70.0.1

• use bcftools mpileup instead of samtools for genotype QC check
• npg_substitution_metrics.pl avoid negative values and made metrics calculations more consistent

67.4.0

• bug fix for mqc skipper script which, because of filtering on
  study name always gave count of unique studies on a run as one
• bam_flagstats autoqc check - detect and parse samtools markdup metrics

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 66.0

• GUI for utility QC (inactive)
• add new bcfstats qc check + viewer change
• skip incomplete tag zero results in genotype_call POSTing to LIMs
• minor changes to genotype qc check to support checking against externally
  supplied genotypes instead if they exist
• handle target samtools stats file - parsing, archiving and viewing.
• queries to qc_store should always have support for tracking db look-up
• methods for loading autoqc results moved from npg_qc::autoqc::collection
  to npg_qc::autoqc::qc_store
• little-used method load_run of npg_qc::autoqc::qc_store class, which did
  not support propagation of tracking db handle, is removed
• unused public methods in npg_qc::autoqc namespace removed
• mqc outcomes API - a new method, get_library_outcomes, for retrieving
  library qc outcomes as boolean values
• deciding whether the entity is subject to manual QC:
  remove special provisions for GCLP;
  enforce that libraries and lanes cannot be qc-ed on the same page
• enable saving qc outcomes for multi-component compositions
• SeqQC GUI changes for multi-component compositions:
  enable display of autoqc results;
  enable manual QC
• changes to allow for SeqQC display of results corresponding to multi-
  component compositions
• Illumina QC data loader restricted to loading cluster density data, its
  data pre-loading functionality dropped
• amend spatial_filter check to take a directory name to search instead
  of an explicit list of input files (that approach became unworkable
  with highly plexed lanes)
• add result_file_path attribute to file-based result objects
• samtools stats file parser
• qX_yield and gc_fraction autoqc checks to use samtools stats files
  instead of fastqcheck file
• SeqQC:
  links for latest ivc and analysis removed since the target files are
  no longer produced;
  link for full rna seqc analysis follows info in the result object
• remove can_run restriction of verify_bam_id check for (cD|R)NA libraries

64.6.3

• update parsing of spatial filter stats in spatial_filter QC check to handle newer format

64.6.2

QC viewer changes for genotype call (GbS)

64.6.1

• tweak to GbS library type check in genotype call as arrived as GBS (now case-insensitive).
• Exit rna seqc gracefully if bam has no reads
• more stringent ref check now required for Pf3D7_v3.fa/hs37d5__Pf3D7_v3.fa
  in genotype check

64.6

• new globin metrics
• changes for GbS genotype calling check
• RNA-SeQC enhancements
• tag_hops_power and tag_hops_percent columns added to tag metrics
• run_timeline component fixes for Illumina QC loader
• tag_sniff enhancements

64.5

• qc outcomes model: code generalisation to simplify addition of further qc types
• switch to node 6.12.2 in travis
• stop generating DBIx classes for unused tables
• tiny tweaks to rna and verify bam id help links
• ensure, where practical, that saving and retrieving qc outcomes works for multi-component compositions
• add functionality to allow more columns to be added to table dynamically
• add data for new extra column for sample_name in summary table
• treat all dynamically added methods in the same way

64.4.1

patch release - fix bam_flagstats check library_size bug