fixed align parameters in basic-config as these were remnants from an…

[riasc]

… older version

Summary by CodeRabbit

• Bug Fixes
  • Corrected misspellings and streamlined configuration settings for improved clarity.
• New Features
  • Added an additional configuration option in the alignment section.
• Documentation
  • Updated guidance for typing options to clearly reflect available modes.

[coderabbitai]

Walkthrough

This update corrects and clarifies a configuration file used in integration testing. The header in the alignment section is fixed from "alingment" to "alignment", and several parameters have been renamed for consistency (e.g., chimsegmin → chimSegmentMin). A new parameter, chimScoreSeparation, is added. In the HLA typing section, comments are updated to indicate that the modes for MHC-I_mode and MHC-II_mode now support a "custom" option. Additionally, the parameter minovlps has been removed.

Changes

File(s)	Change Summary
.tests/integration/config_basic/config.yaml .tests/integration/config.yaml	- Corrected header spelling from "alingment" to "alignment". - Removed parameter minovlps. - Renamed alignment parameters: chimsegmin → chimSegmentMin, chimoverhang → chimJunctionOverhangMin, chimmax → chimScoreMin, chimmaxdrop → chimScoreDropMax. - Added chimScoreSeparation. - Updated HLA typing comments to include "custom" as a mode.

Poem

I'm a hopping rabbit in fields of code so bright,
Fixing names and comments in the quiet night.
Parameters realigned with a careful brush,
Removing clutter without a rush.
With every line, clarity springs anew—
A joyful carrot dance for changes true!

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

.tests/integration/config_basic/config.yaml (1)

91-92: HLA Typing Section – Updated Mode Comments

The inline comments for MHC-I_mode and MHC-II_mode have been revised to indicate that a "custom" option is now supported. This clarification helps users understand that apart from existing values (e.g., "DNA, RNA" and "BOTH"), a custom configuration can be provided for specifying alleles manually if necessary.

Please verify that the chosen default values ("DNA, RNA" for MHC-I and "BOTH" for MHC-II) align with the intended workflow and documentation.

📜 Review details

Configuration used: CodeRabbit UI
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Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 9b16385 and 9529551.

📒 Files selected for processing (1)

• .tests/integration/config_basic/config.yaml (2 hunks)

[coderabbitai]

🛠️ Refactor suggestion

Alignment Section Parameter Renaming and Update

These changes update legacy parameter names in the alignment section:

• chimSegmentMin replaces the old chimsegmin.
• chimScoreMin replaces the old chimmax.
• chimJunctionOverhangMin replaces the old chimoverhang.
• chimScoreDropMax replaces the old chimmaxdrop.
• A new parameter chimScoreSeparation has been added with a value of 10.

This improves clarity and consistency with current naming conventions. Please ensure that any downstream modules or scripts referencing these parameters have also been updated accordingly.