Merge pull request #620 from wtsi-npg/devel

prep for release 66.5

Build.PL

@@ -75,6 +75,7 @@ my $requires = {
                 'URI::Escape'                     => 0,
                 'Vcf'                             => 0,
 
+                'WTSI::DNAP::Utilities::Timestamp'         => 0,
                 'npg_common::Alignment'                    => 0,
                 'npg_common::extractor::fastq'             => 0,
                 'npg_common::roles::software_location'     => 0,
@@ -98,6 +99,7 @@ my $requires = {
                 'npg_tracking::illumina::runfolder'        => 0,
                 'npg_tracking::Schema'                     => 0,
                 'npg_tracking::util::abs_path'             => 0,
+                'npg_tracking::util::pipeline_config'      => 0,
                 'npg_tracking::util::types'                => 0,
                 'npg::util'                                => 0,
                 'st::api::base'                            => 0,

Changes

@@ -1,5 +1,13 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
+release 66.5
+ - update spatial_filter results parsing
+ - add target autosome stats to bam_flagstats qc check
+ - allow 'last_modified' date in mqc tables to be pre-set
+ - new autoqc check 'review' to evaluate results of other
+   checks against configurable criteria
+ - SeqQC: add a visual que for failed autoqc review results
+
 release 66.4
  - allow to finalise undecided library manual qc outcomes for
    all entities

MANIFEST

@@ -31,6 +31,7 @@ lib/npg_qc/autoqc/checks/insert_size.pm
 lib/npg_qc/autoqc/checks/pulldown_metrics.pm
 lib/npg_qc/autoqc/checks/qX_yield.pm
 lib/npg_qc/autoqc/checks/ref_match.pm
+lib/npg_qc/autoqc/checks/review.pm
 lib/npg_qc/autoqc/checks/rna_seqc.pm
 lib/npg_qc/autoqc/checks/samtools_stats.pm
 lib/npg_qc/autoqc/checks/sequence_error.pm
@@ -62,6 +63,7 @@ lib/npg_qc/autoqc/results/pulldown_metrics.pm
 lib/npg_qc/autoqc/results/qX_yield.pm
 lib/npg_qc/autoqc/results/ref_match.pm
 lib/npg_qc/autoqc/results/result.pm
+lib/npg_qc/autoqc/results/review.pm
 lib/npg_qc/autoqc/results/rna_seqc.pm
 lib/npg_qc/autoqc/results/samtools_stats.pm
 lib/npg_qc/autoqc/results/sequence_error.pm
@@ -207,6 +209,7 @@ t/60-autoqc-checks-insert_size.t
 t/60-autoqc-checks-pulldown_metrics.t
 t/60-autoqc-checks-qX_yield.t
 t/60-autoqc-checks-ref_match.t
+t/60-autoqc-checks-review.t
 t/60-autoqc-checks-rna_seqc.t
 t/60-autoqc-checks-sequence_error.t
 t/60-autoqc-checks-spatial_filter.t
@@ -236,6 +239,7 @@ t/60-autoqc-results-pulldown_metrics.t
 t/60-autoqc-results-qX_yield.t
 t/60-autoqc-results-ref_match.t
 t/60-autoqc-results-result.t
+t/60-autoqc-results-review.t
 t/60-autoqc-results-rna_seqc.t
 t/60-autoqc-results-samtools_stats.t
 t/60-autoqc-results-sequence_error.t
@@ -251,6 +255,8 @@ t/70-report-genotype_call.t
 t/80-autoqc-qc-script.t
 t/data/autoqc/bam_flagstats/16960_1_0.tar.gz
 t/data/autoqc/bam_flagstats/17448_1_9.tar.gz
+t/data/autoqc/bam_flagstats/25837_1_13.tar.gz
+t/data/autoqc/bam_flagstats/29006_8_1.tar.gz
 t/data/autoqc/bam_flagstats/24135_1#1.bam_flagstats.json
 t/data/autoqc/bam_flagstats/24135_1#1.flagstat
 t/data/autoqc/bam_flagstats/4783_5_bam_flagstats.json
@@ -470,6 +476,18 @@ t/data/autoqc/rendered/json_single_run/3612_7.insert_size.json
 t/data/autoqc/rendered/json_single_run/3612_7.qX_yield.json
 t/data/autoqc/rendered/json_single_run/3612_8.insert_size.json
 t/data/autoqc/rendered/json_single_run/3612_8.qX_yield.json
+t/data/autoqc/review/product_release.yml
+t/data/autoqc/review/samplesheet_27483.csv
+t/data/autoqc/review/samplesheet_29524.csv
+t/data/autoqc/review/29524#2.composition.json
+t/data/autoqc/review/29524#17.bam_flagstats.json
+t/data/autoqc/review/29524#2.bam_flagstats.json
+t/data/autoqc/review/29524#2.bcfstats.json
+t/data/autoqc/review/29524#2.qX_yield.json
+t/data/autoqc/review/29524#2.verify_bam_id.json
+t/data/autoqc/review/29524#2_phix.bam_flagstats.json
+t/data/autoqc/review/29524#3.bam_flagstats.json
+t/data/autoqc/review/29524#7.bam_flagstats.json
 t/data/autoqc/rna_seqc/data/17550_1#1.bam
 t/data/autoqc/rna_seqc/data/17550_3#8.bam
 t/data/autoqc/rna_seqc/samplesheet_17550.csv

lib/npg_qc/Schema/Mqc/OutcomeDict.pm

@@ -2,11 +2,15 @@ package npg_qc::Schema::Mqc::OutcomeDict;
 
 use Moose::Role;
 use Readonly;
+use Carp;
 
 our $VERSION = '0';
 
 Readonly::Scalar my $FINAL       => 'final';
 Readonly::Scalar my $PRELIMINARY => 'preliminary';
+Readonly::Scalar my $ACCEPTED    => 'Accepted';
+Readonly::Scalar my $REJECTED    => 'Rejected';
+Readonly::Scalar my $UNDECIDED   => 'Undecided';
 
 sub is_final_outcome_description {
   my ($self, $desc) = @_;
@@ -20,12 +24,12 @@ sub is_final_outcome {
 
 sub is_accepted {
   my $self = shift;
-  return $self->short_desc =~ /\AAccepted/smx; #The short description includes the word accepted.
+  return $self->short_desc =~ /\A $ACCEPTED/smx; #The short description includes the word accepted.
 }
 
 sub is_rejected {
   my $self = shift;
-  return $self->short_desc =~ /\ARejected/smx; #The short description includes the word rejected.
+  return $self->short_desc =~ /\A $REJECTED/smx; #The short description includes the word rejected.
 }
 
 sub is_final_accepted {
@@ -35,7 +39,7 @@ sub is_final_accepted {
 
 sub is_undecided {
   my $self = shift;
-  return $self->short_desc =~ /\AUndecided/smx;
+  return $self->short_desc =~ /\A $UNDECIDED/smx;
 }
 
 sub pk_value {
@@ -59,6 +63,19 @@ sub matching_final_short_desc {
   return $desc;
 }
 
+sub generate_short_description {
+  my ($self, $is_final, $is_accepted) = @_;
+
+  defined $is_final or croak 'Final flag should be defined';
+  my $decision = $is_accepted ? $ACCEPTED :
+        (defined $is_accepted ? $REJECTED : $UNDECIDED);
+  if (defined $is_accepted || $is_final) {
+    $decision .= q[ ] . ($is_final ? $FINAL : $PRELIMINARY);
+  }
+
+  return $decision;
+}
+
 no Moose::Role;
 
 1;
@@ -133,6 +150,32 @@ __END__
     print $dict_row->short_desc; # Rejected final
     print $dict_row->matching_final_short_desc(); # Rejected final
 
+=head2 generate_short_description
+
+  Package-level method for generating descriptions matching short
+  descriptions in the dictionary tables. Note that not every description
+  is available in all dictionary tables.
+
+    my $is_final = 1;
+    my $is_accepted = 1;
+
+    __PACKAGE__->generate_short_description($is_final, $is_accepted);
+    # returns 'Accepted final'
+
+    __PACKAGE__->generate_short_description($is_final);
+    # returns 'Undecided final'
+
+    $is_accepted = 0;
+    __PACKAGE__->generate_short_description($is_final);
+    # returns 'Rejected final'
+
+    $is_final = 0;
+    __PACKAGE__->generate_short_description($is_final, $is_accepted);
+    # returns 'Rejected preliminary'
+
+    __PACKAGE__->generate_short_description($is_final);
+    # returns 'Undecided' !!!
+
 =head1 DIAGNOSTICS
 
 =head1 CONFIGURATION AND ENVIRONMENT
@@ -145,6 +188,8 @@ __END__
 
 =item Readonly
 
+=item Carp
+
 =back
 
 =head1 INCOMPATIBILITIES
@@ -157,7 +202,7 @@ Jaime Tovar <lt>jmtc@sanger.ac.uk<gt>
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2017 Genome Research Ltd
+Copyright (C) 2019 Genome Research Ltd
 
 This file is part of NPG.
 

lib/npg_qc/Schema/Mqc/OutcomeEntity.pm

@@ -63,7 +63,9 @@ sub add_common_ent_methods {
 around [qw/update insert/] => sub {
   my $orig = shift;
   my $self = shift;
-  $self->last_modified($self->get_time_now);
+  if (!$self->is_column_changed('last_modified')) {
+    $self->last_modified($self->get_time_now);
+  }
   my $return_super = $self->$orig(@_);
   $self->_create_historic();
   return $return_super;

lib/npg_qc/Schema/Result/BamFlagstats.pm

@@ -264,6 +264,61 @@ The coverage threshold used in the perc target greater than depth calculation
 
 The percentage of the target covered at greater than the depth specified
 
+=head2 target_autosome_filter
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 30
+
+Filter used to produce the target autosome stats file
+
+=head2 target_autosome_length
+
+  data_type: 'bigint'
+  extra: {unsigned => 1}
+  is_nullable: 1
+
+The total length of the target autosome regions
+
+=head2 target_autosome_mapped_reads
+
+  data_type: 'bigint'
+  extra: {unsigned => 1}
+  is_nullable: 1
+
+The number of mapped reads passing the filter
+
+=head2 target_autosome_proper_pair_mapped_reads
+
+  data_type: 'bigint'
+  extra: {unsigned => 1}
+  is_nullable: 1
+
+The number of proper pair mapped reads passing the filter
+
+=head2 target_autosome_mapped_bases
+
+  data_type: 'bigint'
+  extra: {unsigned => 1}
+  is_nullable: 1
+
+The number of mapped bases passing the filter
+
+=head2 target_autosome_coverage_threshold
+
+  data_type: 'integer'
+  is_nullable: 1
+
+The coverage threshold used in the perc target autosome greater than depth calculation
+
+=head2 target_autosome_percent_gt_coverage_threshold
+
+  data_type: 'float'
+  is_nullable: 1
+  size: [5,2]
+
+The percentage of the target autosome covered at greater than the depth specified
+
 =cut
 
 __PACKAGE__->add_columns(
@@ -343,6 +398,20 @@ __PACKAGE__->add_columns(
   { data_type => 'integer', is_nullable => 1 },
   'target_percent_gt_coverage_threshold',
   { data_type => 'float', is_nullable => 1, size => [5, 2] },
+  'target_autosome_filter',
+  { data_type => 'varchar', is_nullable => 1, size => 30 },
+  'target_autosome_length',
+  { data_type => 'bigint', extra => { unsigned => 1 }, is_nullable => 1 },
+  'target_autosome_mapped_reads',
+  { data_type => 'bigint', extra => { unsigned => 1 }, is_nullable => 1 },
+  'target_autosome_proper_pair_mapped_reads',
+  { data_type => 'bigint', extra => { unsigned => 1 }, is_nullable => 1 },
+  'target_autosome_mapped_bases',
+  { data_type => 'bigint', extra => { unsigned => 1 }, is_nullable => 1 },
+  'target_autosome_coverage_threshold',
+  { data_type => 'integer', is_nullable => 1 },
+  'target_autosome_percent_gt_coverage_threshold',
+  { data_type => 'float', is_nullable => 1, size => [5, 2] },
 );
 
 =head1 PRIMARY KEY
@@ -408,8 +477,8 @@ __PACKAGE__->belongs_to(
 with 'npg_qc::Schema::Composition', 'npg_qc::Schema::Flators', 'npg_qc::autoqc::role::result', 'npg_qc::autoqc::role::bam_flagstats';
 
 
-# Created by DBIx::Class::Schema::Loader v0.07049 @ 2018-06-14 16:17:33
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:7FncD4g/I8dgGfG9B9a0CQ
+# Created by DBIx::Class::Schema::Loader v0.07049 @ 2019-04-17 14:56:54
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:YsrYNzYhK4jAltTpq12t+g
 
 
 # You can replace this text with custom code or comments, and it will be preserved on regeneration