API documentation

dentist.commands.collectPileUps.filter This is a collection of helpers for the alignment filtering.
dentist.commands.collectPileUps.pileups This is the algorithm for building pile ups.
dentist.commands.processPileUps.cropper This package contains methods for cropping a pile up.
dentist.commands.bed2mask The bed2mask command creates a Dazzler mask from a BED file.
dentist.commands.buildPartialAssembly This is the buildPartialAssembly command of DENTIST.
dentist.commands.chainLocalAlignments This is the chainLocalAlignments command of DENTIST.
dentist.commands.checkResults This is the checkResults command of DENTIST.
dentist.commands.checkScaffolding This is the checkScaffolding command of DENTIST.
dentist.commands.collectPileUps This is the collectPileUps command of DENTIST.
dentist.commands.filterMask This is the filterMask command of DENTIST.
dentist.commands.findClosableGaps This is the findClosableGaps command of DENTIST.
dentist.commands.generateDazzlerOptions This is the generateDazzlerOptions command of DENTIST.
dentist.commands.maskRepetitiveRegions This is the maskRepetitiveRegions command of DENTIST.
dentist.commands.mergeInsertions This is the mergeInsertions command of DENTIST.
dentist.commands.mergeMasks This is the mergeMasks command of DENTIST.
dentist.commands.output This is the output command of DENTIST.
dentist.commands.processPileUps This is the processPileUps command of DENTIST.
dentist.commands.propagateMask This is the propagateMask command of DENTIST.
dentist.commands.showInsertions This is the showInsertions command of DENTIST.
dentist.commands.showMask This is the showMask command of DENTIST.
dentist.commands.showPileUps This is the showPileUps command of DENTIST.
dentist.commands.translateCoords This is the translate-coords command of DENTIST.
dentist.commands.validateConfig This is the validateConfig command of DENTIST.
dentist.commands.validateRegions This is the validate-regions command of DENTIST.
dentist.common.alignments.base Defines alignment central data structures AlignmentChain and FlatLocalAlignment as well as derived types and helper functions.
dentist.common.alignments.chaining Implementation of local alignment chaining. The main function is chainLocalAlignments.
dentist.common.binio.common Collection of common structure and functions for working with binary data.
dentist.common.binio.insertiondb This package contains methods to handle the proprietary binary data container for Insertions.
dentist.common.binio.pileupdb This package contains methods to handle the proprietary binary data container for PileUps.
dentist.common.alignments Everything to handle local alignments and friends.
dentist.common.binio This package contains methods to handle the proprietary binary data containers used to store information between stages of the algorithm. Currently, there are two containers:
dentist.common.commands Enums with sub-commands of dentist. This is mostly relevant if you are trying to add a new command to DENTIST.
dentist.common.configfile Validate and parse config files.
dentist.common.external This package holds function for easy verification of external tools' existence.
dentist.common.insertions Everything to handle insertions. Insertions are generated by DENTIST command process-pile-ups. They are essentially a consensus sequence alongside alignment that allow precise splicing into the assembly. In addition, the IDs of the reads involved in the consensus are included.
dentist.common.scaffold Work with scaffold graphs. A scaffold graph is an undirected graph with optional edge payloads.
dentist.util.algorithm Some additional alogorithm functions.
dentist.util.containers Useful containers. Currently only HashSet.
dentist.util.fasta Some functions to work with FASTA data.
dentist.util.graphalgo A selection of graph algorithms.
dentist.util.log Central logging facility for DENTIST.
dentist.util.math Some additional mathematical functions.
dentist.util.process Convenience wrappers for executing subprocesses.
dentist.util.range Some additional range functions.
dentist.util.region Defines Region and common operation with these. A Region is a set of tagged intervals where differently tagged intervals are distinct.
dentist.util.saturationmath Efficient implementation of saturation math.
dentist.util.string Some additional string functions.
dentist.util.tempfile Create temporary files and folders. These are wrappers around the corresponding functions in core.sys.posix.stdlib.
dentist.commandline Defines the behavior of the DENTIST command line client. The central component of this file is OptionsFor which encapsulates the complete CLI interface.
dentist.commands Exposes the execute function from each command. The functions are accessed by the command name, for example, dentist.commands.collectPileUps.execute is available as collectPileUps.
dentist.common This package holds common code for the DENTIST algorithm.
dentist.dazzler Defines bindings to and utilities for the Dazzler tool suite.
app Application entry point.
dentist Exposes the run function to execute DENTIST commands. It takes an array of CLI arguments to select the command and construct its options.