ONT preset values are commented out in code. Why?

philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

MIT License

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ONT preset values are commented out in code. Why? #104

Open TimD1 opened 2 years ago

TimD1 commented 2 years ago

Hi, I noticed that the preset for ONT (-x ont) is commented out in the code: https://github.com/philres/ngmlr/blob/8d7677929001d1d13c6b4593c409a52044180dca/src/ArgParser.cpp#L258-L266 This makes the behavior for -x ont identical to -x pacbio, the default behavior. Are those the intended parameters that should be used for ONT reads? Have the ONT values not undergone sufficient testing yet?