Man pages for PacificBiosciences/pbcommandR
R Package for generating reports using SMRT-Link
| chkClass | Helper function for verifying arguments |
| chkPng | Check the file ends as a png |
| dictToResolvedToolContract | Convert a dict to a Resolved Task Contract |
| dToToolContract | convert the json to ToolContract instance |
| examplefastaReport | Example Task for Testing with emitting a report |
| examplefilterFastaTask | Example Task for testing inputs = [FileTypes.Fasta] outputs =... |
| FileType-class | File Type |
| FileTypes | Registry for all the PacBio defined file types |
| getExamplePlotGroup | Example Plot Group |
| getParser | Fundamental argument parser to emit tool contracts and Run... |
| getPBColorScale | Get the default color scheme, adding more colors if they are... |
| getPBFillScale | Get the default color scheme for fills, adding more colors if... |
| getPBTheme | Returns a default there for making plots. |
| InputFileType-class | Tool Contract Task Input File Type |
| loadJsonFromFile | General func to load JSON from a file |
| loadReseqConditionsFromPath | Load Condition |
| loadResolvedToolContractFromPath | Load a Resolved Tool contract from json file |
| loadToolContractFromPath | Load Tool Contract from Path |
| mainRegisteryMainArgs | CLI entry point. Parses CLI args and calls registery Runner |
| OutputFileType-class | Tool Contract Task Input File Type |
| pbreporter | Sugar object to make it easier to generate reports. |
| pbReseqJob | Create a resequencing job tool wrapper using a function that... |
| printConditionCSV | Convert a resolved condition JSON into a CSV for resubmission... |
| RegisteredToolContract-class | Registered Tool Contract |
| ReseqCondition-class | Model For Reseq Condition |
| ReseqConditions-class | Model for ReseqConditions |
| ResolvedToolContract-class | Resolved Tool Contract |
| ResolvedToolContractTask-class | Resolved Tool Contract Task |
| ResourceTypes | Symbol types used in Tool Contract and Resolved Tool... |
| SymbolTypes | Symbol types used in Tool Contract and Resolved Tool... |
| TaskTypes | PacBio Defined task types |
| ToolContract-class | Tool Contract |
| ToolContractTask-class | Tool Contract |
| toolContractToD | Convert Tool Contract into list/dict |
| ToolDriver-class | Tool Driver has the driver exe and env (to be added) |
| writeToolContract | Write Tool Contract to JSON file |
