diff --git a/Changes b/Changes index ae7a48c2..84d815b5 100644 --- a/Changes +++ b/Changes @@ -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. diff --git a/MANIFEST b/MANIFEST index af114f86..6a01731d 100644 --- a/MANIFEST +++ b/MANIFEST @@ -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 diff --git a/lib/npg_qc/autoqc/checks/rna_seqc.pm b/lib/npg_qc/autoqc/checks/rna_seqc.pm index 3096f692..0ce7cd18 100644 --- a/lib/npg_qc/autoqc/checks/rna_seqc.pm +++ b/lib/npg_qc/autoqc/checks/rna_seqc.pm @@ -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, diff --git a/lib/npg_qc/autoqc/role/pulldown_metrics.pm b/lib/npg_qc/autoqc/role/pulldown_metrics.pm index 962077b2..eb4bded5 100644 --- a/lib/npg_qc/autoqc/role/pulldown_metrics.pm +++ b/lib/npg_qc/autoqc/role/pulldown_metrics.pm @@ -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 @@ -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 @@ -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 @@ -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 @@ -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; } @@ -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; } } @@ -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 @@ -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 @@ -271,7 +282,6 @@ sub bait_bases_coverage_percent { } } - return $bbc; } @@ -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}; @@ -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; } diff --git a/npg_qc_viewer/root/src/ui_lanes/lane.tt2 b/npg_qc_viewer/root/src/ui_lanes/lane.tt2 index 53707e0c..52407fad 100644 --- a/npg_qc_viewer/root/src/ui_lanes/lane.tt2 +++ b/npg_qc_viewer/root/src/ui_lanes/lane.tt2 @@ -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; @@ -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 %] NA      NA
 [% FILTER format('%2.2f');on_bait;END %]       @@ -448,6 +449,9 @@ END [% FILTER format('%2.2f');on_bait;END %]       [% FILTER format('%2.2f');on_target;END %] [% END %] +[% ELSE %] +n/a +[% END %] [%- END -%] [% BLOCK substitution_metrics -%] diff --git a/t/60-autoqc-db_loader.t b/t/60-autoqc-db_loader.t index e90c75a7..cbe1c072 100644 --- a/t/60-autoqc-db_loader.t +++ b/t/60-autoqc-db_loader.t @@ -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; diff --git a/t/60-autoqc-results-pulldown_metrics.t b/t/60-autoqc-results-pulldown_metrics.t index ea895d03..e9c5a4a7 100644 --- a/t/60-autoqc-results-pulldown_metrics.t +++ b/t/60-autoqc-results-pulldown_metrics.t @@ -1,11 +1,6 @@ -######### -# Author: mg8 -# Created: 2 May 2012 -# - use strict; use warnings; -use Test::More tests => 10; +use Test::More tests => 11; use Test::Exception; use_ok ('npg_qc::autoqc::results::pulldown_metrics'); @@ -41,4 +36,31 @@ use_ok ('npg_qc::autoqc::results::pulldown_metrics'); cmp_ok(sprintf("%.1f", $pulldown->on_bait_bases_percent), '==', 61.0, 'Percentage on bait is calculated correctly'); } -1; \ No newline at end of file +subtest 'invoke methods for a partially defined result' => sub { + plan tests => 23; + + my $pulldown; + lives_ok { + $pulldown = npg_qc::autoqc::results::pulldown_metrics->load( + 't/data/autoqc/pulldown_metrics/48367_2_2.pulldown_metrics.json' + ); + } 'Load pulldown JSON with most data absent'; + for my $method (qw/ + bait_design_efficiency unique_reads_percent unique_reads_aligned_percent + on_bait_reads_percent near_bait_reads_percent on_target_reads_percent + selected_bases_percent on_bait_bases_percent near_bait_bases_percent + off_bait_bases_percent on_bait_vs_selected_percent + on_target_bases_percent zero_coverage_targets_percent + target_bases_coverage_percent bait_bases_coverage_percent + bait_bases_coverage_percent hs_penalty picard_version_base_count + /) { + my $value; + lives_ok { $value = $pulldown->$method } "no error invoking '$method'"; + if (defined $value) { + ok ((ref $value eq 'HASH') && (scalar keys %{$value} == 0), + q[if the value is defined, it's an empty hash]); + } + } +}; + +1; diff --git a/t/data/autoqc/pulldown_metrics/48367_2_2.pulldown_metrics.json b/t/data/autoqc/pulldown_metrics/48367_2_2.pulldown_metrics.json new file mode 100644 index 00000000..1f69beb0 --- /dev/null +++ b/t/data/autoqc/pulldown_metrics/48367_2_2.pulldown_metrics.json @@ -0,0 +1 @@ +{"__CLASS__":"npg_qc::autoqc::results::pulldown_metrics-71.1.0","comments":"Failed to find bait interval files in repository for TWIST Respiratory Virus Research Panel","composition":{"__CLASS__":"npg_tracking::glossary::composition-98.1.0","components":[{"__CLASS__":"npg_tracking::glossary::composition::component::illumina-98.1.0","id_run":48367,"position":2,"tag_index":2}]},"id_run":48367,"info":{"Check":"npg_qc::autoqc::checks::pulldown_metrics","Check_version":"71.1.0"},"pass":"0","position":2,"tag_index":2} \ No newline at end of file