what's Validation stringency?

Question

[2012secondseason]

Hi

I am wondering about Validation Stringency option. What are the principles and criteria for this?

And when & in what tools should I use this option?

Thank you in advance

Answer 1

[Pierre Lindenbaum]

in picard/htsjdk ValidationStringency ( https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/ValidationStringency.html ) is an enumeration indicating how an error should be handled:

LENIENT

Emit warnings but keep going if possible.

SILENT

Like LENIENT, only don't emit warning messages.

STRICT

Do the right thing, throw an exception if something looks wrong.

concrete usage here: https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/samtools/SAMLineParser.java#L456

[2012secondseason]

I understand. Thank you very much!

[Pierre Lindenbaum]

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