Samtools: Stats: fix "Percent Mapped" plot when samtools was run with read filtering

[lindenb]

This PR fixes a problem with samtools stats #1971

I'm not a python dev, so I hope it's ok !

• This comment contains a description of changes (with reason)
• CHANGELOG.md has been updated

[ewels]

Thanks for this @lindenb!

It looks like this metric has been completely missed until now..

• Is it always there? (It'll crash if not currently)
• Are there any plots / tables that should include this as a category as well?

Cheers,

Phil

[lindenb]

Is it always there? (It'll crash if not currently)

no, as far as I understand , the error is only raised when using :

    -d, --remove-dups                   Exclude from statistics reads marked as duplicates

    -f, --required-flag  <str|int>      Required flag, 0 for unset. See also `samtools flags` [0]
    -F, --filtering-flag <str|int>      Filtering flag, 0 for unset. See also `samtools flags` [0]

the reads are then filtered = ignored from the other counts. If no user uses those flags, the filtered count will always be 0 = no bug

Are there any plots / tables that should include this as a category as well?

🤷

sorry, I'm away from my lab, I don't know if the current MQC table displays the number of filtered reads.

[vladsavelyev]

@lindenb - thanks a lot for the contribution, it looks good to me, but would you be able to submit a test example that reproduces the bug into MultiQC_TestData? Thank you!

[vladsavelyev]

Asking for a test example, otherwise good to me

[lindenb]

@lindenb - thanks a lot for the contribution, it looks good to me, but would you be able to submit a test example that reproduces the bug into MultiQC_TestData? Thank you!

@vladsavelyev thanks for the review & done : MultiQC/test-data#267

[vladsavelyev]

Looks good to me!

[ewels]

Thanks @lindenb!