Performance improvement - input step

[keiranmraine]

This section should be revised so that the "valid_seqs" are appended to the first samtools view command and filtered eariler:

BRASS/perl/lib/Sanger/CGP/Brass/Implement.pm

Lines 130 to 145 in 5f07ea5

	my $command = _which('samtools');
	$command .= ' view -F 3854 -q 6 -u '.$input;
	$command .= ' | ';
	$command .= _which('bedtools');
	$command .= sprintf $BED_INTERSECT_V, 'stdin', $options->{'depth'};
	$command .= ' | ';
	$command .= _which('bamcollate2');
	$command .= sprintf $BAMCOLLATE, $tmp, $index;
	$command .= ' | ';
	$command .= "$^X ";
	$command .= _which('brassI_prep_bam.pl');
	$command .= sprintf $PREP_BAM, $input.'.bas', $rg_prefix;
	$command .= " -i ".join(',', valid_seqs($options));
	$command .= ' | ';
	$command .= _which('bamsort');
	$command .= sprintf $BAMSORT, $tmp, $index, $outbam, $outbam, $outbam, $helper_threads, $helper_threads;

This has been tested previously in an abandoned branch.