Merge pull request #227 from wtsi-npg/devel

pull from devel to master to create release 6.31.0

Changes

@@ -1,6 +1,12 @@
 LIST OF CHANGES
 ---------------
 
+release 6.31.0
+ - Additional columns added to the iseq_product_metrics table to support
+   BGE library metrics reporting.
+ - Add columns to pac_bio_product_metrics to store tag level yield
+   related metrics and bring other tables up to date
+
 release 6.30.0
  - To help with detecting recent changes, add `last_changed` column
    to PacBio NPG tables and update relevant DBIx classes.

lib/WTSI/DNAP/Warehouse/Schema/Result/IseqProductMetric.pm

@@ -391,6 +391,13 @@ mate_mapped_defferent_chr_5 as percentage of all
   is_nullable: 1
   size: [5,2]
 
+=head2 mean_bait_target_coverage
+
+  data_type: 'float'
+  is_nullable: 1
+
+Mean coverage of the design target regions of a bait library (if used and known)
+
 =head2 verify_bam_id_average_depth
 
   data_type: 'float'
@@ -570,6 +577,30 @@ The coverage threshold used in the target perc target greater than depth calcula
 
 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 autosome target stats file
+
+=head2 target_autosome_length
+
+  data_type: 'bigint'
+  extra: {unsigned => 1}
+  is_nullable: 1
+
+The total length of the autosomes only target regions
+
+=head2 target_autosome_mapped_bases
+
+  data_type: 'bigint'
+  extra: {unsigned => 1}
+  is_nullable: 1
+
+The number of mapped bases passing the autosome target filters
+
 =head2 target_autosome_coverage_threshold
 
   data_type: 'integer'
@@ -871,6 +902,8 @@ __PACKAGE__->add_columns(
     is_nullable => 1,
     size => [5, 2],
   },
+  'mean_bait_target_coverage',
+  { data_type => 'float', is_nullable => 1 },
   'verify_bam_id_average_depth',
   {
     data_type => 'float',
@@ -927,6 +960,12 @@ __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_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',
@@ -1073,8 +1112,8 @@ __PACKAGE__->belongs_to(
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:35:44
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Rf7TGwVeXRjNW5a9wU8baQ
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-12-13 14:21:19
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:JGzaGF0Y9fdlAH5ZG6PYsA
 
 
 # You can replace this text with custom code or comments, and it will be preserved on regeneration

lib/WTSI/DNAP/Warehouse/Schema/Result/LabwareLocation.pm

@@ -68,6 +68,15 @@ Barcode associated with storage location
 
 Fully qualifed address of the nested location
 
+=head2 location_name
+
+  data_type: 'varchar'
+  default_value: (empty string)
+  is_nullable: 0
+  size: 255
+
+Name of location where labware is stored
+
 =head2 coordinate_position
 
   data_type: 'integer'
@@ -136,6 +145,8 @@ __PACKAGE__->add_columns(
   { data_type => 'varchar', is_nullable => 0, size => 255 },
   'full_location_address',
   { data_type => 'varchar', is_nullable => 0, size => 255 },
+  'location_name',
+  { data_type => 'varchar', default_value => '', is_nullable => 0, size => 255 },
   'coordinate_position',
   { data_type => 'integer', is_nullable => 1 },
   'coordinate_row',
@@ -196,8 +207,8 @@ __PACKAGE__->add_unique_constraint(
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-07-21 23:04:20
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:CRLExOSkBH1meg87TdA4+g
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2024-01-19 13:58:19
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:MlRPMXGHbVYnpWjeFULpXQ
 
 
 # You can replace this text with custom code or comments, and it will be preserved on regeneration

lib/WTSI/DNAP/Warehouse/Schema/Result/PacBioProductMetric.pm

@@ -79,6 +79,53 @@ Product id
 
 The final QC outcome of the product as 0(failed), 1(passed) or NULL
 
+=head2 hifi_read_bases
+
+  data_type: 'bigint'
+  extra: {unsigned => 1}
+  is_nullable: 1
+
+The number of HiFi bases
+
+=head2 hifi_num_reads
+
+  data_type: 'integer'
+  extra: {unsigned => 1}
+  is_nullable: 1
+
+The number of HiFi reads
+
+=head2 hifi_read_length_mean
+
+  data_type: 'integer'
+  extra: {unsigned => 1}
+  is_nullable: 1
+
+The mean HiFi read length
+
+=head2 barcode_quality_score_mean
+
+  data_type: 'smallint'
+  extra: {unsigned => 1}
+  is_nullable: 1
+
+The mean barcode HiFi quality score
+
+=head2 hifi_read_quality_mean
+
+  data_type: 'smallint'
+  extra: {unsigned => 1}
+  is_nullable: 1
+
+The mean HiFi base quality
+
+=head2 hifi_bases_percent
+
+  data_type: 'float'
+  is_nullable: 1
+
+The HiFi bases expressed as a percentage of the total HiFi bases
+
 =head2 last_changed
 
   data_type: 'datetime'
@@ -101,6 +148,18 @@ __PACKAGE__->add_columns(
   { data_type => 'char', is_nullable => 0, size => 64 },
   'qc',
   { data_type => 'tinyint', is_nullable => 1 },
+  'hifi_read_bases',
+  { data_type => 'bigint', extra => { unsigned => 1 }, is_nullable => 1 },
+  'hifi_num_reads',
+  { data_type => 'integer', extra => { unsigned => 1 }, is_nullable => 1 },
+  'hifi_read_length_mean',
+  { data_type => 'integer', extra => { unsigned => 1 }, is_nullable => 1 },
+  'barcode_quality_score_mean',
+  { data_type => 'smallint', extra => { unsigned => 1 }, is_nullable => 1 },
+  'hifi_read_quality_mean',
+  { data_type => 'smallint', extra => { unsigned => 1 }, is_nullable => 1 },
+  'hifi_bases_percent',
+  { data_type => 'float', is_nullable => 1 },
   'last_changed',
   {
     data_type => 'datetime',
@@ -191,8 +250,8 @@ __PACKAGE__->belongs_to(
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:47:29
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:hTT2fzNhcm/86YuT61o2Qw
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2024-01-19 13:58:19
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:CBgNobCW7fHYVGPcg8ToYQ
 
 use Carp;
 

scripts/update_schema_6.31.0.sql

@@ -0,0 +1,38 @@
+-- Add columns for metrics useful for BGE project.
+
+ALTER TABLE `iseq_product_metrics` \
+  ADD COLUMN `mean_bait_target_coverage` float DEFAULT NULL \
+    COMMENT 'Mean coverage of the design target regions of a bait library (if used and known)' \
+    AFTER `on_or_near_bait_percent`, \
+  ADD COLUMN `target_autosome_filter` varchar(30) DEFAULT NULL \
+    COMMENT 'Filter used to produce the autosome target stats file' \
+    AFTER `target_percent_gt_coverage_threshold`, \
+  ADD COLUMN `target_autosome_length` bigint unsigned DEFAULT NULL \
+    COMMENT 'The total length of the autosomes only target regions' \
+    AFTER `target_autosome_filter`, \
+  ADD COLUMN `target_autosome_mapped_bases` bigint unsigned DEFAULT NULL \
+    COMMENT 'The number of mapped bases passing the autosome target filters' \
+    AFTER `target_autosome_length`;
+
+
+-- Add columns to pac_bio_product_metrics to store tag level yield.
+
+ALTER TABLE `pac_bio_product_metrics` \
+  ADD COLUMN  `hifi_read_bases`  bigint unsigned DEFAULT NULL \
+    COMMENT 'The number of HiFi bases' \
+    AFTER `qc`, \
+  ADD COLUMN  `hifi_num_reads` int unsigned DEFAULT NULL \
+    COMMENT 'The number of HiFi reads' \
+    AFTER `hifi_read_bases`, \
+  ADD COLUMN  `hifi_read_length_mean` int unsigned DEFAULT NULL \
+    COMMENT 'The mean HiFi read length' \
+    AFTER `hifi_num_reads`, \
+  ADD COLUMN  `hifi_read_quality_mean` smallint unsigned DEFAULT NULL \
+    COMMENT 'The mean HiFi base quality' \
+    AFTER  `hifi_read_length_mean`, \
+  ADD COLUMN  `hifi_bases_percent` float DEFAULT NULL \
+    COMMENT 'The HiFi bases expressed as a percentage of the total HiFi bases' \
+    AFTER  `hifi_read_quality_mean`, \
+  ADD COLUMN  `barcode_quality_score_mean` smallint unsigned DEFAULT NULL \
+    COMMENT 'The mean barcode HiFi quality score' \
+    AFTER `hifi_read_length_mean`;