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Patch for James 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4526 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-20 02:39:16 +00:00
parent f7ce18553e
commit c305b41da4
1 changed files with 3 additions and 3 deletions
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6
perl/createTranscriptToGenomicInfoTables.pl
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@ -42,11 +42,11 @@ open(UNSORTED, "< $unsorted_table") or die "can't open $unsorted_table: $!";
my $line = <UNSORTED>;
print SORTED "$line";
close(UNSORTED);
$cmd = "grep haplotypeReference -v $unsorted_table | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $ref.fai";
print SORTED `$cmd`;
close(SORTED);
$cmd = "grep haplotypeReference -v $unsorted_table | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $ref.fai >> $out";
system($cmd);
# clean up
unlink $unsorted_table;