OptionsFor

Options for the different commands.

struct OptionsFor (

DentistCommand command

) {

enum needWorkdir;

string trueAssemblyFile;

string trueAssemblyDb;

string shortReadAssemblyFile;

string shortReadAssemblyDb;

string refFile;

string refDb;

string readsDb;

string resultFile;

string resultDb;

string shortReadAssemblyAlignmentInputFile;

string shortReadAssemblyAlignmentFile;

string selfAlignmentInputFile;

string selfAlignmentFile;

string readsAlignmentInputFile;

string readsAlignmentFile;

string resultsAlignmentInputFile;

string resultsAlignmentFile;

string repeatMask;

string mappedRegionsMask;

OutputCoordinate[] outputCoordinates;

string mappedRegionsMask;

string repeatMask;

string assemblyFile;

coord_t bucketSize;

uint numDaccordThreads;

string assemblyGraphFile;

id_t onlyContigId;

string alignmentTabular;

string gapDetailsTabular;

double bestPileUpMargin;

OptionFlag shouldExtendContigs;

size_t fastaLineWidth;

ProvideMethod provideMethod;

JoinPolicy joinPolicy;

OptionFlag useJson;

OptionFlag keepTemp;

string[] additionalMasks;

id_t maxCoverageReads;

id_t[2] coverageBoundsReads;

id_t maxCoverageSelf;

id_t[2] coverageBoundsSelf;

size_t minAnchorLength;

size_t minInsertionLength;

size_t minExtensionLength;

enum defaultMinSpanningReads;

size_t minReadsPerPileUp;

size_t minSpanningReads;

id_t readCoverage;

double readsErrorRate;

double referenceErrorRate;

uint numThreads;

trace_point_t tracePointDistance;

size_t verbosity;

enum workdirTemplate;

string workdir;

}

Members

Manifest constants

workdirTemplate enum workdirTemplate;: Last part of the working directory name. A directory in the temp directory as returned by std.file.tmpDir with the naming scheme will be created to hold all data for the computation.

Variables

workdir string workdir;: This is a temporary directory to store all working data.

OptionsFor

Members

Manifest constants

Variables

Meta

Source