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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 => 21, 'die';
use feature qw( say );
use FindBin qw( $Bin );
BEGIN { use_ok 'Bio::DB::HTS::Tabix'; }
my $test_file = $Bin . '/data/test.tsv.gz';
my $tbx = Bio::DB::HTS::Tabix->new( filename => $test_file, warnings => 0 );
my $h = $tbx->header ;
ok( $h, "#CHROM FROM TO GERP" ) ;
my @ha = $tbx->header_array ;
ok( $ha[0], "#CHROM FROM TO GERP" ) ;
ok my $iter = $tbx->query("12:8000000-8000008"), "can query a region";
#make sure we can call next
ok my $row = $iter->next, 'can get a value from the iterator';
is $row, "12\t8000000\t8000000\t-2.94", 'row value is correct';
my $num_rows = 0;
++$num_rows while $iter->next;
is $num_rows, 7, "correct number of values come back from the iterator";
#check seqnames
my $seqnames = $tbx->seqnames;
isa_ok($seqnames, 'ARRAY');
is_deeply $seqnames, [1, 12, 'X', 'HLA-A*01:01:01:01'], 'seqnames are correct';
## test chr names containing ':'
#
ok $iter = $tbx->query_full('HLA-A*01:01:01:01',1,10), "can query a region with ':' in chr";
ok $row = $iter->next, 'can get a value from the iterator';
is $row, "HLA-A*01:01:01:01\t1\t500\t0.65", "row value is correct with ':' in chr";
ok $iter = $tbx->query_full('HLA-A*01:01:01:01',1,), "can query a region with ':' in chr, no end";
ok $row = $iter->next, 'can get a value from the iterator';
is $row, "HLA-A*01:01:01:01\t1\t500\t0.65", "row value is correct with ':' in chr, no end";
ok $iter = $tbx->query_full('HLA-A*01:01:01:01'), "can query a region with ':' in chr, no coord";
ok $row = $iter->next, 'can get a value from the iterator';
is $row, "HLA-A*01:01:01:01\t1\t500\t0.65", "row value is correct with ':' in chr, no coord";
#
## end strange chr name testing
$iter = $tbx->query("fake");
ok(!$iter, 'querying non existent chrom');
$tbx->close;
#More in depth header tests
$test_file = $Bin . '/data/data.vcf.gz';
$tbx = Bio::DB::HTS::Tabix->new( filename => $test_file, warnings => 0 );
@ha = $tbx->header_array ;
ok( $ha[0], "##fileformat=VCFv4.2" ) ;
ok( $ha[5], "##reference=human_b36_both.fasta" ) ;
$tbx->close;
done_testing;
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