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LIST OF CHANGES
---------------
release 6.12.0
- a new iseq_product_ampliconstats table to store per sample
per amplicon statistics that is generated by 'samtools
ampliconstats'
release 6.11.0
- iseq_heron_product_metrics table:
set index on the id_run column,
add pp_name and pp_version columns to capture info
about the pipeline, which generated the data
release 6.10.0
- add id_run column to the iseq_heron_product_metrics table
- to allow for deletion of iseq_product_metrica rows, drop
the foreign key constraint on the id_iseq_product column in
the iseq_heron_product_metrics table, keep the relation
definition in the DBIx class
- update the DBIx class for the cgap_heron table
release 6.9.0
- ml warehouse LIMS drivers - define additional delegated
to sample objects methods
- DBIx class for a new iseq_heron_product_metrics table
- DBIx classes updates for latest changes in ml warehouse database
release 6.8.0
- capture latest changes/additions in ml warehouse database
release 6.7.0
- PSD added pac_bio_run_name field to pac_bio_run table to support
runs being created in traction as well as SequenceScape LIMs
- iseq_product_metrics table - a new column to store the outcome
of product uqc
- iseq_external_product_metrics - a new column to store product
destination
- iseq_run_lane_metrics table - added columns to store per-lane
Illumina InterOp data
release 6.6.0
- add instrument_external_name column to the iseq_run_lane_metrics
table
release 6.5.0
- more detailed comments for some columns.
- 'annotation' column reduced to 15 chars since it's not free text
- added columns for whole genome yield and end of phase2 analysis
date
- fixed spelling in one of the columns, ie changed column name
from archive_conformation_date to archive_confirmation_date
release 6.4.0
- iseq_external_product_component table redesign to allow for
rows on iseq_product_metrics table to be deleted and recreated
without making data in the linking table invalid
- yield column in the iseq_external_product_component table changed
from integer to float to correctly accommodate source data
- code to creating rows in the iseq_external_product_component table,
which will be run on row creation the and sometimes on row update
for rows of the iseq_external_product_metrics table; this code will
also be used to create a backlog of linking rows for existing
iseq_external_product_metrics table rows
release 6.3.0
- table update for iseq_external_product_metrics:
drops id_iseq_pr_metrics_tmp and a foreign key based on it
since maintenence will be difficult,
adds index on id_iseq_product to enable using this column
in joining to iseq_product_metrics table on a similar column,
adds an indexed id_run column in case stats by run is needed
- insert and update DBIx IseqExternalProductMetric class
customisation to ensure that composition data and id_run
columns are filled in
release 6.2.1
- nrd_assessment column comment update: include 'NA' as a valid value
release 6.2
- update definition of iseq_external_product_metric table
- fastqc columns become varchars
- rename column qc to qc_overall_assessment
- new column qc_status
- update DBIx classes to match new table definition
release 6.1
- update DBIx classes from prod database
- update definition of iseq_external_product_metric table
release 6.0
- add new tables for externally processed data
releaes 5.1
- allow to store longer composition JSON strings in the iseq_product_metrics
table
release 5.0
- added target autosome fields to iseq_product_metrics
- added DBIx binding for the bmap_flowcell table for the
BioNano Saphyr instrument
release 4.0
- iseq_product_metrics table: make id_iseq_product column not nullable,
set unique constraint on it
- a new table iseq_product_components - linking table for product records
in iseq_product_metrics
release 3.1
- add column 'nrd_percent' for non-reference discordance to the
'iseq_product_metrics' table
release 3.0
- 'last_changed' columns added to both 'iseq_product_metrics' and
'iseq_run_lane_metrics' tables
- 'workflow_type' and 'instrument_side' columns added to the
'iseq_run_lane_metrics' table
- 'qc_seq' column addedto the 'iseq_run_lane_metrics' table
- redundant 'iseq_pm_run_index' indexed dropped from 'iseq_product_metrics'
table
- changes to enable saving results for merged entities to'iseq_product_metrics':
NOT NULL constraint dropped from 'id_run' and 'position' columns;
nullable 'id_iseq_product' column added to save composition digest;
nullable 'iseq_composition_tmp' added to save a short form of composition
JSON, needed because we do not have the linking table yet
release 2.11
- added metric column to iseq_product_metrics for RNA: MT expression in pct of TPM.
- add target fields to iseq_product_metrics
release 2.10
- added metrics columns to iseq_product_metrics for GbS
release 2.9
- added metrics columns to iseq_product_metrics (for RNA)
- superfluous database indexes dropped
- DBIx schema update for primer_panel
- added columns tag_hops_percent and tag_hops_power to iseq_run_lane_metrics table
release 2.8
- added DBIx binding for oseq_flowcell table (describes LIMS info for ONT)
- Travis build - for Perl v 5.22 change to interpreter with threaded support
release 2.7
- DBIx binding update
release 2.6
- ensure lists of study users email addresses do not contain empty or undefined entries
release 2.5
- add column run_priority to iseq_run_lane_metrics table
release 2.4
- change in use of cycles value; expected_cycles calculated from iseq_flowcell read lengths and length of tag sequence(s).
release 2.3
- library_type added to LibraryDigest entity
release 2.2
- DBIx schema update
release 2.1
- small change to LibraryDigest to support non SS tracked libraries.
- use custom build base class to get correct version in a distribution
- Travis tweaks
+ add deployment to GitHub Releases
+ add newer 5.22 Perl to travis build matrix and allow container builds (sudo false)
release 2.0
- update to test script and data for filters in LibraryDigest
- added DBIx class for the new pacbio LIMs data table
release 1.8
- parameterized WTSI::DNAP::Warehouse::Schema::Query::IseqFlowcell role
to allow for query on run id
- iseq_product_metrics table: add columns to store in-house qc values
release 1.7
- extend field size for mean_bait_coverage RT#495558, Change request No6
release 1.6
- change the comment on iseq_run_lane_metrics.unexpected_tags_percent
- update DBIx schema to reflect this change and propagate any changes
to other tables of the live database
release 1.5
- Ability to query by id_study_lims in LibraryDigest
- Added unexpected tag and chimeric fields to iseq_product_metric and iseq_run_lane_metric tables
- Ability to restrict by (legacy) library id
- Added extra fields to entity which are needed by library merging script for adding to iRODS meta data.
Key changed to included cycle count as well as paired_flag. Corresponding test updated.
release 1.4
- update DBIx binding to include second index sequence
- check that flowcell LIMs id and barcode map 1:1 (RT#481156)
release 1.3
- mapping for additional lims interface fields for sample data
release 1.2
- value of the GCLP data lims flag has changed - reflect this
release 1.1
- bug fix in readonly variable declaration
release 1.0
- DBIx schema update following database schema changes
- contains_human_dna and contaminated_human_dna columns have been converted
from varchar to tinyint, inflators/deflators for these columns dropped
release 0.7
- new module - library digest - retrieves information about libraries,
groups it either by library or by sample
release 0.6
- added a role providing methods to determine what LIMs system the record originated from
release 0.5
- ensure contains_human_dna and contaminated_human_dna behave in a boolean manner
- update mapping of library_id lims field to database fields
- ensure missing study link does not lead to code failure when accessing e-mails of followers, etc.
- add mapping for lane_id
release 0.4
- following db schema changes, update the DBIx binding
release 0.3
- added WTSI::DNAP::Warehouse::Schema::Query::IseqFlowcell - a role for querying
the flowcell table knowing one of flowcell identifies
- DBIx object for flowcell row: fields neccessary for NPG lims interface
added
release 0.2
- foreign key into the flowcell table dropped from the run lane metrics table
- a few autoqc results columns dropped from the run lane metrics table
- extra column for verify_bam_id results added to the product metrics table
- columns for modality of the insert size results added to the product metrics table
release 0.1
- initial release