Merge branch 'htslib-1620' into develop

samtools · Jul 20, 2023 · acea5b7 · acea5b7
2 parents e0e3bd4 + 9288357
commit acea5b7
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Showing 8 changed files with 86 additions and 3 deletions.
diff --git a/test/test.pl b/test/test.pl
@@ -288,6 +288,19 @@
 run_test(\&test_vcf_norm,$opts,in=>'norm.symbolic',fai=>'norm.symbolic',out=>'norm.symbolic.1.out',args=>'--old-rec-tag ORI');
 run_test(\&test_vcf_norm,$opts,in=>'norm.right-align',fai=>'norm.right-align',out=>'norm.right-align.1.out',args=>'--old-rec-tag ORI');
 run_test(\&test_vcf_norm,$opts,in=>'norm.right-align',fai=>'norm.right-align',out=>'norm.right-align.2.out',args=>'--old-rec-tag ORI -g {PATH}/norm.right-align.gff');
+run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.1.out',args=>'',reg=>'-r 1');
+run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.1.out',args=>'',reg=>'-r 1:1-2');
+run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.1.out',args=>'',reg=>'-r 1:1,1:2');
+run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.2.out',args=>'',reg=>'-r 1:1-1');
+run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.3.out',args=>'',reg=>'-r {1:1}');
+run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.3.out',args=>'',reg=>'-r {1:1}:1-2');
+run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.3.out',args=>'',reg=>'-r {1:1}:1,{1:1}:2');
+run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.4.out',args=>'',reg=>'-r {1:1}:1-1');
+run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.5.out',args=>'',reg=>'-r {1:1-1}');
+run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.5.out',args=>'',reg=>'-r {1:1-1}:1-2');
+run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.5.out',args=>'',reg=>'-r {1:1-1}:1,{1:1-1}:2');
+run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.6.out',args=>'',reg=>'-r {1:1-1}:1-1');
+run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',args=>'',reg=>'-r {1:1-1}-2',expected_failure=>1);
 run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.1.out',args=>'-aUc1 -C1 -s NA00002 -v snps',reg=>'');
 run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.2.out',args=>'-f PASS -Xks NA00003',reg=>'-r20,Y');
 run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.3.out',args=>'-xs NA00003',reg=>'');
@@ -1078,7 +1091,13 @@ sub test_cmd
 
     my ($ret,$out,$err) = _cmd3("$args{cmd}");
     if ( length($err) ) { $err =~ s/\n/\n\t\t/gs; $err = "\n\n\t\t$err\n"; }
-    if ( $ret ) { failed($opts,$test,"Non-zero status $ret$err"); return; }
+    if ( $ret && !$args{expected_failure} ) { failed($opts,$test,"Non-zero status $ret$err"); return; }
+    if ( $args{expected_failure} )
+    {
+        if ( !$ret ) { failed($opts,$test,"Expected failure but the test returned $ret$err"); }
+        else { passed($opts,$test,"ok, expected non-zero status"); }
+        return;
+    }
     if ( $$opts{redo_outputs} && -e "$$opts{path}/$args{out}" )
     {
         rename("$$opts{path}/$args{out}","$$opts{path}/$args{out}.old");
@@ -1150,9 +1169,10 @@ sub failed
 }
 sub passed
 {
-    my ($opts,$test) = @_;
+    my ($opts,$test,$reason) = @_;
     $$opts{nok}++;
-    print ".. ok\n\n";
+    if ( !defined $reason ) { $reason = 'ok'; }
+    print ".. $reason\n\n";
 }
 sub is_file_newer
 {

diff --git a/test/weird-chr-names.1.out b/test/weird-chr-names.1.out
@@ -0,0 +1,9 @@
+##fileformat=VCFv4.3
+##FILTER=<ID=PASS,Description="All filters passed">
+##reference=ref.fa
+##contig=<ID=1>
+##contig=<ID=1:1>
+##contig=<ID=1:1-1>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	1	.	C	T	.	.	.
+1	2	.	C	T	.	.	.
diff --git a/test/weird-chr-names.2.out b/test/weird-chr-names.2.out
@@ -0,0 +1,8 @@
+##fileformat=VCFv4.3
+##FILTER=<ID=PASS,Description="All filters passed">
+##reference=ref.fa
+##contig=<ID=1>
+##contig=<ID=1:1>
+##contig=<ID=1:1-1>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	1	.	C	T	.	.	.
diff --git a/test/weird-chr-names.3.out b/test/weird-chr-names.3.out
@@ -0,0 +1,9 @@
+##fileformat=VCFv4.3
+##FILTER=<ID=PASS,Description="All filters passed">
+##reference=ref.fa
+##contig=<ID=1>
+##contig=<ID=1:1>
+##contig=<ID=1:1-1>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1:1	1	.	C	T	.	.	.
+1:1	2	.	C	T	.	.	.
diff --git a/test/weird-chr-names.4.out b/test/weird-chr-names.4.out
@@ -0,0 +1,8 @@
+##fileformat=VCFv4.3
+##FILTER=<ID=PASS,Description="All filters passed">
+##reference=ref.fa
+##contig=<ID=1>
+##contig=<ID=1:1>
+##contig=<ID=1:1-1>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1:1	1	.	C	T	.	.	.
diff --git a/test/weird-chr-names.5.out b/test/weird-chr-names.5.out
@@ -0,0 +1,9 @@
+##fileformat=VCFv4.3
+##FILTER=<ID=PASS,Description="All filters passed">
+##reference=ref.fa
+##contig=<ID=1>
+##contig=<ID=1:1>
+##contig=<ID=1:1-1>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1:1-1	1	.	C	T	.	.	.
+1:1-1	2	.	C	T	.	.	.
diff --git a/test/weird-chr-names.6.out b/test/weird-chr-names.6.out
@@ -0,0 +1,8 @@
+##fileformat=VCFv4.3
+##FILTER=<ID=PASS,Description="All filters passed">
+##reference=ref.fa
+##contig=<ID=1>
+##contig=<ID=1:1>
+##contig=<ID=1:1-1>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1:1-1	1	.	C	T	.	.	.
diff --git a/test/weird-chr-names.vcf b/test/weird-chr-names.vcf
@@ -0,0 +1,12 @@
+##fileformat=VCFv4.3
+##reference=ref.fa
+##contig=<ID=1>
+##contig=<ID=1:1>
+##contig=<ID=1:1-1>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	1	.	C	T	.	.	.
+1	2	.	C	T	.	.	.
+1:1	1	.	C	T	.	.	.
+1:1	2	.	C	T	.	.	.
+1:1-1	1	.	C	T	.	.	.
+1:1-1	2	.	C	T	.	.	.