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increase coverage cap for picard_collecthsmetrics
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@jemten
jemten committed Nov 24, 2022
1 parent 5cd0569 commit 0148fb8
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Showing 3 changed files with 53 additions and 57 deletions.
1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
- Set default annotation overlap for structural variants to 0.5 (previously 0.8), due to change in TIDDIT
- Turn on Stringtie and gffcompare by default
- Run varg on research vcf
- Increase max for coverage calculation to 500x

### Tools

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98 changes: 45 additions & 53 deletions lib/MIP/Program/Picardtools.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@ BEGIN {
}

Readonly my $BASE_COMMAND => q{picard};
Readonly my $MAX_COVERAGE => 500;

sub picardtools_addorreplacereadgroups {

Expand Down Expand Up @@ -149,11 +150,9 @@ sub picardtools_addorreplacereadgroups {
store => \$readgroup_sample,
strict_type => 1,
},
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append =>
{ store => \$stderrfile_path_append, strict_type => 1, },

temp_directory => { store => \$temp_directory, strict_type => 1, },
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
temp_directory => { store => \$temp_directory, strict_type => 1, },
};

check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
Expand Down Expand Up @@ -269,8 +268,7 @@ sub picardtools_base {

my @commands = @{$commands_ref};

unshift @commands,
( get_executable_base_command( { base_command => $BASE_COMMAND, } ), );
unshift @commands, ( get_executable_base_command( { base_command => $BASE_COMMAND, } ), );

if ( $create_index ne q{false} ) {

Expand Down Expand Up @@ -347,10 +345,9 @@ sub picardtools_bedtointervallist {
store => \$sequence_dictionary,
strict_type => 1,
},
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append =>
{ store => \$stderrfile_path_append, strict_type => 1, },
temp_directory => { store => \$temp_directory, strict_type => 1, },
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
temp_directory => { store => \$temp_directory, strict_type => 1, },
};

check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
Expand Down Expand Up @@ -653,8 +650,7 @@ sub picardtools_intervallisttools {
}

## Infile
push @commands, q{-INPUT} . $SPACE . join $SPACE . q{-INPUT} . $SPACE,
@{$infile_paths_ref};
push @commands, q{-INPUT} . $SPACE . join $SPACE . q{-INPUT} . $SPACE, @{$infile_paths_ref};

## Output
push @commands, q{-OUTPUT} . $SPACE . $outfile_path;
Expand Down Expand Up @@ -748,12 +744,11 @@ sub picardtools_mergesamfiles {
store => \$referencefile_path,
strict_type => 1,
},
regionsfile_path => { store => \$regionsfile_path, strict_type => 1, },
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append =>
{ store => \$stderrfile_path_append, strict_type => 1, },
temp_directory => { store => \$temp_directory, strict_type => 1, },
threading => {
regionsfile_path => { store => \$regionsfile_path, strict_type => 1, },
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
temp_directory => { store => \$temp_directory, strict_type => 1, },
threading => {
allow => [qw{ true false }],
store => \$threading,
strict_type => 1,
Expand Down Expand Up @@ -798,8 +793,7 @@ sub picardtools_mergesamfiles {
}

## Infile
push @commands, q{-INPUT} . $SPACE . join $SPACE . q{-INPUT} . $SPACE,
@{$infile_paths_ref};
push @commands, q{-INPUT} . $SPACE . join $SPACE . q{-INPUT} . $SPACE, @{$infile_paths_ref};

## Output
push @commands, q{-OUTPUT} . $SPACE . $outfile_path;
Expand Down Expand Up @@ -911,10 +905,9 @@ sub picardtools_markduplicates {
store => \$referencefile_path,
strict_type => 1,
},
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append =>
{ store => \$stderrfile_path_append, strict_type => 1, },
temp_directory => { store => \$temp_directory, strict_type => 1, },
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
temp_directory => { store => \$temp_directory, strict_type => 1, },
};

check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
Expand Down Expand Up @@ -954,13 +947,11 @@ sub picardtools_markduplicates {
}
if ($optical_duplicate_distance) {

push @commands,
q{-OPTICAL_DUPLICATE_PIXEL_DISTANCE} . $SPACE . $optical_duplicate_distance;
push @commands, q{-OPTICAL_DUPLICATE_PIXEL_DISTANCE} . $SPACE . $optical_duplicate_distance;
}

## Infile
push @commands, q{-INPUT} . $SPACE . join $SPACE . q{-INPUT} . $SPACE,
@{$infile_paths_ref};
push @commands, q{-INPUT} . $SPACE . join $SPACE . q{-INPUT} . $SPACE, @{$infile_paths_ref};

## Output
push @commands, q{-OUTPUT} . $SPACE . $outfile_path;
Expand Down Expand Up @@ -1051,10 +1042,9 @@ sub picardtools_gatherbamfiles {
store => \$referencefile_path,
strict_type => 1,
},
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append =>
{ store => \$stderrfile_path_append, strict_type => 1, },
temp_directory => { store => \$temp_directory, strict_type => 1, },
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
temp_directory => { store => \$temp_directory, strict_type => 1, },
};

check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
Expand Down Expand Up @@ -1089,8 +1079,7 @@ sub picardtools_gatherbamfiles {
);

## Infile
push @commands, q{-INPUT} . $SPACE . join $SPACE . q{-INPUT} . $SPACE,
@{$infile_paths_ref};
push @commands, q{-INPUT} . $SPACE . join $SPACE . q{-INPUT} . $SPACE, @{$infile_paths_ref};

## Output
push @commands, q{-OUTPUT} . $SPACE . $outfile_path;
Expand Down Expand Up @@ -1180,10 +1169,9 @@ sub picardtools_collectmultiplemetrics {
store => \$referencefile_path,
strict_type => 1,
},
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append =>
{ store => \$stderrfile_path_append, strict_type => 1, },
temp_directory => { store => \$temp_directory, strict_type => 1, },
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
temp_directory => { store => \$temp_directory, strict_type => 1, },
};

check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
Expand Down Expand Up @@ -1246,6 +1234,7 @@ sub picardtools_collecthsmetrics {
## Function : Perl wrapper for writing picardtools collecthsmetrics recipe to $filehandle. Based on picardtools 2.20.7.
## Returns : @commands
## Arguments: $bait_interval_file_paths_ref => Interval list file(s) that contains the locations of the baits used {REF}
## : $coverage_cap => Coverage cap for sensitivity calculations, Picard default: 200
## : $create_index => Create index
## : $filehandle => Sbatch filehandle to write to
## : $infile_path => Infile paths
Expand Down Expand Up @@ -1274,6 +1263,7 @@ sub picardtools_collecthsmetrics {
my $temp_directory;

## Default(s)
my $coverage_cap;
my $create_index;
my $java_use_large_pages;

Expand All @@ -1285,6 +1275,12 @@ sub picardtools_collecthsmetrics {
store => \$bait_interval_file_paths_ref,
strict_type => 1,
},
coverage_cap => {
allow => qr/ \A \d+ \z /xms,
default => $MAX_COVERAGE,
store => \$coverage_cap,
strict_type => 1,
},
create_index => {
allow => [qw{ true false }],
default => q{false},
Expand Down Expand Up @@ -1318,9 +1314,8 @@ sub picardtools_collecthsmetrics {
store => \$referencefile_path,
strict_type => 1,
},
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append =>
{ store => \$stderrfile_path_append, strict_type => 1, },
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
target_interval_file_paths_ref => {
default => [],
defined => 1,
Expand Down Expand Up @@ -1371,6 +1366,8 @@ sub picardtools_collecthsmetrics {
q{-TARGET_INTERVALS} . $SPACE . join $SPACE . q{-TARGET_INTERVALS} . $SPACE,
@{$target_interval_file_paths_ref};

push @commands, q{-COVERAGE_CAP} . $SPACE . $coverage_cap;

## Infile
push @commands, q{-INPUT} . $SPACE . $infile_path;

Expand Down Expand Up @@ -1507,8 +1504,7 @@ sub picardtools_sortvcf {
push @commands, q{-SEQUENCE_DICTIONARY} . $SPACE . $sequence_dictionary;

## Infile
push @commands, q{-INPUT} . $SPACE . join $SPACE . q{-INPUT} . $SPACE,
@{$infile_paths_ref};
push @commands, q{-INPUT} . $SPACE . join $SPACE . q{-INPUT} . $SPACE, @{$infile_paths_ref};

## Output
push @commands, q{-OUTPUT} . $SPACE . $outfile_path;
Expand Down Expand Up @@ -1589,8 +1585,7 @@ sub sort_vcf {
filehandle => $filehandle,
infile_paths_ref => \@{$infile_paths_ref},
java_use_large_pages => $active_parameter_href->{java_use_large_pages},
java_jar =>
catfile( $active_parameter_href->{picardtools_path}, q{picard.jar} ),
java_jar => catfile( $active_parameter_href->{picardtools_path}, q{picard.jar} ),
memory_allocation => q{Xmx4g},
outfile_path => $outfile,
referencefile_path => $active_parameter_href->{human_genome_reference},
Expand Down Expand Up @@ -1680,9 +1675,7 @@ sub picardtools_collectrnaseqmetrics {
strict_type => 1,
},
strand_specificity => {
allow => [
qw{ FIRST_READ_TRANSCRIPTION_STRAND NONE SECOND_READ_TRANSCRIPTION_STRAND }
],
allow => [qw{ FIRST_READ_TRANSCRIPTION_STRAND NONE SECOND_READ_TRANSCRIPTION_STRAND }],
required => 1,
store => \$strand_specificity,
strict_type => 1,
Expand Down Expand Up @@ -1812,10 +1805,9 @@ sub picardtools_updatevcfsequencedictionary {
store => \$sequence_dictionary,
strict_type => 1,
},
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append =>
{ store => \$stderrfile_path_append, strict_type => 1, },
temp_directory => { store => \$temp_directory, strict_type => 1, },
stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
temp_directory => { store => \$temp_directory, strict_type => 1, },
};

check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
Expand Down
11 changes: 7 additions & 4 deletions t/picardtools_collecthsmetrics.t
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Original file line number Diff line number Diff line change
Expand Up @@ -22,16 +22,13 @@ use Readonly;
use lib catdir( dirname($Bin), q{lib} );
use MIP::Constants qw{ $COMMA $SPACE };


BEGIN {

use MIP::Test::Fixtures qw{ test_import };

### Check all internal dependency modules and imports
## Modules with import
my %perl_module = (
q{MIP::Program::Picardtools} => [qw{ picardtools_collecthsmetrics }],
);
my %perl_module = ( q{MIP::Program::Picardtools} => [qw{ picardtools_collecthsmetrics }], );

test_import( { perl_module_href => \%perl_module, } );
}
Expand All @@ -47,6 +44,8 @@ diag( q{Test picardtools_collecthsmetrics from Picardtools.pm}
. $SPACE
. $EXECUTABLE_NAME );

Readonly my $MAX_COVERAGE => 500;

## Base arguments
my @function_base_commands = qw{ picard CollectHsMetrics };

Expand Down Expand Up @@ -99,6 +98,10 @@ my %specific_argument = (
. $SPACE
. catfile(qw{ indirectory exome_padded_interval_list_1 }),
},
coverage_cap => {
input => $MAX_COVERAGE,
expected_output => q{-COVERAGE_CAP} . $SPACE . $MAX_COVERAGE,
},
target_interval_file_paths_ref => {
inputs_ref => [ catfile(qw{ indirectory exome_interval_list_1 }) ],
expected_output => q{-TARGET_INTERVALS}
Expand Down

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