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Lookahead Covariates moved to UG_feature_branch
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53 changes: 53 additions & 0 deletions
53
src/main/java/org/broadinstitute/hellbender/utils/recalibration/covariates/AltCovariate.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,53 @@ | ||
| package org.broadinstitute.hellbender.utils.recalibration.covariates; | ||
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| import htsjdk.samtools.SAMFileHeader; | ||
| import org.broadinstitute.hellbender.utils.BaseUtils; | ||
| import org.broadinstitute.hellbender.utils.read.GATKRead; | ||
| import org.broadinstitute.hellbender.utils.recalibration.RecalibrationArgumentCollection; | ||
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| public final class AltCovariate implements Covariate { | ||
| private static final long serialVersionUID = 1L; | ||
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| public AltCovariate(final RecalibrationArgumentCollection RAC){ | ||
| } | ||
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| // Used to pick out the covariate's value from attributes of the read | ||
| @Override | ||
| public void recordValues(final GATKRead read, final SAMFileHeader header, final ReadCovariates values, final boolean recordIndelValues) { | ||
| final int readLength = read.getLength(); | ||
| final byte[] readBases = read.getBasesNoCopy(); | ||
| for (int i = 0; i < readLength; i++) { | ||
| final int baseIndex = BaseUtils.simpleBaseToBaseIndex(readBases[i]); | ||
| values.addCovariate(baseIndex, 0, 0, i); | ||
| } | ||
| } | ||
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| @Override | ||
| public String formatKey(final int key){ | ||
| if ( key < 0 ) { | ||
| return "N"; | ||
| } else { | ||
| return String.format("%c", (char)BaseUtils.baseIndexToSimpleBase(key)); | ||
| } | ||
| } | ||
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| @Override | ||
| public int keyFromValue(final Object value) { | ||
| if ( (value instanceof String)) { | ||
| final byte base = ((String)value).getBytes()[0]; | ||
| if ( base == 'N' ) { | ||
| return -1; | ||
| } else { | ||
| return BaseUtils.simpleBaseToBaseIndex(base); | ||
| } | ||
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| } else { | ||
| return (Integer)value; | ||
| } | ||
| } | ||
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| @Override | ||
| public int maximumKeyValue() { | ||
| return BaseUtils.Base.values().length; | ||
| } | ||
| } |
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