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package org.broadinstitute.gatk.tools.walkers.annotator ;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AS_StandardAnnotation ;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ExperimentalAnnotation ;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord ;
import org.broadinstitute.gatk.utils.variant.GATKVCFConstants ;
import java.util.Arrays ;
import java.util.List ;
/ * *
* Allele specific Rank Sum Test for insert sizes of REF versus ALT reads
*
* < p >
* This annotation tests whether the insert sizes of reads supporting the REF allele and ALT allele are roughly equal .
* In case of multiple alternate alleles , each alternate allele is considered separately .
*
* < / p >
* < h3 > Statistical notes < / h3 >
* < p > See the < a href = "http://www.broadinstitute.org/gatk/guide/article?id=4732" > method document < / a > for a more detailed explanation of the rank sum test . < / p >
*
* * /
public class AS_InsertSizeRankSum extends AS_RankSumTest implements ExperimentalAnnotation {
@Override
public List < String > getKeyNames ( ) { return Arrays . asList ( GATKVCFConstants . AS_INSERT_SIZE_RANK_SUM_KEY ) ; }
@Override
public String getRawKeyName ( ) { return GATKVCFConstants . AS_RAW_INSERT_SIZE_RANK_SUM_KEY ; }
@Override
protected Double getElementForRead ( final GATKSAMRecord read , final int refLoc ) {
return ( double ) Math . abs ( read . getInferredInsertSize ( ) ) ;
}
}
Takuto Sato