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`MalformedReadFilter` seemingly overly aggressive?
I recently came across(blog post) a scenario in which a subset of my reads had triggered the
MalformedReadFilter during indel realignment. I'm curious to know about the definition of "malformed", as whilst invalid, I wouldn't have described incorrect mate names and alignment positions for unmapped reads as "malformed" and capable of causing job crashes...
Not a bug - I'm just curious to know of any implementation details or reasoning about the