99% working version of BCF2 encoder / decoder
-- fixed final bugs with PL encoding / decoding -- Ready for testing by other members of the group -- Current performance numbers aren't so great, but they will improve in the next phase of BCF2 optimizations -- Fixed a nasty bug in the filter field -- Not that some (many?) GATK tools won't work with BCF because they internally assume values are Strings not their true types Read 1500 genotypes file in VCF -> VCF : 11 seconds Read 1500 genotypes file in VCF -> BCF : 9.5 seconds VariantEval 1500 genotypes file in VCF : 3 seconds VariantEval 1500 genotypes file in BCF : 3 seconds
This commit is contained in:
Mark DePristo
parent
b5bce8d3f9
commit
64d4238e2f
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@ -266,13 +266,17 @@ public class BCF2Codec implements FeatureCodec<VariantContext> {
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}
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private void decodeFilter( final VariantContextBuilder builder ) {
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final Object filters = decoder.decodeTypedValue();
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final Object value = decoder.decodeTypedValue();
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if ( filters == null ) {
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if ( value == null )
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builder.unfiltered();
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}
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else {
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builder.filters(new LinkedHashSet<String>(asStrings(filters)));
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if ( value instanceof Integer )
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builder.filter(getDictionaryString((Integer)value));
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else {
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for ( int offset : (List<Integer>)value )
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builder.filter(getDictionaryString(offset));
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}
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}
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}
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@ -320,12 +324,21 @@ public class BCF2Codec implements FeatureCodec<VariantContext> {
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final Integer value = (Integer)values.get(i);
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if ( value != BCF2Type.INT8.getMissingJavaValue() )
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log10PError = value / -10.0;
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} else if ( field.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) ) {
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final List<Integer> pls = (List<Integer>)values.get(i);
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if ( pls != null ) { // we have a PL field
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log10Likelihoods = new double[pls.size()];
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for ( int j = 0; j < log10Likelihoods.length; j++ )
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log10Likelihoods[j] = pls.get(j) / -10.0;
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}
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} else if ( field.equals(VCFConstants.GENOTYPE_FILTER_KEY) ) {
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throw new ReviewedStingException("Genotype filters not implemented in GATK BCF2");
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//filters = new HashSet<String>(values.get(i));
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} else { // add to attributes
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if ( attributes == null ) attributes = new HashMap<String, Object>(nFields);
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attributes.put(field, values.get(i));
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if ( values.get(i) != null ) { // don't add missing values
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if ( attributes == null ) attributes = new HashMap<String, Object>(nFields);
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attributes.put(field, values.get(i));
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}
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}
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}
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@ -370,7 +383,10 @@ public class BCF2Codec implements FeatureCodec<VariantContext> {
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}
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private final String getDictionaryString() {
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final int offset = (Integer)decoder.decodeTypedValue();
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return getDictionaryString((Integer) decoder.decodeTypedValue());
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}
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private final String getDictionaryString(final int offset) {
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final String field = dictionary.get(offset);
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return field;
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}
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@ -383,24 +399,4 @@ public class BCF2Codec implements FeatureCodec<VariantContext> {
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throw new UserException.MalformedBCF2(String.format("No contig at index %d present in the sequence dictionary from the BCF2 header (%s)", contigOffset, contigNames));
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}
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}
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// ----------------------------------------------------------------------
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//
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// Utility functions
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//
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// ----------------------------------------------------------------------
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private final Collection<String> asStrings(final Object o) {
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return asCollection(String.class, o);
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}
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private final <T> Collection<T> asCollection(final Class<T> c, final Object o) {
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if ( o == null )
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return Collections.emptyList();
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else if ( o instanceof List ) {
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return (List<T>)o;
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} else {
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return (Set<T>)Collections.singleton(o);
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}
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}
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}
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@ -145,7 +145,7 @@ public class BCF2Decoder {
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for ( int i = 0; i < size; i++ ) {
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ints.add(decodeSingleValue(type));
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}
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return ints;
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return ints.get(0) == null ? null : ints;
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}
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}
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@ -185,6 +185,21 @@ public class BCF2Encoder {
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//
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// --------------------------------------------------------------------------------
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public final BCF2Type determineIntegerType(final int[] values) {
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// literally a copy of the code below, but there's no general way to unify lists and arrays in java
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BCF2Type maxType = BCF2Type.INT8;
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for ( final int value : values ) {
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final BCF2Type type1 = determineIntegerType(value);
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switch ( type1 ) {
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case INT8: break;
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case INT16: maxType = BCF2Type.INT16; break;
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case INT32: return BCF2Type.INT32; // fast path for largest possible value
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default: throw new ReviewedStingException("Unexpected integer type " + type1 );
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}
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}
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return maxType;
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}
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public final BCF2Type determineIntegerType(final List<Integer> values) {
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BCF2Type maxType = BCF2Type.INT8;
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for ( final int value : values ) {
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@ -214,9 +214,7 @@ public class Genotype implements Comparable<Genotype> {
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return x;
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else {
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x = getLikelihoods(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, false);
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if ( x != null ) return x;
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else
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throw new IllegalStateException("BUG: genotype likelihood field in " + this.getSampleName() + " sample are not either a string or a genotype likelihood class!");
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return x;
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}
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}
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@ -24,19 +24,15 @@
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package org.broadinstitute.sting.utils.variantcontext;
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import org.apache.commons.lang.ArrayUtils;
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import org.broad.tribble.TribbleException;
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import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import java.util.*;
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public class GenotypeLikelihoods implements List<Double> {
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public static final boolean CAP_PLS = false;
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public static final int PL_CAP = 255;
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import java.util.EnumMap;
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public class GenotypeLikelihoods {
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//
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// There are two objects here because we are lazy in creating both representations
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// for this object: a vector of log10 Probs and the PL phred-scaled string. Supports
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@ -57,14 +53,18 @@ public class GenotypeLikelihoods implements List<Double> {
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return new GenotypeLikelihoods(log10Likelihoods);
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}
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public final static GenotypeLikelihoods fromPLs(final int[] pls) {
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return new GenotypeLikelihoods(PLsToGLs(pls));
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}
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//
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// You must use the factory methods now
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//
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protected GenotypeLikelihoods(String asString) {
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private GenotypeLikelihoods(String asString) {
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likelihoodsAsString_PLs = asString;
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}
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protected GenotypeLikelihoods(double[] asVector) {
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private GenotypeLikelihoods(double[] asVector) {
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log10Likelihoods = asVector;
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}
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@ -85,6 +85,11 @@ public class GenotypeLikelihoods implements List<Double> {
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return log10Likelihoods;
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}
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public int[] getAsPLs() {
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final double[] GLs = getAsVector();
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return GLs == null ? null : GLsToPLs(GLs);
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}
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public String toString() {
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return getAsString();
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}
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@ -181,66 +186,84 @@ public class GenotypeLikelihoods implements List<Double> {
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return null;
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}
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private final static String convertLikelihoodsToPLString(double[] GLs) {
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private final static String convertLikelihoodsToPLString(final double[] GLs) {
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if ( GLs == null )
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return VCFConstants.MISSING_VALUE_v4;
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StringBuilder s = new StringBuilder();
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double adjust = Double.NEGATIVE_INFINITY;
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for ( double l : GLs ) adjust = Math.max(adjust, l);
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final StringBuilder s = new StringBuilder();
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boolean first = true;
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for ( double l : GLs ) {
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for ( final int pl : GLsToPLs(GLs) ) {
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if ( ! first )
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s.append(",");
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else
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first = false;
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long PL = Math.round(-10 * (l - adjust));
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if ( CAP_PLS )
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PL = Math.min(PL, PL_CAP);
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s.append(Long.toString(PL));
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s.append(pl);
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}
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return s.toString();
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}
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// -------------------------------------------------------------------------------------
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//
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// List interface functions
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//
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// -------------------------------------------------------------------------------------
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private final static int[] GLsToPLs(final double[] GLs) {
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final int[] pls = new int[GLs.length];
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final double adjust = maxPL(GLs);
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private final void notImplemented() {
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throw new ReviewedStingException("BUG: code not implemented");
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for ( int i = 0; i < GLs.length; i++ ) {
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pls[i] = (int)Math.round(-10 * (GLs[i] - adjust));
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}
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return pls;
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}
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@Override public int size() { return this.log10Likelihoods.length; }
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@Override public Double get(final int i) { return log10Likelihoods[i];}
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@Override public Double set(final int i, final Double aDouble) { return log10Likelihoods[i] = aDouble; }
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@Override public boolean isEmpty() { return false; }
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@Override public Iterator<Double> iterator() { return Arrays.asList(ArrayUtils.toObject(log10Likelihoods)).iterator(); }
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@Override public Object[] toArray() { return ArrayUtils.toObject(log10Likelihoods); }
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private final static double maxPL(final double[] GLs) {
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double adjust = Double.NEGATIVE_INFINITY;
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for ( double l : GLs ) adjust = Math.max(adjust, l);
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return adjust;
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}
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// none of these are implemented
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@Override public boolean contains(final Object o) { notImplemented(); return false; }
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@Override public <T> T[] toArray(final T[] ts) { notImplemented(); return null; }
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@Override public boolean add(final Double aDouble) { notImplemented(); return false; }
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@Override public boolean remove(final Object o) {notImplemented(); return false; }
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@Override public boolean containsAll(final Collection<?> objects) { notImplemented(); return false; }
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@Override public boolean addAll(final Collection<? extends Double> doubles) { notImplemented(); return false; }
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@Override public boolean addAll(final int i, final Collection<? extends Double> doubles) { notImplemented(); return false; }
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@Override public boolean removeAll(final Collection<?> objects) { notImplemented(); return false; }
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@Override public boolean retainAll(final Collection<?> objects) { notImplemented(); return false; }
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@Override public void clear() { notImplemented(); }
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@Override public void add(final int i, final Double aDouble) { notImplemented(); }
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@Override public Double remove(final int i) { notImplemented(); return null; }
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@Override public int indexOf(final Object o) { notImplemented(); return -1; }
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@Override public int lastIndexOf(final Object o) { notImplemented(); return 0; }
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@Override public ListIterator<Double> listIterator() { notImplemented(); return null; }
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@Override public ListIterator<Double> listIterator(final int i) { notImplemented(); return null; }
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@Override public List<Double> subList(final int i, final int i1) { notImplemented(); return null; }
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private final static double[] PLsToGLs(final int pls[]) {
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double[] likelihoodsAsVector = new double[pls.length];
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for ( int i = 0; i < pls.length; i++ ) {
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likelihoodsAsVector[i] = pls[i] / -10.0;
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}
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return likelihoodsAsVector;
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}
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// // -------------------------------------------------------------------------------------
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// //
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// // List interface functions
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// //
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// // -------------------------------------------------------------------------------------
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//
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// private final void notImplemented() {
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// throw new ReviewedStingException("BUG: code not implemented");
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// }
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//
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// @Override public int size() { return getAsVector().length; }
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// @Override public Double get(final int i) { return getAsVector()[i];}
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// @Override public Double set(final int i, final Double aDouble) { return getAsVector()[i] = aDouble; }
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// @Override public boolean isEmpty() { return false; }
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// @Override public Iterator<Double> iterator() { return Arrays.asList(ArrayUtils.toObject(getAsVector())).iterator(); }
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// @Override public Object[] toArray() { return ArrayUtils.toObject(getAsVector()); }
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//
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// // none of these are implemented
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// @Override public boolean contains(final Object o) { notImplemented(); return false; }
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// @Override public <T> T[] toArray(final T[] ts) { notImplemented(); return null; }
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// @Override public boolean add(final Double aDouble) { notImplemented(); return false; }
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// @Override public boolean remove(final Object o) {notImplemented(); return false; }
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// @Override public boolean containsAll(final Collection<?> objects) { notImplemented(); return false; }
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// @Override public boolean addAll(final Collection<? extends Double> doubles) { notImplemented(); return false; }
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// @Override public boolean addAll(final int i, final Collection<? extends Double> doubles) { notImplemented(); return false; }
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// @Override public boolean removeAll(final Collection<?> objects) { notImplemented(); return false; }
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// @Override public boolean retainAll(final Collection<?> objects) { notImplemented(); return false; }
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// @Override public void clear() { notImplemented(); }
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// @Override public void add(final int i, final Double aDouble) { notImplemented(); }
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// @Override public Double remove(final int i) { notImplemented(); return null; }
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// @Override public int indexOf(final Object o) { notImplemented(); return -1; }
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// @Override public int lastIndexOf(final Object o) { notImplemented(); return 0; }
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// @Override public ListIterator<Double> listIterator() { notImplemented(); return null; }
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// @Override public ListIterator<Double> listIterator(final int i) { notImplemented(); return null; }
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// @Override public List<Double> subList(final int i, final int i1) { notImplemented(); return null; }
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// -------------------------------------------------------------------------------------
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//
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@ -1296,7 +1296,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
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private final Object decodeValue(final String field, final Object value, final VCFCompoundHeaderLine format) {
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if ( value instanceof String ) {
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if ( field.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) )
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return value.equals(".") ? null : new GenotypeLikelihoods((String)value);
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return GenotypeLikelihoods.fromPLField((String)value);
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final String string = (String)value;
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if ( string.indexOf(",") != -1 ) {
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@ -242,7 +242,13 @@ public class VariantContextBuilder {
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* @return
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*/
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public VariantContextBuilder filters(final String ... filters) {
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filters(new HashSet<String>(Arrays.asList(filters)));
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filters(new LinkedHashSet<String>(Arrays.asList(filters)));
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return this;
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}
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public VariantContextBuilder filter(final String filter) {
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if ( this.filters == null ) this.filters = new LinkedHashSet<String>(1);
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this.filters.add(filter);
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return this;
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}
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@ -209,8 +209,8 @@ class BCF2Writer extends IndexingVariantContextWriter {
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addGQ(vc);
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} else if ( field.equals(VCFConstants.GENOTYPE_FILTER_KEY) ) {
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addGenotypeFilters(vc);
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// } else if ( field.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) ) {
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// addPLs(vc);
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} else if ( field.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) ) {
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addPLs(vc);
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} else {
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addGenericGenotypeField(vc, field);
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}
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@ -350,18 +350,33 @@ class BCF2Writer extends IndexingVariantContextWriter {
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}
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}
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// private final void addPLs(final VariantContext vc) throws IOException {
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// startGenotypeField(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, 1, BCF2Type.INT16);
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// for ( final Genotype g : vc.getGenotypes() ) {
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// if ( g.hasLog10PError() ) {
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// final int GQ = (int)Math.round(Math.min(g.getPhredScaledQual(), VCFConstants.MAX_GENOTYPE_QUAL));
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// if ( GQ > VCFConstants.MAX_GENOTYPE_QUAL ) throw new ReviewedStingException("Unexpectedly large GQ " + GQ + " at " + vc);
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// encoder.encodeRawValue(GQ, BCF2Type.INT8);
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// } else {
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// encoder.encodeRawMissingValues(1, BCF2Type.INT8);
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// }
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// }
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// }
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/**
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* Horrible special case to deal with the GenotypeLikelihoods class
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* @param vc
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* @throws IOException
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*/
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private final void addPLs(final VariantContext vc) throws IOException {
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final String field = VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY;
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final int numPLs = getNGenotypeFieldValues(field, vc);
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final int[] allPLs = new int[numPLs * vc.getNSamples()];
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// collect all of the PLs into a single vector of values
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int i = 0;
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for ( final Genotype g : vc.getGenotypes() ) {
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final GenotypeLikelihoods gls = g.getLikelihoods();
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final int[] pls = gls != null ? g.getLikelihoods().getAsPLs() : null;
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if ( pls == null )
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for ( int j = 0; j < numPLs; j++) allPLs[i++] = -1;
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else
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for ( int pl : pls ) allPLs[i++] = pl;
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}
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// determine the best size
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final BCF2Type type = encoder.determineIntegerType(allPLs);
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startGenotypeField(field, numPLs, type);
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for ( int pl : allPLs )
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encoder.encodePrimitive(pl == -1 ? type.getMissingBytes() : pl, type);
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}
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private final void addGenotypes(final VariantContext vc) throws IOException {
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if ( vc.getNAlleles() > 127 )
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|
|
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@ -29,6 +29,7 @@ package org.broadinstitute.sting.utils.codecs.bcf2;
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// the imports for unit testing.
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import org.apache.commons.lang.ArrayUtils;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.exceptions.StingException;
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import org.testng.Assert;
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@ -239,6 +240,32 @@ public class BCF2EncoderDecoderUnitTest extends BaseTest {
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}
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}
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|
||||
@DataProvider(name = "BestIntTypeTests")
|
||||
public Object[][] BestIntTypeTests() {
|
||||
List<Object[]> tests = new ArrayList<Object[]>();
|
||||
tests.add(new Object[]{Arrays.asList(1), BCF2Type.INT8});
|
||||
tests.add(new Object[]{Arrays.asList(1, 10), BCF2Type.INT8});
|
||||
tests.add(new Object[]{Arrays.asList(1, 10, 100), BCF2Type.INT8});
|
||||
tests.add(new Object[]{Arrays.asList(1, -1), BCF2Type.INT8});
|
||||
tests.add(new Object[]{Arrays.asList(1, 1000), BCF2Type.INT16});
|
||||
tests.add(new Object[]{Arrays.asList(1, 1000, 10), BCF2Type.INT16});
|
||||
tests.add(new Object[]{Arrays.asList(1, 1000, 100), BCF2Type.INT16});
|
||||
tests.add(new Object[]{Arrays.asList(1000), BCF2Type.INT16});
|
||||
tests.add(new Object[]{Arrays.asList(100000), BCF2Type.INT32});
|
||||
tests.add(new Object[]{Arrays.asList(100000, 10), BCF2Type.INT32});
|
||||
tests.add(new Object[]{Arrays.asList(100000, 100), BCF2Type.INT32});
|
||||
tests.add(new Object[]{Arrays.asList(100000, 1, -10), BCF2Type.INT32});
|
||||
tests.add(new Object[]{Arrays.asList(-100000, 1, -10), BCF2Type.INT32});
|
||||
return tests.toArray(new Object[][]{});
|
||||
}
|
||||
|
||||
@Test(dataProvider = "BestIntTypeTests")
|
||||
public void determineBestEncoding(final List<Integer> ints, final BCF2Type expectedType) throws IOException {
|
||||
BCF2Encoder encoder = new BCF2Encoder();
|
||||
Assert.assertEquals(encoder.determineIntegerType(ints), expectedType);
|
||||
Assert.assertEquals(encoder.determineIntegerType(ArrayUtils.toPrimitive(ints.toArray(new Integer[0]))), expectedType);
|
||||
}
|
||||
|
||||
@Test(dataProvider = "BCF2EncodingTestProviderBasicTypes")
|
||||
public void testBCF2EncodingVectorsWithMissing(final List<BCF2TypedValue> toEncode) throws IOException {
|
||||
for ( final BCF2TypedValue tv : toEncode ) {
|
||||
|
|
|
|||
|
|
@ -47,14 +47,14 @@ public class GenotypeLikelihoodsUnitTest {
|
|||
|
||||
@Test
|
||||
public void testFromVector2() {
|
||||
GenotypeLikelihoods gl = new GenotypeLikelihoods(v);
|
||||
GenotypeLikelihoods gl = GenotypeLikelihoods.fromLog10Likelihoods(v);
|
||||
assertDoubleArraysAreEqual(gl.getAsVector(), v);
|
||||
Assert.assertEquals(gl.getAsString(), vPLString);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testFromString1() {
|
||||
GenotypeLikelihoods gl = new GenotypeLikelihoods(vPLString);
|
||||
GenotypeLikelihoods gl = GenotypeLikelihoods.fromPLField(vPLString);
|
||||
assertDoubleArraysAreEqual(gl.getAsVector(), new double[]{-9.3, 0, -3.9});
|
||||
Assert.assertEquals(gl.getAsString(), vPLString);
|
||||
}
|
||||
|
|
@ -68,13 +68,13 @@ public class GenotypeLikelihoodsUnitTest {
|
|||
|
||||
@Test (expectedExceptions = UserException.MalformedVCF.class)
|
||||
public void testErrorBadFormat() {
|
||||
GenotypeLikelihoods gl = new GenotypeLikelihoods("adf,b,c");
|
||||
GenotypeLikelihoods gl = GenotypeLikelihoods.fromPLField("adf,b,c");
|
||||
gl.getAsVector();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testGetAsMap(){
|
||||
GenotypeLikelihoods gl = new GenotypeLikelihoods(v);
|
||||
GenotypeLikelihoods gl = GenotypeLikelihoods.fromLog10Likelihoods(v);
|
||||
//Log scale
|
||||
EnumMap<Genotype.Type,Double> glMap = gl.getAsMap(false);
|
||||
Assert.assertEquals(v[Genotype.Type.HOM_REF.ordinal()-1],glMap.get(Genotype.Type.HOM_REF));
|
||||
|
|
@ -89,7 +89,7 @@ public class GenotypeLikelihoodsUnitTest {
|
|||
Assert.assertEquals(vl[Genotype.Type.HOM_VAR.ordinal()-1],glMap.get(Genotype.Type.HOM_VAR));
|
||||
|
||||
//Test missing likelihoods
|
||||
gl = new GenotypeLikelihoods(".");
|
||||
gl = GenotypeLikelihoods.fromPLField(".");
|
||||
glMap = gl.getAsMap(false);
|
||||
Assert.assertNull(glMap);
|
||||
|
||||
|
|
@ -108,7 +108,7 @@ public class GenotypeLikelihoodsUnitTest {
|
|||
|
||||
@Test
|
||||
public void testGetLog10GQ(){
|
||||
GenotypeLikelihoods gl = new GenotypeLikelihoods(vPLString);
|
||||
GenotypeLikelihoods gl = GenotypeLikelihoods.fromPLField(vPLString);
|
||||
|
||||
//GQ for the best guess genotype
|
||||
Assert.assertEquals(gl.getLog10GQ(Genotype.Type.HET),-3.9);
|
||||
|
|
@ -120,7 +120,7 @@ public class GenotypeLikelihoodsUnitTest {
|
|||
Assert.assertEquals(gl.getLog10GQ(Genotype.Type.HOM_VAR), Math.log10(1.0 - test[Genotype.Type.HOM_VAR.ordinal()-1]));
|
||||
|
||||
//Test missing likelihoods
|
||||
gl = new GenotypeLikelihoods(".");
|
||||
gl = GenotypeLikelihoods.fromPLField(".");
|
||||
Assert.assertEquals(gl.getLog10GQ(Genotype.Type.HOM_REF),Double.NEGATIVE_INFINITY);
|
||||
Assert.assertEquals(gl.getLog10GQ(Genotype.Type.HET),Double.NEGATIVE_INFINITY);
|
||||
Assert.assertEquals(gl.getLog10GQ(Genotype.Type.HOM_VAR),Double.NEGATIVE_INFINITY);
|
||||
|
|
|
|||
|
|
@ -50,7 +50,7 @@ public class VCFJarClassLoadingUnitTest {
|
|||
|
||||
ClassLoader classLoader = new URLClassLoader(jarURLs, null);
|
||||
classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.VariantContext");
|
||||
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.bcf.BCF2Codec");
|
||||
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec");
|
||||
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCFCodec");
|
||||
classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec");
|
||||
classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter");
|
||||
|
|
|
|||
|
|
@ -296,22 +296,30 @@ public class VariantContextTestProvider {
|
|||
}
|
||||
|
||||
if ( ENABLE_PL_TESTS ) {
|
||||
// testing PLs
|
||||
addGenotypeTests(site,
|
||||
new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{0, -1, -2}),
|
||||
new Genotype("g2", Arrays.asList(ref, ref), -1, new double[]{0, -2, -3}));
|
||||
if ( site.getNAlleles() == 2 ) {
|
||||
// testing PLs
|
||||
addGenotypeTests(site,
|
||||
new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{0, -1, -2}),
|
||||
new Genotype("g2", Arrays.asList(ref, ref), -1, new double[]{0, -2, -3}));
|
||||
|
||||
addGenotypeTests(site,
|
||||
new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{-1, 0, -2}),
|
||||
new Genotype("g2", Arrays.asList(ref, ref), -1, new double[]{0, -2, -3}));
|
||||
addGenotypeTests(site,
|
||||
new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{-1, 0, -2}),
|
||||
new Genotype("g2", Arrays.asList(ref, ref), -1, new double[]{0, -2, -3}));
|
||||
|
||||
addGenotypeTests(site,
|
||||
new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{-1, 0, -2}),
|
||||
new Genotype("g2", Arrays.asList(ref, ref), -1, new double[]{0, -2000, -1000}));
|
||||
addGenotypeTests(site,
|
||||
new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{-1, 0, -2}),
|
||||
new Genotype("g2", Arrays.asList(ref, ref), -1, new double[]{0, -2000, -1000}));
|
||||
|
||||
addGenotypeTests(site, // missing PLs
|
||||
new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{-1, 0, -2}),
|
||||
new Genotype("g2", Arrays.asList(ref, ref), -1));
|
||||
addGenotypeTests(site, // missing PLs
|
||||
new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{-1, 0, -2}),
|
||||
new Genotype("g2", Arrays.asList(ref, ref), -1));
|
||||
}
|
||||
else if ( site.getNAlleles() == 3 ) {
|
||||
// testing PLs
|
||||
addGenotypeTests(site,
|
||||
new Genotype("g1", Arrays.asList(ref, ref), -1, new double[]{0, -1, -2, -3, -4, -5}),
|
||||
new Genotype("g2", Arrays.asList(ref, ref), -1, new double[]{0, -2, -3, -4, -5, -6}));
|
||||
}
|
||||
}
|
||||
|
||||
// test attributes
|
||||
|
|
|
|||
Loading…
Reference in New Issue