Mercurial > repos > yutaka-saito > bsfcall
diff bsfcall_wrapper.pl @ 1:20930a8f700b
rename some files
author | yutaka-saito |
---|---|
date | Sun, 19 Apr 2015 22:39:26 +0900 |
parents | bsf-call_wrapper.pl@06f8460885ff |
children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bsfcall_wrapper.pl Sun Apr 19 22:39:26 2015 +0900 @@ -0,0 +1,51 @@ +#!/usr/bin/perl + +use strict; +use warnings; + +use FindBin; + +print STDOUT "The tool script is called with:\n", join(" ", ($0, @ARGV)), "\n\n"; + +my ($idx, $in) = ("", ""); +my $default_option = "-o bsf-call.out -W bsfwork"; + +my $tooldir = shift(@ARGV); +$tooldir = $FindBin::Bin; +$ENV{PATH} = "$tooldir/bin:" . $ENV{PATH}; +my $reference_source = shift(@ARGV); +my $read_end = shift(@ARGV); +my $gslot = shift(@ARGV); +#$idx = "$tooldir/data/chrX.sub.fa"; + +if ($reference_source eq "indexed") { + $idx = shift(@ARGV); +} +elsif ($reference_source eq "history") { + my $own = shift(@ARGV); + $idx = "reference.fa"; + &invoke_command("ln -s $own reference.fa"); +} +else { + die "never reach here\n"; +} + +if ($read_end eq "single-end") { + $in = shift(@ARGV); + &invoke_command("$tooldir/bin/bsf-call $default_option -p $gslot $idx $in"); +} +elsif ($read_end eq "paired-end") { + my $in1 = shift(@ARGV); + my $in2 = shift(@ARGV); + $in = $in1 . "," . $in2; + &invoke_command("$tooldir/bin/bsf-call $default_option -p $gslot $idx $in"); +} +else { + die "never reach here\n"; +} + +sub invoke_command { + my ($command) = @_; + print "invoking: $command\n"; + system($command); +}