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Changeset 11:52c5e53aff28 (2013-01-02)

Previous changeset 10:f0bdf862ba39 (2012-12-31) Next changeset 12:4cbf6c6d2f2b (2013-01-17)

Commit message:
Revised perl wrapper.

modified:
flexbar.pl

diff -r f0bdf862ba39 -r 52c5e53aff28 flexbar.pl
--- a/flexbar.pl Mon Dec 31 18:40:01 2012 +0100
+++ b/flexbar.pl Wed Jan 02 12:54:28 2013 +0100

[

@@ -5,12 +5,10 @@
use warnings;
use strict;

-my $format  = pop @ARGV;
-my $folder  = pop @ARGV;
-my $id      = pop @ARGV;
-my $outFile = pop @ARGV;

-my $call = join " ", @ARGV;
+my ($outFile, $id, $folder, $format) = @ARGV[($#ARGV - 3) .. $#ARGV];
+
+my $call = join " ", @ARGV[0..($#ARGV - 4)];

system $call .' --target reads > '. $outFile and exit 1;

@@ -23,11 +21,13 @@
$fileType = $format    if /\.\w+fast\w$/;
$fileType = 'tabular'  if $fileType eq 'lengthdist';

+ my $file = $_;
+
s/_//g;

my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;

- rename $_, $name;
+ rename $file, $name;
rename $name, $folder;
}