Uses of Interface
org.snpeff.snpEffect.commandLine.CommandLine
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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 -
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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 databaseclass
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 structuresclass
SnpEffCmdClosest
Command line: Find closes marker to each variantclass
SnpEffCmdCount
Count reads from a BAM file given a list of intervalsclass
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 menuclass
SnpEffCmdDownload
Command line program: Download and install a (pre built) databaseclass
SnpEffCmdDump
Command line program: Build databaseclass
SnpEffCmdEff
Command line program: Predict variant effectsclass
SnpEffCmdGenes2Bed
Simple test programclass
SnpEffCmdGsa
Command line: Gene-Sets Analysis Perform gene set analysysclass
SnpEffCmdLen
Calculate the maximum interval length by type, for all markers in a genomeclass
SnpEffCmdPdb
PDB distance analysisclass
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 geneclass
SnpEffCmdShow
Command line program: Show a transcript or a geneclass
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 stdoutvoid
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
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