Package org.snpeff.snpEffect.commandLine
package org.snpeff.snpEffect.commandLine
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ClassDescriptionCommand line and arguments The way to run a command from 'main' is usually: public static void main(String[] args) { Command cmd = new Command(); cmd.parseArgs(args); cmd.run(); }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.Command line program: Build databaseParse NetxProt XML file and build a database http://www.nextprot.org/Command line: Calculate coding sequences from a file and compare them to the ones calculated from our data structuresCommand line: Find closes marker to each variantCount reads from a BAM file given a list of intervalsShow all databases configures in snpEff.config Create an HTML 'download' table based on the config file Also creates a list of genome for Galaxy menuCommand line program: Download and install a (pre built) databaseCommand line program: Build databaseCommand line program: Predict variant effectsSimple test programCommand line: Gene-Sets Analysis Perform gene set analysysCalculate the maximum interval length by type, for all markers in a genomePDB distance analysisCommand 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.Command line program: Show a transcript or a geneCommand line program: Show a transcript or a geneCreate an SVG representation of a Marker