diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java index 784da2367..a31fa638f 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java @@ -1,4 +1,4 @@ - package org.broadinstitute.sting.playground.gatk.walkers.annotator; +package org.broadinstitute.sting.playground.gatk.walkers.annotator; import java.io.File; import java.util.Collection; @@ -31,40 +31,10 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils; import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter; -/* - General documentation - todo put this in wiki? - - The GenomicAnnotator - - Input Files: - - Input files are specified using the -B,, arg. - - - One of the -B args should have the "variants" and contain the genotypes to be annotated. - - - Data files are also provided using the -B arg and should have be "table". - Table format: - - the coordinates must be position-based rather than offset-based (eg. 1-based half-open) - - special rows: - - can contain comment lines starting with # - - at the top of the file, there must be a header line of the form: - HEADER columnName1 columnName2 etc. TODO finalize this - - special columns: - - first column must be of the form chr:pos or chr:start-end. - - alt/ref haplotypes: - - if there is a column named "hap_ref", a variant will only be annotated with a given row if that row's "hap_ref" allele exactly matches the variant's reference sequence. - - - - - - - - - - - */ /** - * Annotates variant calls with context information. Users can specify which of the available annotations to use. + * Annotates variant calls with information from user-provided tabular files. + * See: {TODO: put wiki url} */ //@Requires(value={DataSource.READS, DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type=VariationRod.class)) @Allows(value={DataSource.READS, DataSource.REFERENCE})