Add tests for #1123

samtools · Dec 16, 2019 · 4b54f9d · 4b54f9d
1 parent 2782d9f
commit 4b54f9d
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Showing 11 changed files with 72 additions and 0 deletions.
diff --git a/test/test.pl b/test/test.pl
@@ -226,6 +226,11 @@
 test_vcf_view($opts,in=>'idx.2',out=>'idx.2.out',args=>q[-H -R {PATH}/idx.2.bed]);
 test_vcf_view($opts,in=>'idx.3',out=>'idx.3.out',args=>q[-H -R {PATH}/idx.3.bed]);
 test_vcf_view($opts,in=>'idx.4',out=>'idx.4.out',args=>q[-H -R {PATH}/idx.4.bed]);
+test_vcf_64bit($opts,in=>'view64bit.1',out=>'view64bit.1.out',do_bcf=>1);
+test_vcf_64bit($opts,in=>'view64bit.2',out=>'view64bit.2.out',do_bcf=>1);
+test_vcf_64bit($opts,in=>'view64bit.3',out=>'view64bit.3.out');     # large coordinates don't work with BCF
+test_vcf_64bit($opts,in=>'view64bit.4',out=>'view64bit.4.out',do_bcf=>1);
+test_vcf_64bit($opts,in=>'view64bit.5',out=>'view64bit.5.out',do_bcf=>1);
 test_vcf_filter($opts,in=>'view.filter',out=>'view.filter.6.out',args=>q[-S. -e'TXT0="text"'],reg=>'');
 test_vcf_filter($opts,in=>'view.filter',out=>'view.filter.7.out',args=>q[-S. -e'FMT/FRS[*:1]="BB"'],reg=>'');
 test_vcf_filter($opts,in=>'view.filter',out=>'view.filter.8.out',args=>q[-S. -e'FMT/FGS[*:0]="AAAAAA"'],reg=>'');
@@ -959,6 +964,16 @@ sub test_vcf_view
         test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $args{args} $$opts{tmp}/$args{in}.vcf.gz $args{reg} | $$opts{bin}/bcftools view | grep -v ^##bcftools_", exp_fix=>1);
     }
 }
+sub test_vcf_64bit
+{
+    my ($opts,%args) = @_;
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view $$opts{path}/$args{in}.vcf -H", exp_fix=>1);
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view $$opts{path}/$args{in}.vcf     | $$opts{bin}/bcftools view -H", exp_fix=>1);
+    if ( $args{do_bcf} )
+    {
+        test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view $$opts{path}/$args{in}.vcf -Ou | $$opts{bin}/bcftools view -H", exp_fix=>1);
+    }
+}
 sub test_vcf_call
 {
     my ($opts,%args) = @_;

diff --git a/test/view64bit.1.out b/test/view64bit.1.out
@@ -0,0 +1,2 @@
+chr1	1	.	G	C	.	.	MPOS=.;XPOS=.,.,.;NALOD=-0.8279;NLOD=15.45;POPAF=6
+chr1	2	.	G	C	.	.	MPOS=.;XPOS=.,.,.;NALOD=-0.8279;NLOD=15.45;POPAF=6
diff --git a/test/view64bit.1.vcf b/test/view64bit.1.vcf
@@ -0,0 +1,10 @@
+##fileformat=VCFv4.2
+##INFO=<ID=MPOS,Number=A,Type=Integer,Description="dummy">
+##INFO=<ID=XPOS,Number=.,Type=Integer,Description="dummy">
+##INFO=<ID=NALOD,Number=A,Type=Float,Description="dummy">
+##INFO=<ID=NLOD,Number=A,Type=Float,Description="dummy">
+##INFO=<ID=POPAF,Number=A,Type=Float,Description="dummy">
+##contig=<ID=chr1,length=248956422>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+chr1	1	.	G	C	.	.	MPOS=-2147483641;XPOS=-2147483641,-2147483641,-2147483641;NALOD=-8.279e-01;NLOD=15.45;POPAF=6.00
+chr1	2	.	G	C	.	.	MPOS=-2147483648;XPOS=-2147483648,-2147483648,-2147483648;NALOD=-8.279e-01;NLOD=15.45;POPAF=6.00
diff --git a/test/view64bit.2.out b/test/view64bit.2.out
@@ -0,0 +1 @@
+chr1	1	.	G	C	.	.	MPOS=.;XPOS=.,.,.	MPOS:XPOS	.:.,.,.
diff --git a/test/view64bit.2.vcf b/test/view64bit.2.vcf
@@ -0,0 +1,8 @@
+##fileformat=VCFv4.2
+##INFO=<ID=MPOS,Number=A,Type=Integer,Description="dummy">
+##INFO=<ID=XPOS,Number=.,Type=Integer,Description="dummy">
+##FORMAT=<ID=MPOS,Number=.,Type=Integer,Description="dummy">
+##FORMAT=<ID=XPOS,Number=.,Type=Integer,Description="dummy">
+##contig=<ID=chr1,length=248956422>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
+chr1	1	.	G	C	.	.	MPOS=42949672950;XPOS=42949672950,42949672950,42949672950	MPOS:XPOS	42949672950:42949672950,42949672950,42949672950
diff --git a/test/view64bit.3.out b/test/view64bit.3.out
@@ -0,0 +1 @@
+chr1	42949672950	.	G	C	.	.	MPOS=.;XPOS=.,.,.	MPOS:XPOS	.:.,.,.
diff --git a/test/view64bit.3.vcf b/test/view64bit.3.vcf
@@ -0,0 +1,8 @@
+##fileformat=VCFv4.2
+##INFO=<ID=MPOS,Number=A,Type=Integer,Description="dummy">
+##INFO=<ID=XPOS,Number=.,Type=Integer,Description="dummy">
+##FORMAT=<ID=MPOS,Number=.,Type=Integer,Description="dummy">
+##FORMAT=<ID=XPOS,Number=.,Type=Integer,Description="dummy">
+##contig=<ID=chr1,length=248956422>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
+chr1	42949672950	.	G	C	.	.	MPOS=42949672950;XPOS=42949672950,42949672950,42949672950	MPOS:XPOS	42949672950:42949672950,42949672950,42949672950
diff --git a/test/view64bit.4.out b/test/view64bit.4.out
@@ -0,0 +1 @@
+chr1	1	.	G	C	.	.	MPOS=.;XPOS=.,.,.	MPOS:XPOS	.:.,.,.
diff --git a/test/view64bit.4.vcf b/test/view64bit.4.vcf
@@ -0,0 +1,8 @@
+##fileformat=VCFv4.2
+##INFO=<ID=MPOS,Number=A,Type=Integer,Description="dummy">
+##INFO=<ID=XPOS,Number=.,Type=Integer,Description="dummy">
+##FORMAT=<ID=MPOS,Number=.,Type=Integer,Description="dummy">
+##FORMAT=<ID=XPOS,Number=.,Type=Integer,Description="dummy">
+##contig=<ID=chr1,length=248956422>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
+chr1	1	.	G	C	.	.	MPOS=.;XPOS=.,.,.	MPOS:XPOS	.:.,.,.
diff --git a/test/view64bit.5.out b/test/view64bit.5.out
@@ -0,0 +1,6 @@
+chr1	1	.	G	C	.	.	END=42949672,1,.;MPOS=100000000	XX	1,-2147483640,.,.,.,2147483647,.
+chr1	1	.	G	C	.	.	END=-2147483640	XX	-2147483640
+chr1	1	.	G	C	.	.	END=.	XX	.
+chr1	1	.	G	C	.	.	END=.	XX	.
+chr1	1	.	G	C	.	.	END=.	XX	.
+chr1	1	.	G	C	.	.	END=.	XX	.
diff --git a/test/view64bit.5.vcf b/test/view64bit.5.vcf
@@ -0,0 +1,12 @@
+##fileformat=VCFv4.2
+##INFO=<ID=END,Number=A,Type=Integer,Description="dummy">
+##INFO=<ID=MPOS,Number=A,Type=Integer,Description="dummy">
+##FORMAT=<ID=XX,Number=A,Type=Integer,Description="dummy">
+##contig=<ID=chr1,length=248956422>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1
+chr1	1	.	G	C	.	.	END=42949672,1,5000000000;MPOS=100000000	XX	1,-2147483640,-2147483641,-2147483647,-2147483648,2147483647,2147483648
+chr1	1	.	G	C	.	.	END=-2147483640	XX	-2147483640
+chr1	1	.	G	C	.	.	END=-2147483641	XX	-2147483641
+chr1	1	.	G	C	.	.	END=-2147483647	XX	-2147483647
+chr1	1	.	G	C	.	.	END=-2147483648	XX	-2147483648
+chr1	1	.	G	C	.	.	END=-2147483649	XX	-2147483649