PepQueryMHC v1.0.2

Changes in "annotate mode"

• Change class category
  • IF: In-frame in CDS (previous: PC, protein coding)
  • OOF: Out-of-frame in CDS (previous: FS, frameshift)
  • UTR: Untranslated region (previous: UTR)
  • ncRNA: Non-coding RNA (previous: ncRNA)
  • IR: Intron-retention (previous: IR)
  • asRNA: antisense RNA (previous asRNA)
  • IGR: Intergenic region (previous: IGR)
  • Unknown: Unknown region (previous: Unknown)
  • ES: Exon-skipping (previous: AS)
  • EE: Exon-exclusion (previous: AS)
• Change penalties and annotation rules
  • We introduce a concept of class to classify categories:
    • Class I: Exonic class such as IF, OOF, UTR, ncRNA
    • Class II: Intronic class, IR
    • Class III: Antisense class, asRNA
    • Class IV: Intergenic class, IGR
    • Class V: Exon-structural variations, EE, ES
    • Else: Unkown
  • Penalty of annotation is calculated by summing all maximum penalties in each class.
    • e.g., an annotation for UTR;IF;IR will be calculated max(UTR, IF) + max(IR).
  • Penalties:
    • IF: 0
    • UTR, FS: 20
    • ncRNA: 30
    • IR: 60
    • asRNA: 120
    • IGR: 240
    • Unknown: 480
    • Warning tag: 1000
    • ES: 15
    • EE: 15
  • Present a representative annotation
    • Annotation can stretch from UTR to OOF with ES and EE, leading to printing verbose annotation (e.g., UTR;OOF;ES;EE).
      To make it clean, worst priority annotation from Class I to Class IV is selected as the representative annotation. The example will be present "UTR;ES;EE".

Full Changelog: v1.0.1...v1.0.2