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Performance improvement - input step #100

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@keiranmraine

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@keiranmraine

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

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.

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