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chanzuckerberg / shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
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Refactor ReadGraph creation method 2 and add additional output method #251

Closed rlorigro closed 3 years ago

rlorigro commented 3 years ago

This adds the option to generate a labeled table of candidates with the following values:

ReadName0,ReadName1,SameStrand,passesReadGraph2Criteria,inReadGraph,

And the automated thresholds that are selected during ReadGraph creation method 2 are now stored in:

assemblerInfo->automatedAlignedFractionThreshold
assemblerInfo->automatedMarkerCountThreshold
assemblerInfo->automatedMaxDriftThreshold
assemblerInfo->automatedMaxSkipThreshold
assemblerInfo->automatedMaxTrimThreshold

And can be reused to check whether an alignment passed the thresholds at any time using Assembler::passesReadGraph2Criteria(const AlignmentInfo& info)