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package org.broadinstitute.gatk.tools.walkers.annotator ;
import htsjdk.variant.variantcontext.Allele ;
import htsjdk.variant.variantcontext.Genotype ;
import htsjdk.variant.variantcontext.GenotypeBuilder ;
import htsjdk.variant.variantcontext.VariantContext ;
import htsjdk.variant.vcf.VCFFormatHeaderLine ;
import htsjdk.variant.vcf.VCFHeaderLineCount ;
import htsjdk.variant.vcf.VCFHeaderLineType ;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible ;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.GenotypeAnnotation ;
import org.broadinstitute.gatk.utils.contexts.AlignmentContext ;
import org.broadinstitute.gatk.utils.contexts.ReferenceContext ;
import org.broadinstitute.gatk.utils.genotyper.MostLikelyAllele ;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap ;
import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker ;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord ;
import java.util.Collections ;
import java.util.List ;
import java.util.Map ;
/ * *
* Number of forward and reverse reads that support each allele ( including REF )
*
* < p > The StrandAlleleCountsBySample annotation produces read counts per allele and per strand . Note that , as with the < a href = "https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_annotator_DepthPerAlleleBySample.php" > AD < / a > annotation , the allele counts here should not be used to make assumptions about the called genotype . < / p >
*
* < p > This annotation produces 2 values per allele at each site , corresponding to the number of reads that support the following ( in that order ) : < / p >
* < ul >
* < li > the reference allele on the forward strand < / li >
* < li > the reference allele on the reverse strand < / li >
* < li > the first alternate allele on the forward strand < / li >
* < li > the first alternate allele on the reverse strand < / li >
* < li > the second alternate allele on the forward strand < / li >
* < li > < i > . . . etc < / i > < / li >
* < / ul >
*
* < h3 > Example < / h3 >
* < pre > GT : AD : GQ : PL : SB : SAC 1 / 2 : 1 , 18 , 12 : 99 : 1022 , 326 , 382 , 537 , 0 , 487 : 1 , 0 , 4 , 8 : 1 , 0 , 3 , 15 , 4 , 8 < / pre >
* < p > In this example , the reference allele is supported by 1 read on the forward strand , the first alternate allele is supported by 3 forward and 15 reverse reads , and the second alternate allele is supported by 4 forward and 8 reverse reads . < / p >
*
* < h3 > Related annotations < / h3 >
* < ul >
* < li > < b > < a href = "https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_annotator_DepthPerAlleleBySample.php" > DepthPerAlleleBySample < / a > < / b > displays the number of reads supporting each allele , without stratifying by strand . < / li >
* < / ul >
* /
public class StrandAlleleCountsBySample extends GenotypeAnnotation {
public final static String STRAND_COUNT_BY_SAMPLE_KEY_NAME = "SAC" ;
@Override
public void annotate ( final RefMetaDataTracker tracker ,
final AnnotatorCompatible walker ,
final ReferenceContext ref ,
final AlignmentContext stratifiedContext ,
final VariantContext vc ,
final Genotype g ,
final GenotypeBuilder gb ,
final PerReadAlleleLikelihoodMap alleleLikelihoodMap ) {
if ( ! isAppropriateInput ( alleleLikelihoodMap , g ) )
return ;
gb . attribute ( STRAND_COUNT_BY_SAMPLE_KEY_NAME , getStrandCounts ( Collections . singletonMap ( g . getSampleName ( ) , alleleLikelihoodMap ) , vc ) ) ;
}
@Override
public List < String > getKeyNames ( ) { return Collections . singletonList ( STRAND_COUNT_BY_SAMPLE_KEY_NAME ) ; }
@Override
public List < VCFFormatHeaderLine > getDescriptions ( ) {
return Collections . singletonList (
new VCFFormatHeaderLine ( getKeyNames ( ) . get ( 0 ) , VCFHeaderLineCount . UNBOUNDED , VCFHeaderLineType . Integer ,
"Number of reads on the forward and reverse strand supporting each allele (including reference)" ) ) ;
}
private boolean isAppropriateInput ( final PerReadAlleleLikelihoodMap map , final Genotype g ) {
return ! ( map = = null | | g = = null | | ! g . isCalled ( ) ) ;
}
/ * *
* This method was inspired by ( copied from ) StrandBiasTest . getContingencyTable ( ) . Unlike getContingencyTable , it
* returns values for all alleles rather than only reference and the most likely allele . Since this is not useful
* for StrandBias calculations , it ' s here and it skips the Nx2 table format used in that method
* /
private int [ ] getStrandCounts ( final Map < String , PerReadAlleleLikelihoodMap > stratifiedPerReadAlleleLikelihoodMap , final VariantContext vc ) {
if ( stratifiedPerReadAlleleLikelihoodMap = = null ) { throw new IllegalArgumentException ( "stratifiedPerReadAlleleLikelihoodMap cannot be null" ) ; }
if ( vc = = null ) { throw new IllegalArgumentException ( "input vc cannot be null" ) ; }
final int [ ] table = new int [ vc . getNAlleles ( ) * 2 ] ;
for ( final PerReadAlleleLikelihoodMap maps : stratifiedPerReadAlleleLikelihoodMap . values ( ) ) {
for ( final Map . Entry < GATKSAMRecord , Map < Allele , Double > > el : maps . getLikelihoodReadMap ( ) . entrySet ( ) ) {
final MostLikelyAllele mostLikelyAllele = PerReadAlleleLikelihoodMap . getMostLikelyAllele ( el . getValue ( ) ) ;
final GATKSAMRecord read = el . getKey ( ) ;
if ( mostLikelyAllele . isInformative ( ) )
updateTable ( table , vc . getAlleleIndex ( mostLikelyAllele . getAlleleIfInformative ( ) ) , read ) ;
}
}
return table ;
}
private void updateTable ( final int [ ] table , final int alleleIndex , final GATKSAMRecord read ) {
if ( alleleIndex < 0 | | ( alleleIndex + 1 ) * 2 > table . length ) return ;
final int offset = alleleIndex * 2 ;
//Unstranded reads are not meaningful for this annotation, they can be found in the AD annotation
if ( ! read . isStrandless ( ) ) {
final boolean isFW = ! read . getReadNegativeStrandFlag ( ) ;
table [ offset + ( isFW ? 0 : 1 ) ] + + ;
}
}
}
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