fix: bug when rescaling BAM

[fgvieira]

Fix #3686

QC

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Summary by CodeRabbit

• New Features
  • Updated the rescaling configuration so that when rescaling is enabled for BAM file processing, both required parameters are applied. This improvement ensures that command-line operations align with current expectations for proper rescaling behavior.

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📝 Walkthrough

Walkthrough

The pull request updates the construction of the rescaled_bam variable in the mapdamage2 wrapper. When a rescaled BAM file is specified, the command-line arguments now include both --rescale and --rescale-out options. This change adjusts the parameters passed to the mapDamage tool without altering the public interface.

Changes

File	Summary of Changes
bio/mapdamage2/wrapper.py	Updated the rescaled_bam construction to include both --rescale and --rescale-out options.

Sequence Diagram(s)

sequenceDiagram
    participant Wrapper as mapdamage2 Wrapper
    participant MapDamage as mapDamage Tool
    Wrapper->>Wrapper: Check if rescaled_bam is defined
    alt rescaled_bam is defined
        Wrapper->>MapDamage: Build command with "--rescale" and "--rescale-out" options
    else
        Wrapper->>MapDamage: Build command without rescaling options
    end
    MapDamage-->>Wrapper: Return processing result

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Suggested reviewers

• johanneskoester

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[cmeesters]

@fgvieira I am sorry, but I do not get it. You include --rescale-out in your command line, the code and webpage of mapDamage only shows --rescale-only. Honestly? I am a bit puzzled.

[fgvieira]

The command line arguments are not super clear (ginolhac/mapDamage#59) and there are some hidden arguments:

https://github.com/ginolhac/mapDamage/blob/484bb3094de69422c2308385aa2bfaf0ef12fa27/mapdamage/config.py#L338-L344