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bamcheck fix for projects with -d or -t in their path #16

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bamcheck fix for projects with -d or -t in their path #16

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25 changes: 19 additions & 6 deletions modules/VRPipe/Steps/bamcheck.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -44,14 +44,18 @@ class VRPipe::Steps::bamcheck with VRPipe::StepRole {
default_value => 'bamcheck'
),
bamcheck_options => VRPipe::StepOption->create(
description => 'options to bamcheck, excluding -r and -t (which are set by reference_fasta and exome_targets_file options)',
description => 'options to bamcheck, excluding -r, -t and -d (which are set by reference_fasta, exome_targets_file options and exclude_duplicates)',
optional => 1
),
reference_fasta => VRPipe::StepOption->create(description => 'absolute path to genome reference file'),
exome_targets_file => VRPipe::StepOption->create(
description => 'absolute path to a file describing the targets/baits used for exome pulldown (tab-delimited [chr,start,end], where start is 1-based, and end is inclusive)',
optional => 1
)
),
exclude_duplicates => VRPipe::StepOption->create(
description => 'exclude reads marked as duplicated from the calculated statistics',
optional => 1
),
};
}

Expand All @@ -66,13 +70,18 @@ class VRPipe::Steps::bamcheck with VRPipe::StepRole {
my $options = $self->options;
my $bamcheck_exe = $options->{bamcheck_exe};
my $opts = VRPipe::Steps::bamcheck->get_bamcheck_options($options);
my $targeted = 0;
my $dups = 0;
$targeted = 1 if exists($options->{exome_targets_file}) && $options->{exome_targets_file};
$dups = 1 if exists($options->{exclude_duplicates}) && $options->{exclude_duplicates};

my $req = $self->new_requirements(memory => 500, time => 1);
foreach my $bam_file (@{ $self->inputs->{bam_files} }) {
my $ifile = $bam_file->path;
my $check_file = $self->output_file(output_key => 'bamcheck_files', basename => $ifile->basename . '.bamcheck', type => 'txt');
my $ofile = $check_file->path;
$self->dispatch_wrapped_cmd('VRPipe::Steps::bamcheck', 'stats_from_bamcheck', ["$bamcheck_exe $opts $ifile > $ofile", $req, { output_files => [$check_file] }]);
my $cmd = qq[use VRPipe::Steps::bamcheck; VRPipe::Steps::bamcheck->stats_from_bamcheck('$bamcheck_exe $opts $ifile > $ofile', $targeted, $dups);];
$self->dispatch_vrpipecode($cmd, $req, { output_files => [$check_file] });
}
};
}
Expand Down Expand Up @@ -114,6 +123,10 @@ class VRPipe::Steps::bamcheck with VRPipe::StepRole {
$self->throw("exome_targets_file must be an absolute path") unless $targets->is_absolute;
$opts .= ' -t ' . $targets;
}
my $dups = $options->{exclude_duplicates};
if ($dups) {
$opts .= ' -d';
}

my $user_opts = $options->{bamcheck_options};
if ($user_opts) {
Expand All @@ -127,7 +140,7 @@ class VRPipe::Steps::bamcheck with VRPipe::StepRole {
return $opts;
}

method stats_from_bamcheck (ClassName|Object $self: Str $cmd_line) {
method stats_from_bamcheck (ClassName|Object $self: Str $cmd_line!, Bool $targeted, Bool $dups) {
my ($bam_path, $check_path) = $cmd_line =~ / (\S+) > (\S+)$/;
$bam_path || $self->throw("bad cmd line [$cmd_line]");
my $bam_file = VRPipe::File->get(path => $bam_path);
Expand All @@ -145,10 +158,10 @@ class VRPipe::Steps::bamcheck with VRPipe::StepRole {
$check_file->disconnect;

my $hash_key_prefix = '';
if ($cmd_line =~ /-d/) {
if ($dups) {
$hash_key_prefix = 'rmdup_';
}
elsif ($cmd_line =~ /-t/) {
elsif ($targeted) {
$hash_key_prefix = 'targeted_';
}

Expand Down