Documentation

ErrorThrowing

A walker that simply throws errors.

Category Toy Walkers (DevZone)

Traversal LocusWalker

PartitionBy LOCUS


Overview

Allows us to test that the engine is behaving as expected with error handling

Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by ErrorThrowing.

Parallelism options

This tool can be run in multi-threaded mode using these options.

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

Command-line Arguments

Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

ErrorThrowing specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Required Inputs
--exception
 -E
NA Java class of exception to throw
Optional Parameters
--failMethod
 -fail
MAP Determines which method to fail in

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.


--exception / -E

Java class of exception to throw

R String


--failMethod / -fail

Determines which method to fail in

The --failMethod argument is an enumerated type (FailMethod), which can have one of the following values:

MAP
REDUCE
TREE_REDUCE

FailMethod  MAP


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA