void init_string_individual_field_by_sample(VariantBuilder& builder, const string& field, const vector<string>& samples,
const vector<string>& values, bool use_indices) {
auto header = builder.header();
auto sample_idx = 0;
for ( const auto& sample : samples ) {
// Don't set values for samples with no data
if ( ! values[sample_idx].empty() ) {
use_indices ? builder.set_string_individual_field(header.field_index(field), sample_idx, values[sample_idx]) :
builder.set_string_individual_field(field, sample, values[sample_idx]);
}
++sample_idx;
}
}
void init_genotype_field_by_sample(VariantBuilder& builder, const vector<string>& samples,
const vector<vector<int32_t>>& values, bool use_indices, bool perform_move) {
auto sample_idx = 0;
for ( const auto& sample : samples ) {
// Don't set values for samples with no data
if ( ! values[sample_idx].empty() ) {
use_indices ? (perform_move ? builder.set_genotype(sample_idx, move(values[sample_idx])) : builder.set_genotype(sample_idx, values[sample_idx])) :
(perform_move ? builder.set_genotype(sample, move(values[sample_idx])) : builder.set_genotype(sample, values[sample_idx]));
}
++sample_idx;
}
}
/**********************************************
* Individual fields: tests for setting in bulk
* (ie., setting an entire field at once)
**********************************************/
BOOST_AUTO_TEST_CASE( bulk_set_integer_individual_fields ) {
auto header = SingleVariantReader{"testdata/test_variants_for_variantbuilder.vcf"}.header();
auto builder = VariantBuilder{header};
builder.set_chromosome(0).set_alignment_start(5).set_ref_allele("A");
// Run each test below with both lvalues and rvalues
for ( bool perform_move : { true, false } ) {
// Run each test below using both field indices and field names
for ( bool use_field_index : { true, false } ) {
auto nested_vector = vector<vector<int32_t>>{};
auto expected = vector<vector<int32_t>>{};
// Flat vector with one value per sample
expected = {{1}, {2}, {3}};
auto flat_vector = initialize_flat_multi_sample_integer_vector(builder, expected);
auto variant = use_field_index ? (perform_move ? builder.set_integer_individual_field(header.field_index("ZIFMT"), move(flat_vector)).build() : builder.set_integer_individual_field(header.field_index("ZIFMT"), flat_vector).build()) :
(perform_move ? builder.set_integer_individual_field("ZIFMT", move(flat_vector)).build() : builder.set_integer_individual_field("ZIFMT", flat_vector).build());
check_integer_individual_field(variant, "ZIFMT", expected);
// Flat vector with multiple values per sample
expected = {{1, 2, 3}, {4, 5, 6}, {7, 8, 9}};
flat_vector = initialize_flat_multi_sample_integer_vector(builder, expected);
variant = use_field_index ? (perform_move ? builder.set_integer_individual_field(header.field_index("ZIFMT"), move(flat_vector)).build() : builder.set_integer_individual_field(header.field_index("ZIFMT"), flat_vector).build()) :
(perform_move ? builder.set_integer_individual_field("ZIFMT", move(flat_vector)).build() : builder.set_integer_individual_field("ZIFMT", flat_vector).build());
check_integer_individual_field(variant, "ZIFMT", expected);
// Flat vector with variable number of values per sample, and a missing sample
expected = {{1, 2, 3}, {1, bcf_int32_vector_end, bcf_int32_vector_end}, {bcf_int32_missing, bcf_int32_vector_end, bcf_int32_vector_end}};
flat_vector = initialize_flat_multi_sample_integer_vector(builder, vector<vector<int32_t>>{{1, 2, 3}, {1}, {}});
variant = use_field_index ? (perform_move ? builder.set_integer_individual_field(header.field_index("ZIFMT"), move(flat_vector)).build() : builder.set_integer_individual_field(header.field_index("ZIFMT"), flat_vector).build()) :
(perform_move ? builder.set_integer_individual_field("ZIFMT", move(flat_vector)).build() : builder.set_integer_individual_field("ZIFMT", flat_vector).build());
check_integer_individual_field(variant, "ZIFMT", expected);
// Uniform-length nested vector
nested_vector = {{1, 2, 3}, {4, 5, 6}, {7, 8, 9}};
expected = nested_vector;
variant = use_field_index ? (perform_move ? builder.set_integer_individual_field(header.field_index("ZIFMT"), move(nested_vector)).build() : builder.set_integer_individual_field(header.field_index("ZIFMT"), nested_vector).build()) :
(perform_move ? builder.set_integer_individual_field("ZIFMT", move(nested_vector)).build() : builder.set_integer_individual_field("ZIFMT", nested_vector).build());
check_integer_individual_field(variant, "ZIFMT", expected);