Uses of Interface
org.snpeff.snpEffect.commandLine.CommandLine

Packages that use CommandLine

Package	Description
org.snpeff
org.snpeff.fastq
org.snpeff.snpEffect
org.snpeff.snpEffect.commandLine
org.snpeff.snpEffect.testCases.integration
org.snpeff.spliceSites

Uses of CommandLine in org.snpeff

Classes in org.snpeff that implement CommandLine

Modifier and Type	Class	Description
class	SnpEff	SnpEff's main command line program

Uses of CommandLine in org.snpeff.fastq

Classes in org.snpeff.fastq that implement CommandLine

Modifier and Type	Class	Description
class	FastqSplit	Split a fastq into N files

Uses of CommandLine in org.snpeff.snpEffect

Subinterfaces of CommandLine in org.snpeff.snpEffect

Modifier and Type	Interface	Description
interface	VcfAnnotator	Annotate a VCF file: E.g.

Classes in org.snpeff.snpEffect that implement CommandLine

Modifier and Type	Class	Description
class	VcfAnnotatorChain	Maintains a list of VcfAnnotators and applies them one by one in the specified order

Uses of CommandLine in org.snpeff.snpEffect.commandLine

Classes in org.snpeff.snpEffect.commandLine that implement CommandLine

Modifier and Type	Class	Description
class	SnpEffCmdAcat	ACAT: Create ACAT score for T2D project Note: This is just used to compile 'ACAT' score in T2D-GENES project, not useful at all for general audience.
class	SnpEffCmdBuild	Command line program: Build database
class	SnpEffCmdBuildNextProt	Parse NetxProt XML file and build a database http://www.nextprot.org/
class	SnpEffCmdCds	Command line: Calculate coding sequences from a file and compare them to the ones calculated from our data structures
class	SnpEffCmdClosest	Command line: Find closes marker to each variant
class	SnpEffCmdCount	Count reads from a BAM file given a list of intervals
class	SnpEffCmdDatabases	Show all databases configures in snpEff.config Create an HTML 'download' table based on the config file Also creates a list of genome for Galaxy menu
class	SnpEffCmdDownload	Command line program: Download and install a (pre built) database
class	SnpEffCmdDump	Command line program: Build database
class	SnpEffCmdEff	Command line program: Predict variant effects
class	SnpEffCmdGenes2Bed	Simple test program
class	SnpEffCmdGsa	Command line: Gene-Sets Analysis Perform gene set analysys
class	SnpEffCmdLen	Calculate the maximum interval length by type, for all markers in a genome
class	SnpEffCmdPdb	PDB distance analysis
class	SnpEffCmdProtein	Command line: Read protein sequences from a file and compare them to the ones calculated from our data structures Note: This is done in order to see potential incompatibility errors between genome sequence and annotation.
class	SnpEffCmdSeq	Command line program: Show a transcript or a gene
class	SnpEffCmdShow	Command line program: Show a transcript or a gene
class	SnpEffCmdTranslocationsReport	Create an SVG representation of a Marker

Uses of CommandLine in org.snpeff.snpEffect.testCases.integration

Methods in org.snpeff.snpEffect.testCases.integration with parameters of type CommandLine

Modifier and Type	Method	Description
java.lang.String	IntegrationTest.command(CommandLine command)	Run a 'command' and return everything printed to stdout
void	IntegrationTest.command(CommandLine command, java.lang.String expectedOutputFile)	Run a command and compare to an expected output (form a file)
java.lang.String	IntegrationTest.showCommand(CommandLine command)	Show command (as a command line)

Uses of CommandLine in org.snpeff.spliceSites

Classes in org.snpeff.spliceSites that implement CommandLine

Modifier and Type	Class	Description
class	SnpEffCmdSpliceAnalysis	Analyze sequences from splice sites