Mercurial > repos > yutaka-saito > bsfcall

comparison bsf-call_wrapper.pl @ 0:06f8460885ff

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author yutaka-saito
date Sun, 19 Apr 2015 20:51:13 +0900
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-1:000000000000 0:06f8460885ff
1 #!/usr/bin/perl
2
3 use strict;
4 use warnings;
5
6 use FindBin;
7
8 print STDOUT "The tool script is called with:\n", join(" ", ($0, @ARGV)), "\n\n";
9
10 my ($idx, $in) = ("", "");
11 my $default_option = "-o bsf-call.out -W bsfwork";
12
13 my $tooldir = shift(@ARGV);
14 $tooldir = $FindBin::Bin;
15 $ENV{PATH} = "$tooldir/bin:" . $ENV{PATH};
16 my $reference_source = shift(@ARGV);
17 my $read_end = shift(@ARGV);
18 my $gslot = shift(@ARGV);
19 #$idx = "$tooldir/data/chrX.sub.fa";
20
21 if ($reference_source eq "indexed") {
22 $idx = shift(@ARGV);
23 }
24 elsif ($reference_source eq "history") {
25 my $own = shift(@ARGV);
26 $idx = "reference.fa";
27 &invoke_command("ln -s $own reference.fa");
28 }
29 else {
30 die "never reach here\n";
31 }
32
33 if ($read_end eq "single-end") {
34 $in = shift(@ARGV);
35 &invoke_command("$tooldir/bin/bsf-call $default_option -p $gslot $idx $in");
36 }
37 elsif ($read_end eq "paired-end") {
38 my $in1 = shift(@ARGV);
39 my $in2 = shift(@ARGV);
40 $in = $in1 . "," . $in2;
41 &invoke_command("$tooldir/bin/bsf-call $default_option -p $gslot $idx $in");
42 }
43 else {
44 die "never reach here\n";
45 }
46
47 sub invoke_command {
48 my ($command) = @_;
49 print "invoking: $command\n";
50 system($command);
51 }