From 889e3c45830f3afa353523270f827a39d02f9870 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sat, 2 Jun 2012 20:21:27 -0400
Subject: [PATCH] Code cleanup before major refactor

---
 .../codecs/bcf2/BCF2LazyGenotypesDecoder.java | 72 -------------------
 .../utils/variantcontext/SlowGenotype.java    |  1 -
 2 files changed, 73 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java
index b1c7a91db..050ff0717 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java
@@ -56,78 +56,6 @@ class BCF2LazyGenotypesDecoder implements LazyGenotypesContext.LazyParser {
         this.nFields = nFields;
     }
 
-//    @Override
-//    public LazyGenotypesContext.LazyData parse(final Object data) {
-//        logger.info("Decoding BCF genotypes for " + nSamples + " samples with " + nFields + " fields each");
-//
-//        // load our bytep[] data into the decoder
-//        final BCF2Decoder decoder = new BCF2Decoder((byte[])data);
-//
-//        // go ahead and decode everyone
-//        final List<String> samples = new ArrayList<String>(codec.getHeader().getGenotypeSamples());
-//
-//        if ( samples.size() != nSamples )
-//            throw new UserException.MalformedBCF2("GATK currently doesn't support reading BCF2 files with " +
-//                    "different numbers of samples per record.  Saw " + samples.size() +
-//                    " samples in header but have a record with " + nSamples + " samples");
-//
-//        final Map<String, List<Object>> fieldValues = decodeGenotypeFieldValues(decoder, nFields, nSamples);
-//        final ArrayList<Genotype> genotypes = new ArrayList<Genotype>(nSamples);
-//        for ( int i = 0; i < nSamples; i++ ) {
-//            // all of the information we need for each genotype, with default values
-//            final String sampleName = samples.get(i);
-//            List<Allele> alleles = null;
-//            boolean isPhased = false;
-//            double log10PError = VariantContext.NO_LOG10_PERROR;
-//            Set<String> filters = null;
-//            Map<String, Object> attributes = null;
-//            double[] log10Likelihoods = null;
-//
-//            for ( final Map.Entry<String, List<Object>> entry : fieldValues.entrySet() ) {
-//                final String field = entry.getKey();
-//                Object value = entry.getValue().get(i);
-//                try {
-//                    if ( field.equals(VCFConstants.GENOTYPE_KEY) ) {
-//                        alleles = decodeGenotypeAlleles(siteAlleles, (List<Integer>)value);
-//                    } else if ( field.equals(VCFConstants.GENOTYPE_QUALITY_KEY) ) {
-//                        if ( value != BCF2Type.INT8.getMissingJavaValue() )
-//                            log10PError = ((Integer)value) / -10.0;
-//                    } else if ( field.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY) ) {
-//                        final List<Integer> pls = (List<Integer>)value;
-//                        if ( pls != null ) { // we have a PL field
-//                            log10Likelihoods = new double[pls.size()];
-//                            for ( int j = 0; j < log10Likelihoods.length; j++ ) {
-//                                final double d = pls.get(j);
-//                                log10Likelihoods[j] = d == -0.0 ? 0.0 : d / -10.0;
-//                            }
-//                        }
-//                    } else if ( field.equals(VCFConstants.GENOTYPE_FILTER_KEY) ) {
-//                        throw new ReviewedStingException("Genotype filters not implemented in GATK BCF2");
-//                        //filters = new HashSet<String>(values.get(i));
-//                    } else { // add to attributes
-//                        if ( value != null ) { // don't add missing values
-//                            if ( attributes == null ) attributes = new HashMap<String, Object>(nFields);
-//                            if ( value instanceof List && ((List)value).size() == 1)
-//                                value = ((List)value).get(0);
-//                            attributes.put(field, value);
-//                        }
-//                    }
-//                } catch ( ClassCastException e ) {
-//                    throw new UserException.MalformedBCF2("BUG: expected encoding of field " + field
-//                            + " inconsistent with the value observed in the decoded value in the "
-//                            + " BCF file.  Value was " + value);
-//                }
-//            }
-//
-//            if ( alleles == null ) throw new UserException.MalformedBCF2("BUG: no alleles found");
-//
-//            final Genotype g = new Genotype(sampleName, alleles, log10PError, filters, attributes, isPhased, log10Likelihoods);
-//            genotypes.add(g);
-//        }
-//
-//        return new LazyGenotypesContext.LazyData(genotypes, codec.getHeader().getSampleNamesInOrder(), codec.getHeader().getSampleNameToOffset());
-//    }
-
     @Override
     public LazyGenotypesContext.LazyData parse(final Object data) {
         logger.info("Decoding BCF genotypes for " + nSamples + " samples with " + nFields + " fields each");
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java
index db480de45..3cca86b30 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/SlowGenotype.java
@@ -25,7 +25,6 @@
 package org.broadinstitute.sting.utils.variantcontext;
 
 
-import org.broad.tribble.util.ParsingUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;