pirl-unc / hitlist / 25187740497

Build # 25187740497

Build Type

push

github

Committed by web-flow

Commit Message

v1.30.18: Surface severity tiers in qc.discrepancies + CLI flag (#204)

Follows up v1.30.17 (#201) by exposing the new four-tier
mhc_class_label_severity through both the QC reports and the export CLI.

qc.discrepancies adds two new columns alongside the existing
suspect_class_label_n:

- borderline_class_label_n  -- bulged class-I (13-14aa) or short
                               class-II (8-10aa); uncommon-but-real
                               biology, NOT counted as suspect.
- implausible_class_label_n -- class-I >=18aa or <=7aa,
                               class-II <=4 or >=31aa; almost always
                               curation drift.

Together they let a curator distinguish "this study has a lot of
bulged peptides" (legitimate) from "this study has rows where the
class label is clearly wrong" (action item).

CLI: hitlist export observations gains
--exclude-class-label-implausible alongside the existing
--exclude-class-label-suspect. The new flag drops only the
implausible tier, retaining bulged class-I 15-17aa peptides for
analyses that want them.

Coverage Stats

3638 of 5141 relevant lines covered (70.76%)

0.71 hits per line

Source File

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