Add synced reader region tests, and move no-index tests

Add some tests to exercise the --regions / --targets synced reader options. Currently this only includes tests for the chromosomes with [:-] characters in the name, but it could be expanded easily to do others. Test files have been borrowed from pull request samtools/bcftools#1938. Move the synced reader no-index tests from test-bcf-sr.pl to test.pl. The former isn't a good place for them as it gets called 10 times, but the no-index test only needs to run once. It also allows the code running the test to be simplified a bit. Also fix the exit code on test-bcf-sr.pl failure from -1 to 1. Co-authored-by: Petr Danecek <[email protected]>
samtools · Jun 27, 2023 · e86126b · e86126b
1 parent 28a8082
commit e86126b
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diff --git a/test/bcf-sr/weird-chr-names.1.out b/test/bcf-sr/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/bcf-sr/weird-chr-names.2.out b/test/bcf-sr/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/bcf-sr/weird-chr-names.3.out b/test/bcf-sr/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/bcf-sr/weird-chr-names.4.out b/test/bcf-sr/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/bcf-sr/weird-chr-names.5.out b/test/bcf-sr/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/bcf-sr/weird-chr-names.6.out b/test/bcf-sr/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/bcf-sr/weird-chr-names.vcf b/test/bcf-sr/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	.	.	.
diff --git a/test/test-bcf-sr.pl b/test/test-bcf-sr.pl
@@ -34,7 +34,6 @@
 
 my $opts = parse_params();
 run_test($opts);
-test_no_index($opts);
 
 exit;
 
@@ -58,7 +57,7 @@ sub error
         "   -v, --verbose           \n",
         "   -h, -?, --help          This help message\n",
         "\n";
-    exit -1;
+    exit 1;
 }
 sub parse_params
 {
@@ -572,60 +571,3 @@ sub pairing_score
     }
     return (1<<(28+$min)) + $cnt;
 }
-
-sub test_no_index {
-    my ($opts) = @_;
-
-    my $vcfdir = "$FindBin::Bin/bcf-sr";
-    if ($^O =~ /^msys/) {
-        $vcfdir = `cygpath -w $vcfdir`;
-        $vcfdir =~ s/\r?\n//;
-        $vcfdir =~ s/\\/\\\\/g;
-    }
-
-    # Positive test
-    open(my $fh, '>', "$$opts{tmp}/no_index_1.txt")
-        || error("$$opts{tmp}/no_index_1.txt : $!");
-    print $fh "$vcfdir/merge.noidx.a.vcf\n";
-    print $fh "$vcfdir/merge.noidx.b.vcf\n";
-    print $fh "$vcfdir/merge.noidx.c.vcf\n";
-    close($fh) || error("$$opts{tmp}/no_index_1.txt : $!");
-
-    my $cmd = "$FindBin::Bin/test-bcf-sr --no-index -p all $$opts{tmp}/no_index_1.txt > $$opts{tmp}/no_index_1.out 2> $$opts{tmp}/no_index_1.err";
-    my ($ret) = _cmd($cmd);
-    if ($ret) {
-        error("The command failed [$ret]: $cmd\n");
-    }
-
-    if ($^O =~ /^msys/) {
-        cmd("diff --strip-trailing-cr $vcfdir/merge.noidx.abc.expected.out $$opts{tmp}/no_index_1.out");
-    } else {
-        cmd("cmp $vcfdir/merge.noidx.abc.expected.out $$opts{tmp}/no_index_1.out");
-    }
-
-    # Check bad input detection
-
-    my @bad_file_tests = (["out-of-order header",
-                           ["merge.noidx.a.vcf", "merge.noidx.hdr_order.vcf"]],
-                          ["out-of-order records",
-                           ["merge.noidx.a.vcf", "merge.noidx.rec_order.vcf"]],
-                          ["out-of-order records",
-                           ["merge.noidx.rec_order.vcf", "merge.noidx.a.vcf"]]);
-    my $count = 2;
-    foreach my $test_params (@bad_file_tests) {
-        my ($badness, $inputs) = @$test_params;
-        open($fh, '>', "$$opts{tmp}/no_index_$count.txt")
-            || error("$$opts{tmp}/no_index_$count.txt : $!");
-        foreach my $input (@$inputs) {
-            print $fh "$vcfdir/$input\n";
-        }
-        close($fh) || error("$$opts{tmp}/no_index_$count.txt : $!");
-
-        $cmd = "$FindBin::Bin/test-bcf-sr --no-index -p all $$opts{tmp}/no_index_$count.txt > $$opts{tmp}/no_index_$count.out 2> $$opts{tmp}/no_index_$count.err";
-        my ($ret) = _cmd($cmd);
-        if ($ret == 0) {
-            error("Failed to detect $badness: $cmd\n");
-        }
-        $count++;
-    }
-}
diff --git a/test/test.pl b/test/test.pl
@@ -54,6 +54,8 @@
 test_vcf_sweep($opts,out=>'test-vcf-sweep.out');
 test_vcf_various($opts);
 test_bcf_sr_sort($opts);
+test_bcf_sr_no_index($opts);
+test_bcf_sr_range($opts);
 test_command($opts,cmd=>'test-bcf-translate -',out=>'test-bcf-translate.out');
 test_convert_padded_header($opts);
 test_rebgzip($opts);
@@ -1033,6 +1035,113 @@ sub test_bcf_sr_sort
     }
 }
 
+sub test_bcf_sr_no_index {
+    my ($opts) = @_;
+
+    my $test = "test_bcf_sr_no_index";
+
+    my $vcfdir = "$$opts{path}/bcf-sr";
+
+    # Positive test
+    test_cmd($opts, out => "bcf-sr/merge.noidx.abc.expected.out",
+             cmd => "$$opts{path}/test-bcf-sr --no-index -p all --args $vcfdir/merge.noidx.a.vcf $vcfdir/merge.noidx.b.vcf $vcfdir/merge.noidx.c.vcf 2> $$opts{tmp}/no_index_1.err");
+
+    # Check bad input detection
+
+    my @bad_file_tests = (["out-of-order header",
+                           ["merge.noidx.a.vcf", "merge.noidx.hdr_order.vcf"]],
+                          ["out-of-order records",
+                           ["merge.noidx.a.vcf", "merge.noidx.rec_order.vcf"]],
+                          ["out-of-order records",
+                           ["merge.noidx.rec_order.vcf", "merge.noidx.a.vcf"]]);
+    my $count = 2;
+    foreach my $test_params (@bad_file_tests) {
+        my ($badness, $inputs) = @$test_params;
+        my @ins = map { "$vcfdir/$_" } @$inputs;
+
+        my $cmd = "$$opts{path}/test-bcf-sr --no-index -p all --args @ins > $$opts{tmp}/no_index_$count.out 2> $$opts{tmp}/no_index_$count.err";
+        print "$test:\n\t$cmd (expected fail)\n";
+        my ($ret) = _cmd($cmd);
+        if ($ret == 0) {
+            failed($opts, $test, "Failed to detect $badness: $cmd\n");
+        } else {
+            passed($opts, $test);
+        }
+        $count++;
+    }
+}
+
+sub test_bcf_sr_range {
+    my ($opts) = @_;
+
+    my $test = "test_bcf_sr_range";
+
+    my $vcfdir = "$$opts{path}/bcf-sr";
+
+    my @tests = (['r', '1', 'weird-chr-names.vcf', 'weird-chr-names.1.out'],
+                 ['r', '1:1-2', 'weird-chr-names.vcf', 'weird-chr-names.1.out'],
+                 ['r', '1:1,1:2', 'weird-chr-names.vcf', 'weird-chr-names.1.out'],
+                 ['r', '1:1-1', 'weird-chr-names.vcf', 'weird-chr-names.2.out'],
+                 ['r', '{1:1}', 'weird-chr-names.vcf', 'weird-chr-names.3.out'],
+                 ['r', '{1:1}:1-2', 'weird-chr-names.vcf', 'weird-chr-names.3.out'],
+                 ['r', '{1:1}:1,{1:1}:2', 'weird-chr-names.vcf', 'weird-chr-names.3.out'],
+                 ['r', '{1:1}:1-1', 'weird-chr-names.vcf', 'weird-chr-names.4.out'],
+                 ['r', '{1:1-1}', 'weird-chr-names.vcf', 'weird-chr-names.5.out'],
+                 ['r', '{1:1-1}:1-2', 'weird-chr-names.vcf', 'weird-chr-names.5.out'],
+                 ['r', '{1:1-1}:1,{1:1-1}:2', 'weird-chr-names.vcf', 'weird-chr-names.5.out'],
+                 ['r', '{1:1-1}:1-1', 'weird-chr-names.vcf', 'weird-chr-names.6.out'],
+                 ['r', '{1:1-1}-2', 'weird-chr-names.vcf', undef], # Expected failure
+                 ['t', '1', 'weird-chr-names.vcf', 'weird-chr-names.1.out'],
+                 ['t', '1:1-2', 'weird-chr-names.vcf', 'weird-chr-names.1.out'],
+                 ['t', '1:1,1:2', 'weird-chr-names.vcf', 'weird-chr-names.1.out'],
+                 ['t', '1:1-1', 'weird-chr-names.vcf', 'weird-chr-names.2.out'],
+                 ['t', '{1:1}', 'weird-chr-names.vcf', 'weird-chr-names.3.out'],
+                 ['t', '{1:1}:1-2', 'weird-chr-names.vcf', 'weird-chr-names.3.out'],
+                 ['t', '{1:1}:1,{1:1}:2', 'weird-chr-names.vcf', 'weird-chr-names.3.out'],
+                 ['t', '{1:1}:1-1', 'weird-chr-names.vcf', 'weird-chr-names.4.out'],
+                 ['t', '{1:1-1}', 'weird-chr-names.vcf', 'weird-chr-names.5.out'],
+                 ['t', '{1:1-1}:1-2', 'weird-chr-names.vcf', 'weird-chr-names.5.out'],
+                 ['t', '{1:1-1}:1,{1:1-1}:2', 'weird-chr-names.vcf', 'weird-chr-names.5.out'],
+                 ['t', '{1:1-1}:1-1', 'weird-chr-names.vcf', 'weird-chr-names.6.out'],
+                 ['t', '{1:1-1}-2', 'weird-chr-names.vcf', undef] # Expected failure
+        );
+
+    my $count = 0;
+    my %converted;
+    foreach my $tst (@tests) {
+        my ($option, $range, $in, $exp_out) = @$tst;
+        $count++;
+        if (!$converted{$in}) {
+            my $cmd = "$$opts{path}/test_view -b -p $$opts{tmp}/$in.bcf -x $$opts{tmp}/$in.bcf.csi $vcfdir/$in";
+            print "$test:\n\t$cmd\n";
+            my ($ret) = _cmd($cmd);
+            if ($ret) {
+                failed($opts, $test);
+                $converted{$in} = 'fail';
+                next;
+            } else {
+                passed($opts, $test);
+                $converted{$in} = "$$opts{tmp}/$in.bcf";
+            }
+        }
+        next if ($converted{$in} eq 'fail');
+        my $cmd = "$$opts{path}/test-bcf-sr -O vcf -o $$opts{tmp}/range_test_$count.out.vcf -$option '$range' --args $converted{$in}";
+        if ($exp_out) {
+            test_compare($opts, $cmd, "$vcfdir/$exp_out",
+                         "$$opts{tmp}/range_test_$count.out.vcf",
+                         fix_newlines => 1);
+        } else {
+            print "$test:\n\t$cmd (expected fail)\n";
+            my ($ret) = _cmd($cmd);
+            if ($ret) {
+                passed($opts, $test);
+            } else {
+                failed($opts, $test);
+            }
+        }
+    }
+}
+
 sub test_command
 {
     my ($opts, %args) = @_;