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# Copyright [2015-2018] EMBL-European Bioinformatics Institute
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
use strict;
use warnings;
use Test::More tests => 177, 'die';
use FindBin qw( $Bin );
use Data::Dumper;
BEGIN {
use lib "$Bin/../lib", "$Bin/../blib/lib", "$Bin/../blib/arch";
use_ok 'Bio::DB::HTS::VCF';
use_ok 'Bio::DB::HTS::VCF::Row';
use_ok 'Bio::DB::HTS::VCF::RowPtr';
use_ok 'Bio::DB::HTS::VCF::Header';
use_ok 'Bio::DB::HTS::VCF::HeaderPtr';
}
{
# Test sweep functions
my $sweep = Bio::DB::HTS::VCF::Sweep->new(filename => $Bin . "/data/test.vcf.gz");
my $h = $sweep->header ;
my $row = $sweep->next_row();
is $row->chromosome($h), "19", "Chromosome value read" ;
#This should one day be fixed to 2 - but the HTSlib API always returns 0 at the moment
#is $row->num_filters(), "2", "Number of filters read" ;
#Once that is corrected, also add a test for the filters themselves
$row = $sweep->previous_row();
is $row->chromosome($h), "X", "Chromosome value read" ;
is $row->position(), 10, "Position value read" ;
is $row->quality(), 10, "Quality value read" ;
$row = $sweep->previous_row();
is $row->reference(), "T", "Quality value read" ;
$row = $sweep->previous_row();
is $row->id(), "microsat1", "ID value read" ;
is $row->num_alleles(), 2, "Number of alleles value read" ;
my $a_team = $row->get_alleles() ;
isa_ok($a_team, 'ARRAY');
is_deeply $a_team, ['GA', 'GAC'], 'alleles are correct';
$sweep->close() ;
}
{
# Test standard functions on a VCF file
ok my $v = Bio::DB::HTS::VCF->new( filename => $Bin . "/data/test.vcf.gz" ), "VCF file open";
is $v->num_variants(), 9, 'correct number of variants identified in file';
my $h = $v->header();
my $header_str = <<"HEADER";
##fileformat=VCFv4.0
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=1000GenomesPilot-NCBI36
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=TT,Number=0,Type=String,Description="Test">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FILTER=<ID=MQ45,Description="MQ45 info">
##FILTER=<ID=DP50,Description="DP50 info">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
##ALT=<ID=CNV,Description="Copy number variable region">
##contig=<ID=19>
##contig=<ID=20>
##contig=<ID=X>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
HEADER
is($h->fmt_text, $header_str, "Header formatted string");
is $h->version(), "VCFv4.0", "VCF Header version matches" ;
is $h->num_samples(), 3, "Number of samples" ;
is_deeply $h->get_sample_names(), ['NA00001','NA00002','NA00003'], "sample names correct" ;
is $h->num_seqnames(), 3, "Number of seqnames" ;
ok my $seqnames = $h->get_seqnames() ;
is_deeply $seqnames, ['19','20','X'], "sequence names correct" ;
ok my $row = $v->next(), "Next row";
is $row->chromosome($h), "19", "Chromosome value read" ;
is $row->position(), "111", "Position value read" ;
is $row->id(), "testid", "ID value read" ;
is $row->num_filters(), 2, "Num Filters OK" ;
is $row->has_filter($h,"DP50"), 1, "Actual Filter present" ;
is $row->has_filter($h,"."), 0, "PASS filter absent" ;
is $row->get_variant_type(1),1, "Variant type matches" ;
#info related tests
my $info_result ;
$info_result = $row->get_info($h);
is_deeply($info_result, { AF => [0.5], DB => [1], DP => [14], H2 => [1], NS => [3], TT => ['TESTSTRING'] }, 'info read correctly');
$info_result = $row->get_info($h,"DB") ;
isa_ok($info_result, 'ARRAY');
is_deeply $info_result, [1], 'info flag read correctly';
is $row->get_info_type($h,"DB"), "Flag", "info flag type correct" ;
$info_result = $row->get_info($h,"AF") ;
isa_ok($info_result, 'ARRAY');
is_deeply $info_result, [0.5], 'info float read correctly';
is $row->get_info_type($h,"AF"), "Float", "info float type correct" ;
$info_result = $row->get_info($h,"TT") ;
isa_ok($info_result, 'ARRAY');
is_deeply $info_result, ["TESTSTRING"], 'info string read correctly';
is $row->get_info_type($h,"TT"), "String", "info String type correct" ;
$info_result = $row->get_info($h,"NS") ;
isa_ok($info_result, 'ARRAY');
is_deeply $info_result, [3], 'info ints read correctly';
is $row->get_info_type($h,"NS"), "Integer", "info int type correct" ;
# format related tests
is_deeply($row->get_format($h, "GT"), [2, 3, 2, 3, 2, 4], 'format int read');
is_deeply($row->get_format($h, "HQ"), [10, 10, 10, 10, 3, 3], 'format int read');
is($row->get_format($h, "INVALID"), "ID_NOT_FOUND", 'format id not present');
is_deeply($row->get_format($h), {
GT => [2, 3, 2, 3, 2, 4],
HQ => [10, 10, 10, 10, 3, 3]
}, "format read");
ok $row = $v->next(), "Next row";
is $row->chromosome($h), "19", "Chromosome value read" ;
is $row->position(), "112", "Position value read" ;
is $row->quality(), "10", "Quality value read" ;
is $row->reference(), "A", "Reference value read" ;
is $row->num_alleles(), 1, "Num Alleles" ;
is $row->is_snp(), 1, "Is SNP" ;
my $a_team = $row->get_alleles() ;
isa_ok($a_team, 'ARRAY');
is_deeply $a_team, ['G'], 'alleles are correct';
is $row->num_filters(), 1, "Num Filters OK" ;
is $row->has_filter($h,"PASS"), 1, "PASS Filter present" ;
is $row->has_filter($h,"DP50"), 0, "Actual Filter absent" ;
is $row->has_filter($h,"sdkjsdf"), -1, "Made up filter not existing" ;
$info_result = $row->get_info($h);
is_deeply($info_result, {}, 'info read correctly');
# format related tests
is_deeply($row->get_format($h, "GT"), [2, 3, 2, 3, 2, 4], 'format int read');
is_deeply($row->get_format($h, "HQ"), [10, 10, 10, 10, 3, 3], 'format int read');
is($row->get_format($h, "INVALID"), "ID_NOT_FOUND", 'format id not present');
is_deeply($row->get_format($h), {
GT => [2, 3, 2, 3, 2, 4],
HQ => [10, 10, 10, 10, 3, 3]
}, "format read");
# Format and genotype tests
ok $row = $v->next(), "Next row";
is $row->chromosome($h), "20", "Chromosome value read" ;
is $row->get_format_type($h,"DP"), "Integer", "int format type correct";
is_deeply($row->get_format($h, "GT"), [2,3,4,3,4,4], "format int read");
is_deeply($row->get_format($h, "GQ"), [48,48,43], 'format int read');
is_deeply($row->get_format($h, "DP"), [1,8,5], 'format int read');
note "!!! Not sure this is correct !!!";
is_deeply($row->get_format($h, "HQ"), [51,51,51,51,'-2147483648','-2147483648'], 'format int read');
is_deeply($row->get_format($h), {
GT => [2,3,4,3,4,4],
GQ => [48,48,43],
DP => [1,8,5],
HQ => [51,51,51,51,'-2147483648','-2147483648']
}, "format read");
my $fmt_result = $row->get_genotypes($h) ;
isa_ok($fmt_result, 'ARRAY');
#TODO resolve how these translate to the strings in htslib
is_deeply $fmt_result, [2,3,4,3,4,4], 'genotypes read correctly' ;
is $row->get_format($h,"IDONTEXIST"), 'ID_NOT_FOUND', 'format id not found';
is $row->get_info($h,"IDONTEXIST"), 'ID_NOT_FOUND', 'info id not found';
$info_result = $row->get_info($h);
is_deeply($info_result, { NS => [3],
DP => [14],
AF => [0.5],
DB => [1],
H2 => [1]
}, 'info read correctly');
# Query tests
ok my $iter = $v->query("20:1000000-1231000"), "can query a region";
ok $row = $iter->next, "can get a value from the iterator";
# 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
is($row->chromosome($h), 20, 'chr');
is($row->position, 1110696, 'position');
is($row->id, 'rs6040355', 'id');
is($row->reference, 'A', 'reference');
is_deeply($row->get_info($h, 'NS'), [2], 'info');
is_deeply($row->get_info($h, 'DP'), [10], 'info');
is_deeply($row->get_info($h, 'AA'), ['T'], 'info');
is_deeply($row->get_info($h, 'DB'), [1], 'info');
ok $row = $iter->next, "can get a value from the iterator";
# 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,.
is($row->chromosome($h), 20, 'chr');
is($row->position, 1230237, 'position');
is($row->id, '.', 'id');
is($row->reference, 'T', 'reference');
is_deeply($row->get_info($h), {
NS => [3],
DP => [13],
AA => ['T']}, 'info');
ok !$iter->next, "no more results";
$v->close();
}
{
# Test standard functions on a BCF file
ok my $v = Bio::DB::HTS::VCF->new( filename => $Bin . "/data/test.bcf" ), "BCF file open";
is $v->num_variants(), 9, 'correct number of variants identified in file';
my $h = $v->header();
my $header_str = <<"HEADER";
##fileformat=VCFv4.0
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=1000GenomesPilot-NCBI36
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=TT,Number=0,Type=String,Description="Test">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FILTER=<ID=MQ45,Description="MQ45 info">
##FILTER=<ID=DP50,Description="DP50 info">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
##ALT=<ID=CNV,Description="Copy number variable region">
##contig=<ID=19>
##contig=<ID=20>
##contig=<ID=X>
##bcftools_viewVersion=1.3.1+htslib-1.3.1
##bcftools_viewCommand=view -o test.bcf -O b test.vcf.gz
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
HEADER
is($h->fmt_text, $header_str, "Header formatted string");
is $h->version(), "VCFv4.0", "VCF Header version matches" ;
is $h->num_samples(), 3, "Number of samples" ;
is_deeply $h->get_sample_names(), ['NA00001','NA00002','NA00003'], "sample names correct" ;
is $h->num_seqnames(), 3, "Number of seqnames" ;
is_deeply $h->get_seqnames(), ['19','20','X'], "sequence names correct" ;
ok my $row = $v->next(), "Next row";
is $row->chromosome($h), "19", "Chromosome value read" ;
is $row->position(), "111", "Position value read" ;
is $row->id(), "testid", "ID value read" ;
is $row->num_filters(), 2, "Num Filters OK" ;
is $row->has_filter($h,"DP50"), 1, "Actual Filter present" ;
is $row->has_filter($h,"."), 0, "PASS filter absent" ;
is $row->get_variant_type(1),1, "Variant type matches" ;
# info related tests
my $info_result ;
$info_result = $row->get_info($h);
is_deeply($info_result, { AF => [0.5], DB => [1], DP => [14], H2 => [1], NS => [3], TT => ['TESTSTRING'] }, 'info read correctly');
$info_result = $row->get_info($h,"DB") ;
isa_ok($info_result, 'ARRAY');
is_deeply $info_result, [1], 'info flag read correctly';
is $row->get_info_type($h,"DB"), "Flag", "info flag type correct" ;
$info_result = $row->get_info($h,"AF") ;
isa_ok($info_result, 'ARRAY');
is_deeply $info_result, [0.5], 'info float read correctly';
is $row->get_info_type($h,"AF"), "Float", "info float type correct" ;
$info_result = $row->get_info($h,"TT") ;
isa_ok($info_result, 'ARRAY');
is_deeply $info_result, ["TESTSTRING"], 'info string read correctly';
is $row->get_info_type($h,"TT"), "String", "info String type correct" ;
$info_result = $row->get_info($h,"NS") ;
isa_ok($info_result, 'ARRAY');
is_deeply $info_result, [3], 'info ints read correctly';
is $row->get_info_type($h,"NS"), "Integer", "info int type correct" ;
# format related tests
is_deeply($row->get_format($h, "GT"), [2, 3, 2, 3, 2, 4], 'format int read');
is_deeply($row->get_format($h, "HQ"), [10, 10, 10, 10, 3, 3], 'format int read');
is($row->get_format($h, "INVALID"), "ID_NOT_FOUND", 'format ID not present');
is_deeply($row->get_format($h), {
GT => [2, 3, 2, 3, 2, 4],
HQ => [10, 10, 10, 10, 3, 3]
}, "format read");
ok $row = $v->next(), "Next row";
is $row->chromosome($h), "19", "Chromosome value read" ;
is $row->position(), "112", "Position value read" ;
is $row->quality(), "10", "Quality value read" ;
is $row->reference(), "A", "Reference value read" ;
is $row->num_alleles(), 1, "Num Alleles" ;
is $row->is_snp(), 1, "Is SNP" ;
my $a_team = $row->get_alleles() ;
isa_ok($a_team, 'ARRAY');
is_deeply $a_team, ['G'], 'alleles are correct';
is $row->num_filters(), 1, "Num Filters OK" ;
is $row->has_filter($h,"PASS"), 1, "PASS Filter present" ;
is $row->has_filter($h,"DP50"), 0, "Actual Filter absent" ;
is $row->has_filter($h,"sdkjsdf"), -1, "Made up filter not existing" ;
$info_result = $row->get_info($h);
is_deeply($info_result, {}, 'info read correctly');
# format related tests
is_deeply($row->get_format($h, "GT"), [2, 3, 2, 3, 2, 4], 'format int read');
is_deeply($row->get_format($h, "HQ"), [10, 10, 10, 10, 3, 3], 'format int read');
is($row->get_format($h, "INVALID"), "ID_NOT_FOUND", 'format ID not present');
is_deeply($row->get_format($h), {
GT => [2, 3, 2, 3, 2, 4],
HQ => [10, 10, 10, 10, 3, 3]
}, "format read");
#Format and genotype tests
ok $row = $v->next(), "Next row";
is $row->chromosome($h), "20", "Chromosome value read" ;
is $row->get_format_type($h,"DP"), "Integer", "int format type correct" ;
is_deeply($row->get_format($h, "GT"), [2,3,4,3,4,4], 'format int read');
is_deeply($row->get_format($h, "GQ"), [48,48,43], 'format int read');
is_deeply($row->get_format($h, "DP"), [1,8,5], 'format int read');
note "!!! Not sure this is correct !!!";
is_deeply($row->get_format($h, "HQ"), [51,51,51,51,'-2147483648','-2147483648'], 'format int read');
is_deeply($row->get_format($h), {
GT => [2,3,4,3,4,4],
GQ => [48,48,43],
DP => [1,8,5],
HQ => [51,51,51,51,'-2147483648','-2147483648']
}, "format read");
my $fmt_result = $row->get_genotypes($h) ;
isa_ok($fmt_result, 'ARRAY');
# TODO resolve how these translate to the strings in htslib
is_deeply $fmt_result, [2,3,4,3,4,4], 'genotypes read correctly' ;
is $row->get_format($h,"IDONTEXIST"), 'ID_NOT_FOUND', 'format id not found';
is $row->get_info($h,"IDONTEXIST"), 'ID_NOT_FOUND', 'info id not found';
$info_result = $row->get_info($h);
is_deeply($info_result, { NS => [3],
DP => [14],
AF => [0.5],
DB => [1],
H2 => [1]
}, 'info read correctly');
# Query tests
ok my $iter = $v->query("20:1000000-1231000"), "can query a region";
ok $row = $iter->next, "can get a value from the iterator";
# 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
is($row->chromosome($h), 20, 'chr');
is($row->position, 1110696, 'position');
is($row->id, 'rs6040355', 'id');
is($row->reference, 'A', 'reference');
is_deeply($row->get_info($h, 'NS'), [2], 'info');
is_deeply($row->get_info($h, 'DP'), [10], 'info');
is_deeply($row->get_info($h, 'AA'), ['T'], 'info');
is_deeply($row->get_info($h, 'DB'), [1], 'info');
ok $row = $iter->next, "can get a value from the iterator";
# 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,.
is($row->chromosome($h), 20, 'chr');
is($row->position, 1230237, 'position');
is($row->id, '.', 'id');
is($row->reference, 'T', 'reference');
is_deeply($row->get_info($h), {
NS => [3],
DP => [13],
AA => ['T']}, 'info');
ok !$iter->next, "no more results";
$v->close();
}
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