Uses of Interface
org.snpeff.snpEffect.commandLine.CommandLine
Packages that use CommandLine
Package
Description
-
Uses of CommandLine in org.snpeff
Classes in org.snpeff that implement CommandLine -
Uses of CommandLine in org.snpeff.fastq
Classes in org.snpeff.fastq that implement CommandLine -
Uses of CommandLine in org.snpeff.snpEffect
Subinterfaces of CommandLine in org.snpeff.snpEffectClasses in org.snpeff.snpEffect that implement CommandLineModifier and TypeClassDescriptionclass
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 CommandLineModifier and TypeClassDescriptionclass
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
Command line program: Build databaseclass
Parse NetxProt XML file and build a database http://www.nextprot.org/class
Command line: Calculate coding sequences from a file and compare them to the ones calculated from our data structuresclass
Command line: Find closes marker to each variantclass
Count reads from a BAM file given a list of intervalsclass
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
Command line program: Download and install a (pre built) databaseclass
Command line program: Build databaseclass
Command line program: Predict variant effectsclass
Simple test programclass
Command line: Gene-Sets Analysis Perform gene set analysysclass
Calculate the maximum interval length by type, for all markers in a genomeclass
PDB distance analysisclass
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
Command line program: Show a transcript or a geneclass
Command line program: Show a transcript or a geneclass
Create an SVG representation of a Marker -
Uses of CommandLine in org.snpeff.spliceSites
Classes in org.snpeff.spliceSites that implement CommandLineModifier and TypeClassDescriptionclass
Analyze sequences from splice sites