1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
|
#!/usr/bin/env perl
#
# Copyright (C) 2012-2013 Genome Research Ltd.
#
# Author: Petr Danecek <pd3@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
use strict;
use warnings;
use Carp;
use FindBin;
use lib "$FindBin::Bin";
use Getopt::Long;
use File::Temp qw/ tempfile tempdir /;
my $opts = parse_params();
test_vcf_api($opts,out=>'test-vcf-api.out');
test_vcf_sweep($opts,out=>'test-vcf-sweep.out');
print "\nNumber of tests:\n";
printf " total .. %d\n", $$opts{nok}+$$opts{nfailed};
printf " passed .. %d\n", $$opts{nok};
printf " failed .. %d\n", $$opts{nfailed};
print "\n";
exit ($$opts{nfailed} > 0);
#--------------------
sub error
{
my (@msg) = @_;
if ( scalar @msg ) { confess @msg; }
print
"About: samtools/htslib consistency test script\n",
"Usage: test.pl [OPTIONS]\n",
"Options:\n",
" -r, --redo-outputs Recreate expected output files.\n",
" -t, --temp-dir <path> When given, temporary files will not be removed.\n",
" -h, -?, --help This help message.\n",
"\n";
exit 1;
}
sub parse_params
{
my $opts = { keep_files=>0, nok=>0, nfailed=>0 };
my $help;
Getopt::Long::Configure('bundling');
my $ret = GetOptions (
't|temp-dir:s' => \$$opts{keep_files},
'r|redo-outputs' => \$$opts{redo_outputs},
'h|?|help' => \$help
);
if ( !$ret or $help ) { error(); }
$$opts{tmp} = $$opts{keep_files} ? $$opts{keep_files} : tempdir(CLEANUP=>1);
if ( $$opts{keep_files} ) { cmd("mkdir -p $$opts{keep_files}"); }
$$opts{path} = $FindBin::RealBin;
$$opts{bin} = $FindBin::RealBin;
$$opts{bin} =~ s{/test/?$}{};
return $opts;
}
sub _cmd
{
my ($cmd) = @_;
my $kid_io;
my @out;
my $pid = open($kid_io, "-|");
if ( !defined $pid ) { error("Cannot fork: $!"); }
if ($pid)
{
# parent
@out = <$kid_io>;
close($kid_io);
}
else
{
# child
exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!");
}
return ($? >> 8, join('',@out));
}
sub cmd
{
my ($cmd) = @_;
my ($ret,$out) = _cmd($cmd);
if ( $ret ) { error("The command failed [$ret]: $cmd\n", $out); }
return $out;
}
sub test_cmd
{
my ($opts,%args) = @_;
if ( !exists($args{out}) )
{
if ( !exists($args{in}) ) { error("FIXME: expected out or in key\n"); }
$args{out} = "$args{in}.out";
}
my ($package, $filename, $line, $test)=caller(1);
$test =~ s/^.+:://;
print "$test:\n";
print "\t$args{cmd}\n";
my ($ret,$out) = _cmd("$args{cmd} 2>&1");
if ( $ret ) { failed($opts,$test); return; }
if ( $$opts{redo_outputs} && -e "$$opts{path}/$args{out}" )
{
rename("$$opts{path}/$args{out}","$$opts{path}/$args{out}.old");
open(my $fh,'>',"$$opts{path}/$args{out}") or error("$$opts{path}/$args{out}: $!");
print $fh $out;
close($fh);
my ($ret,$out) = _cmd("diff -q $$opts{path}/$args{out} $$opts{path}/$args{out}.old");
if ( !$ret && $out eq '' ) { unlink("$$opts{path}/$args{out}.old"); }
else
{
print "\tthe expected output changed, saving:\n";
print "\t old .. $$opts{path}/$args{out}.old\n";
print "\t new .. $$opts{path}/$args{out}\n";
}
}
my $exp = '';
if ( open(my $fh,'<',"$$opts{path}/$args{out}") )
{
my @exp = <$fh>;
$exp = join('',@exp);
close($fh);
}
elsif ( !$$opts{redo_outputs} ) { failed($opts,$test,"$$opts{path}/$args{out}: $!"); return; }
if ( $exp ne $out )
{
open(my $fh,'>',"$$opts{path}/$args{out}.new") or error("$$opts{path}/$args{out}.new");
print $fh $out;
close($fh);
if ( !-e "$$opts{path}/$args{out}" )
{
rename("$$opts{path}/$args{out}.new","$$opts{path}/$args{out}") or error("rename $$opts{path}/$args{out}.new $$opts{path}/$args{out}: $!");
print "\tthe file with expected output does not exist, creating new one:\n";
print "\t\t$$opts{path}/$args{out}\n";
}
else
{
failed($opts,$test,"The outputs differ:\n\t\t$$opts{path}/$args{out}\n\t\t$$opts{path}/$args{out}.new");
}
return;
}
passed($opts,$test);
}
sub failed
{
my ($opts,$test,$reason) = @_;
$$opts{nfailed}++;
if ( defined $reason ) { print "\n\t$reason"; }
print "\n.. failed ...\n\n";
}
sub passed
{
my ($opts,$test) = @_;
$$opts{nok}++;
print ".. ok\n\n";
}
sub is_file_newer
{
my ($afile,$bfile) = @_;
my (@astat) = stat($afile) or return 0;
my (@bstat) = stat($bfile) or return 0;
if ( $astat[9]>$bstat[9] ) { return 1 }
return 0;
}
# The tests --------------------------
sub test_vcf_api
{
my ($opts,%args) = @_;
test_cmd($opts,%args,cmd=>"$$opts{path}/test-vcf-api $$opts{tmp}/test-vcf-api.bcf");
}
sub test_vcf_sweep
{
my ($opts,%args) = @_;
test_cmd($opts,%args,cmd=>"$$opts{path}/test-vcf-sweep $$opts{tmp}/test-vcf-api.bcf");
}
|
