Haplo - fix chromosome match (#487)

* Fix chromosome comparison * Test non numeric chromosome
Ensembl · Jun 6, 2019 · 0f37f44 · 0f37f44
1 parent c9cbd42
commit 0f37f44
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Showing 5 changed files with 25 additions and 4 deletions.
diff --git a/modules/Bio/EnsEMBL/VEP/Constants.pm b/modules/Bio/EnsEMBL/VEP/Constants.pm
@@ -53,7 +53,7 @@ use warnings;
 use base qw(Exporter);
 
 our $VEP_VERSION     = 96;
-our $VEP_SUB_VERSION = 1;
+our $VEP_SUB_VERSION = 2;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS

diff --git a/modules/Bio/EnsEMBL/VEP/Haplo/InputBuffer.pm b/modules/Bio/EnsEMBL/VEP/Haplo/InputBuffer.pm
@@ -138,7 +138,7 @@ sub next {
     return $buffer unless $max;
 
     # Continue to add VF to buffer until VF start > max or VF on different chromosome
-    while($vf && $vf->{start} <= $max && $vf->{chr} == $current_chr) {
+    while($vf && $vf->{start} <= $max && $vf->{chr} eq $current_chr) {
       push @$buffer, $vf;
       $vf = $parser->next;
     }

diff --git a/t/Haplo_InputBuffer.t b/t/Haplo_InputBuffer.t
@@ -123,11 +123,24 @@ SKIP: {
 
   # Chr 21
   $vfs = $ib->next;
-  ok(scalar(@$vfs) == 3 && $vfs->[0]->{chr} == 21, 'The 3 entries from chr21 are in the same buffer');
+  ok(scalar(@$vfs) == 3 && $vfs->[0]->{chr} == 21, 'The 3 entries from chromosome 21 are in the same buffer');
 
   # Chr 22
   $vfs = $ib->next;
-  ok(scalar(@$vfs) == 1 && $vfs->[0]->{chr} == 22, 'The entry from chr22 is in a different buffer');
+  ok(scalar(@$vfs) == 1 && $vfs->[0]->{chr} == 22, 'The entry from chromosome 22 is in a different buffer');
+
+  # Test non numeric chromosomes 
+  my $runner3 = Bio::EnsEMBL::VEP::Haplo::Runner->new({%{$test_cfg->base_testing_cfg}, input_file => $test_cfg->{test_vcf4}});
+
+  $ib = $runner3->get_InputBuffer;
+
+  # chr21
+  $vfs = $ib->next;
+  ok(scalar(@$vfs) == 3 && $vfs->[0]->{chr} eq 'chr21', 'The 3 entries from chr21 are in the same buffer');
+
+  # chr22
+  $vfs = $ib->next;
+  ok(scalar(@$vfs) == 1 && $vfs->[0]->{chr} eq 'chr22', 'The entry from chr22 is in a different buffer');
 
 }
 

diff --git a/t/VEPTestingConfig.pm b/t/VEPTestingConfig.pm
@@ -54,6 +54,7 @@ our %DEFAULTS = (
   test_vcf       => $Bin.'/testdata/input/test.vcf',
   test_vcf2      => $Bin.'/testdata/input/test2.vcf',
   test_vcf3      => $Bin.'/testdata/input/test3.vcf',
+  test_vcf4      => $Bin.'/testdata/input/test4.vcf',
   vr_vcf         => $Bin.'/testdata/input/idt_test.vcf',
   windows_vcf    => $Bin.'/testdata/input/windows.vcf',
   test_gzvcf     => $Bin.'/testdata/input/test.vcf.gz',

diff --git a/t/testdata/input/test4.vcf b/t/testdata/input/test4.vcf
@@ -0,0 +1,7 @@
+##fileformat=VCFv4.1
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	P1
+chr21	25769083	var2_chr21	CT	C	.	PASS	.	GT	0|1
+chr21	25769085	var3_chr21	T	TT	.	PASS	.	GT	0|1
+chr21	25769093	var4_chr21	A	G	.	PASS	.	GT	0|1
+chr22	25769065	var5_chr22	G	T	.	PASS	.	GT	0|1