API documentation
| Module | Description |
|---|---|
| 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.
|
| 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 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.
|