pindel_merge_vcf_bam.pl - output threads

[keiranmraine]

Currently doesn't add helpers to output threads:

cgpPindel/perl/lib/Sanger/CGP/Pindel/OutputGen/BamUtil.pm

Line 41 in df1ee78

const my $BAMSORT => ' inputformat=%s outputformat=%s reference=%s | tee %s | md5sum -b - > %s';

cgpPindel/perl/lib/Sanger/CGP/Pindel/OutputGen/BamUtil.pm

Line 73 in df1ee78

$command .= sprintf $BAMSORT, 'sam', $aln_fmt, $ref, $aln_out, $aln_md5;

Minor improvement to overal runtime expected