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;


Manifest constants

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.


string workdir;

This is a temporary directory to store all working data.