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Merge pull request wtsi-npg#857 from wtsi-npg/devel
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pull from devel to master to create release 72.0.1
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@jmtcsngr
jmtcsngr authored Feb 22, 2024
2 parents e021f08 + 33c55cd commit d9fa1e0
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8 changes: 8 additions & 0 deletions Changes
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@@ -1,5 +1,13 @@
LIST OF CHANGES FOR NPG-QC PACKAGE

release 72.0.1
- Ensured that retrieving values from a partially defined pulldown_metrics
result does not trigger an error. Added a test to demonstrate that such
result can be loaded to the database without problems.
- Updated the SeqQC summary display for pulldown_metrics incomplete results
so that just 'n/a' is displayed.
- autoqc rna seqqc max memory hardcoded limit increased to 8000MB

release 72.0.0

- QC View sorting order to put merged lanes before unmerged.
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1 change: 1 addition & 0 deletions MANIFEST
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Expand Up @@ -465,6 +465,7 @@ t/data/autoqc/pulldown_metrics/pdm.out
t/data/autoqc/pulldown_metrics/samplesheet_pulldown.csv
t/data/autoqc/pulldown_metrics/39193_3_14.pulldown_metrics.json
t/data/autoqc/pulldown_metrics/40739_2_29.pulldown_metrics.json
t/data/autoqc/pulldown_metrics/48367_2_2.pulldown_metrics.json
t/data/autoqc/qc/1937_3.map
t/data/autoqc/qX_yield/npg/instrument/15.xml
t/data/autoqc/qX_yield/npg/run/2549.xml
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2 changes: 1 addition & 1 deletion lib/npg_qc/autoqc/checks/rna_seqc.pm
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Expand Up @@ -302,7 +302,7 @@ sub _command {
if($self->ref_rrna){
$ref_rrna_option = q[-bwa ] . $self->bwa_rrna . q[ -BWArRNA ]. $self->ref_rrna;
}
my $command = $self->java_cmd. sprintf q[ -Xmx4000m -XX:+UseSerialGC -XX:-UsePerfData -jar %s -s %s -o %s -r %s -t %s -ttype %d %s %s],
my $command = $self->java_cmd. sprintf q[ -Xmx8000m -XX:+UseSerialGC -XX:-UsePerfData -jar %s -s %s -o %s -r %s -t %s -ttype %d %s %s],
$self->_java_jar_path,
$self->_input_str,
$self->rna_seqc_report_path,
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105 changes: 58 additions & 47 deletions lib/npg_qc/autoqc/role/pulldown_metrics.pm
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Expand Up @@ -6,7 +6,7 @@ use Readonly;
our $VERSION = '0';
## no critic (Documentation::RequirePodAtEnd)

Readonly::Scalar our $HUNDRED => 100;
Readonly::Scalar our $HUNDRED => 100;

=head1 NAME
Expand All @@ -27,28 +27,27 @@ npg_qc::autoqc::role::pulldown_metrics
=cut

sub criterion {
my $self = shift;

return q[Fail if on bait bases less than 20%];
}

=head2 bait_design_efficiency
Target territory / bait territory. 1 == perfectly efficient, 0.5 = half of baited bases are not target. BAIT_DESIGN_EFFICIENCY in Picard metrics.
Picard metrics BAIT_DESIGN_EFFICIENCY: target territory / bait territory.
1 == perfectly efficient, 0.5 = half of baited bases are not target.
=cut

sub bait_design_efficiency {
my $self = shift;
if ($self->bait_territory && defined $self->target_territory) {
return $self->target_territory/$self->bait_territory;
return $self->target_territory / $self->bait_territory;
}
return;
}

=head2 unique_reads_percent
unique_reads_num / total_reads_num, PCT_PF_UQ_READS in Picard metrics.
Picard metrics PCT_PF_UQ_READS: unique_reads_num / total_reads_num
=cut

Expand All @@ -69,106 +68,120 @@ sub unique_reads_percent {
sub unique_reads_aligned_percent {
my $self = shift;
if ($self->total_reads_num && defined $self->unique_reads_aligned_num) {
return ($self->unique_reads_aligned_num / $self->total_reads_num) * $HUNDRED;
return ($self->unique_reads_aligned_num /
$self->total_reads_num) * $HUNDRED;
}
return;
}

=head2 on_bait_reads_percent
Picard metrics:
PF_UQ_READS_ALIGNED_BAIT : The number of PF unique reads that are aligned overlapping a bait by >= 1bp
Picard metrics PF_UQ_READS_ALIGNED_BAIT:
The number of PF unique reads that are aligned overlapping a bait by >= 1bp
=cut

sub on_bait_reads_percent {
my $self = shift;

if ($self->total_reads_num && defined $self->other_metrics->{PF_UQ_READS_ALIGNED_BAIT}) {
return ($self->other_metrics->{PF_UQ_READS_ALIGNED_BAIT} / $self->total_reads_num) * $HUNDRED;
}
if (defined $self->other_metrics && $self->total_reads_num &&
defined $self->other_metrics->{PF_UQ_READS_ALIGNED_BAIT}) {
return ($self->other_metrics->{PF_UQ_READS_ALIGNED_BAIT} /
$self->total_reads_num) * $HUNDRED;
}
return;
}

=head2 near_bait_reads_percent
Picard metrics :
PF_UQ_READS_ALIGNED_NEAR_BAIT: The number of PF unique reads that dont overlap a bait but align within 250bp
of a bait.
Picard metrics PF_UQ_READS_ALIGNED_NEAR_BAIT:
The number of PF unique reads that dont overlap a bait but align within 250bp
of a bait.
=cut

sub near_bait_reads_percent {
my $self = shift;

if ($self->total_reads_num && defined $self->other_metrics->{PF_UQ_READS_ALIGNED_NEAR_BAIT}) {
return ($self->other_metrics->{PF_UQ_READS_ALIGNED_NEAR_BAIT} / $self->total_reads_num) * $HUNDRED;
if (defined $self->other_metrics && $self->total_reads_num &&
defined $self->other_metrics->{PF_UQ_READS_ALIGNED_NEAR_BAIT}) {
return ($self->other_metrics->{PF_UQ_READS_ALIGNED_NEAR_BAIT} /
$self->total_reads_num) * $HUNDRED;
}
return;
}

=head2 on_target_reads_percent
Picard metrics:
PF_UQ_READS_ALIGNED_TARGET: The number of PF unique reads that are aligned overlapping a target by >= 1bp
Picard metrics PF_UQ_READS_ALIGNED_TARGET:
The number of PF unique reads that are aligned overlapping a target by >= 1bp
=cut

sub on_target_reads_percent {
my $self = shift;

if ($self->total_reads_num && defined $self->other_metrics->{PF_UQ_READS_ALIGNED_TARGET}) {
return ($self->other_metrics->{PF_UQ_READS_ALIGNED_TARGET} / $self->total_reads_num) * $HUNDRED;
if (defined $self->other_metrics && $self->total_reads_num &&
defined $self->other_metrics->{PF_UQ_READS_ALIGNED_TARGET}) {
return ($self->other_metrics->{PF_UQ_READS_ALIGNED_TARGET} /
$self->total_reads_num) * $HUNDRED;
}
return;
}

=head2 selected_bases_percent
(on_bait_bases_num + near_bait_bases_num) / [PF_BASES, PCT_SELECTED_BASES] in Picard metrics.
(on_bait_bases_num + near_bait_bases_num) / [PF_BASES, PCT_SELECTED_BASES]
in Picard metrics.
=cut

sub selected_bases_percent {
my $self= shift;
if ($self->picard_version_base_count && defined $self->on_bait_bases_num && defined $self->near_bait_bases_num) {
return (($self->on_bait_bases_num + $self->near_bait_bases_num) / $self->picard_version_base_count) * $HUNDRED;
if ($self->picard_version_base_count && defined $self->on_bait_bases_num &&
defined $self->near_bait_bases_num) {
return (($self->on_bait_bases_num + $self->near_bait_bases_num) /
$self->picard_version_base_count) * $HUNDRED;
}
return;
}

=head2 on_bait_bases_percent
The percentage of aligned, de-duped, on-bait bases out of the PF bases available. PCT_USABLE_BASES_ON_BAIT in Picard metrics
The percentage of aligned, de-duped, on-bait bases out of the PF bases
available. PCT_USABLE_BASES_ON_BAIT in Picard metrics
=cut

sub on_bait_bases_percent {
my $self = shift;
if($self->picard_version_base_count && defined $self->on_bait_bases_num) {
return ($self->on_bait_bases_num / $self->picard_version_base_count) * $HUNDRED;
return ($self->on_bait_bases_num /
$self->picard_version_base_count) * $HUNDRED;
}
return;
}

=head2 near_bait_bases_percent
The percentage of aligned, de-duped, on-bait bases out of the PF bases available.
The percentage of aligned, de-duped, on-bait bases out of the PF bases
available.
=cut

sub near_bait_bases_percent {
my $self = shift;
if($self->picard_version_base_count && defined $self->near_bait_bases_num) {
return ($self->near_bait_bases_num / $self->picard_version_base_count) * $HUNDRED;
return ($self->near_bait_bases_num /
$self->picard_version_base_count) * $HUNDRED;
}
return;
}

=head2 off_bait_bases_percent
The percentage of aligned PF bases that mapped neither on or near a bait. PCT_OFF_BAIT in Picard metrics
The percentage of aligned PF bases that mapped neither on or near a bait.
PCT_OFF_BAIT in Picard metrics
=cut

Expand All @@ -182,7 +195,7 @@ sub off_bait_bases_percent {

=head2 on_bait_vs_selected_percent
ON_BAIT_VS_SELECTED in Picard metrics
ON_BAIT_VS_SELECTED in Picard metrics
=cut

Expand All @@ -199,14 +212,16 @@ sub on_bait_vs_selected_percent {

=head2 on_target_bases_percent
The percentage of aligned, de-duped, on-target bases out of the PF bases available. PCT_USABLE_BASES_ON_TARGET in Picard metrics
The percentage of aligned, de-duped, on-target bases out of the PF bases
available. PCT_USABLE_BASES_ON_TARGET in Picard metrics
=cut

sub on_target_bases_percent {
my $self = shift;
if ($self->picard_version_base_count && defined $self->on_target_bases_num) {
return ($self->on_target_bases_num / $self->picard_version_base_count) * $HUNDRED;
return ($self->on_target_bases_num /
$self->picard_version_base_count) * $HUNDRED;
}
return;
}
Expand All @@ -232,11 +247,10 @@ sub zero_coverage_targets_percent {
sub target_bases_coverage_percent {
my $self = shift;
my $tbc = {};
if ($self->other_metrics) {
my @keys = keys %{$self->other_metrics};
@keys = grep {/^PCT_TARGET_BASES/smx} @keys;
if (defined $self->other_metrics) {
my @keys = grep {/^PCT_TARGET_BASES/smx} keys %{$self->other_metrics};
foreach my $key (@keys) {
my ($coverage) = $key =~ /_(\d+)X/smx;
my ($coverage) = $key =~ /_(\d+)X/smx;
$tbc->{$coverage} = $self->other_metrics->{$key} * $HUNDRED;
}
}
Expand All @@ -246,8 +260,6 @@ sub target_bases_coverage_percent {
=head2 bait_bases_coverage_percent
Various increments between PCT_BAIT_BASES_1X and PCT_BAIT_BASES_1000X
to be stored in npgqc pulldown_metrics.other_metrics
Represents the fraction of bait bases with a depth of >= Nx
PCT_BAIT_BASES_2X
Expand All @@ -260,9 +272,8 @@ PCT_BAIT_BASES_30X
sub bait_bases_coverage_percent {
my $self = shift;
my $bbc = {};
if ($self->other_metrics) {
my @keys = keys %{$self->other_metrics};
@keys = grep {/^PCT_BAIT_BASES/smx} @keys;
if (defined $self->other_metrics) {
my @keys = grep {/^PCT_BAIT_BASES/smx} keys %{$self->other_metrics};
foreach my $key (@keys) {
# e.g. PCT_BAIT_BASES_30X
# multiply by a 100 as is not already a percentage, despite the name
Expand All @@ -271,7 +282,6 @@ sub bait_bases_coverage_percent {
}
}


return $bbc;
}

Expand All @@ -283,9 +293,8 @@ sub bait_bases_coverage_percent {
sub hs_penalty {
my $self = shift;
my $penalty = {};
if ($self->other_metrics) {
my @keys = keys %{$self->other_metrics};
@keys = grep {/^HS_PENALTY/smx} @keys;
if (defined $self->other_metrics) {
my @keys = grep {/^HS_PENALTY/smx} keys %{$self->other_metrics};
foreach my $key (@keys) {
my ($coverage) = $key =~ /_(\d+)X/smx;
$penalty->{$coverage} = $self->other_metrics->{$key};
Expand All @@ -309,7 +318,9 @@ PF_BASES instead.

sub picard_version_base_count {
my $self = shift;
return (exists $self->other_metrics->{PF_BASES}) ? $self->other_metrics->{PF_BASES} : $self->unique_bases_aligned_num;
return
(defined $self->other_metrics && exists $self->other_metrics->{PF_BASES})
? $self->other_metrics->{PF_BASES} : $self->unique_bases_aligned_num;
}


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6 changes: 5 additions & 1 deletion npg_qc_viewer/root/src/ui_lanes/lane.tt2
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Expand Up @@ -425,7 +425,7 @@ END
[% href='#pdmc_' _ result.id_run _ ':' _ result.position _ ':' _ result.tag_index %]

[%-
mcoverage = 0;
mcoverage;
IF result.unique_bases_aligned_num.defined && result.unique_bases_aligned_num != 0;
mcoverage = result.mean_target_coverage / (result.unique_bases_aligned_num / 1000000000);
END;
Expand All @@ -439,6 +439,7 @@ END
END;
coverage = result.target_bases_coverage_percent.20 ? result.target_bases_coverage_percent.20 : 0;
-%]
[% IF mcoverage.defined %]
[% IF result.interval_files_identical.defined && result.interval_files_identical == 1 %]
<span class="pdmc_na" title="Bait and target intervals identical"><a href="[% href %]">NA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;NA<br/></a></span>
<span class="dark_blue" title="On-bait bases %age"><a href="[% href %]">[% FILTER format('%2.2f');on_bait;END %]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a></span>
Expand All @@ -448,6 +449,9 @@ END
<span class="dark_blue" title="On-bait bases %age"><a href="[% href %]">[% FILTER format('%2.2f');on_bait;END %]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a></span>
<span class="dark_blue" title="On-target bases %age"><a href="[% href %]">[% FILTER format('%2.2f');on_target;END %]</a></span>
[% END %]
[% ELSE %]
n/a
[% END %]
[%- END -%]

[% BLOCK substitution_metrics -%]
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21 changes: 17 additions & 4 deletions t/60-autoqc-db_loader.t
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Expand Up @@ -875,17 +875,30 @@ subtest 'loading review and other results from path' => sub {
};

subtest 'loading partially defined results' => sub {
plan tests => 2;
plan tests => 4;

my $db = $db_helper->create_test_db(q[npg_qc::Schema], 't/data/fixtures');
my $db = $db_helper->create_test_db(q[npg_qc::Schema]);
my $db_loader = npg_qc::autoqc::db_loader->new(
path => ['t/data/autoqc/dbix_loader/short_results'],
schema => $db,
verbose => 0,
verbose => 0
);
lives_ok { $db_loader->load() } 'no error loading an incomplete result';
lives_ok { $db_loader->load() }
'no error loading an incomplete genotype result';
is ($db->resultset('Genotype')->search({})->count(), 1,
'one genotype record is created');

$db_loader = npg_qc::autoqc::db_loader->new(
json_file =>
['t/data/autoqc/pulldown_metrics/48367_2_2.pulldown_metrics.json'],
schema => $db,
verbose => 0
);
lives_ok { $db_loader->load() }
'no error loading an incomplete pulldown_metrics result';
is ($db->resultset('PulldownMetrics')->search({})->count(), 1,
'one genotype record is created');

};

1;
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