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

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TimD1 opened this issue Apr 5, 2022 · 0 comments
Open

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

TimD1 opened this issue Apr 5, 2022 · 0 comments

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@TimD1
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TimD1 commented Apr 5, 2022

Hi, I noticed that the preset for ONT (-x ont) is commented out in the code:

ngmlr/src/ArgParser.cpp

Lines 258 to 266 in 8d76779

} else if (presetArgs.getValue() == "ont") {
// lowQualitySplit = (lowqualitysplitArg.isSet()) ? lowQualitySplit : false;
// smallInversionDetection = (nosmallInversionArg.isSet()) ? smallInversionDetection : false;
// scoreMatch = (scoreMatchArg.isSet()) ? scoreMatch : 3;
// scoreMismatch = (scoreMatchArg.isSet()) ? scoreMismatch : -3;
//scoreGapOpen = (scoreGapOpenArg.isSet()) ? scoreGapOpen : -1;
//scoreGapExtendMax = (scoreGapExtendMaxArg.isSet()) ? scoreGapExtendMax : -1;
//scoreGapExtendMax = (scoreGapExtendMinArg.isSet()) ? scoreGapExtendMin : -0.5;
scoreGapDecay = (scoreGapDecayArg.isSet()) ? scoreGapDecay : 0.15;

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?

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