8740124cda7ca4cbe3beb4db05296a6daf242769,java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/CoverageAndPowerWalker.java,CoverageAndPowerWalker,map,#RefMetaDataTracker#ReferenceContext#AlignmentContext#,46

Before Change


        if ( !suppress_printing )
        {
            Pair<Double,Byte> powpair = boostrapSamplingPowerCalc(context);
            out.printf("%s: %d %d %f%n", context.getLocation(), context.getReads().size(),powpair.second,powpair.first);
        }

        return context.getReads().size();

After Change


    }

    public Pair<Integer,Integer> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
        Pair<Pair<List<SAMRecord>,List<SAMRecord>>,Pair<List<Integer>,List<Integer>>> readsByDirection = PoolUtils.splitReadsByReadDirection(context.getReads(),context.getOffsets());
        if ( ! suppress_printing) {
            Pair<double[],byte[]> powers = calculatePower(readsByDirection, useBootstrap, context);
            out.printf("%s: %d %d %d %d %d %d %f %f %f%n", context.getLocation(), readsByDirection.getFirst().getFirst().size(), readsByDirection.getFirst().getSecond().size(),
            context.getReads().size(), powers.getSecond()[0], powers.getSecond()[1], powers.getSecond()[2],
            powers.getFirst()[0], powers.getFirst()[1], powers.getFirst()[2]);
        }
        return new Pair(readsByDirection.getFirst().getFirst().size(),readsByDirection.getFirst().getSecond().size());
    }

    // helper methods