* Copyright (c) 2012 The Broad Institute

*

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*

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*/

* Filters a lifted-over VCF file for ref bases that have been changed.

*

* "Lifting over" variants means adjusting variant calls from one reference to another. Specifically, the process adjusts the position of the call to match the corresponding position on the target reference.

* For example, if you have variants called from reads aligned to the hg19 reference, and you want to compare them to calls made based on the b37 reference, you need to liftover one of the callsets to the other reference.

*

* FilteredLiftedVariants is intended to be the second of two processing steps for the liftover process. The first step is to run LiftoverVariants on your VCF file.

* The second step is to run FilterLiftedVariants on the output of LiftoverVariants. This will produce valid well-behaved VCF files, where you'll see that the contig names in the header have all been correctly replaced.

*

*/

    @ArgumentCollection

    protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();

    private static final int MAX_VARIANT_SIZE = 100;

    @Output(doc="File to which variants should be written")

    protected VariantContextWriter writer = null;

    private long failedLocs = 0, totalLocs = 0;

    public void initialize() {

        String trackName = variantCollection.variants.getName();

        Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));

        Map<String, VCFHeader> vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));

        final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : Collections.<VCFHeaderLine>emptySet(), samples);

        writer.writeHeader(vcfHeader);

    }

    /**

     * Determines whether records should be filtered; if not, writes them to the output

     *

     * @param ref   the reference context

     * @param vc    the VariantContext to process

     * @return true if the record is not filtered, false otherwise

     */

    protected boolean filterOrWrite(final byte[] ref, final VariantContext vc) {

  if ( ref == null ) throw new IllegalArgumentException("Cannot filter based on a null reference array");

  if ( vc == null ) throw new IllegalArgumentException("Cannot filter a null Variant Context");

        totalLocs++;

        boolean filter = false;

        final byte[] recordRef = vc.getReference().getBases();

        // this can happen for records that get placed at the ends of chromosomes

        if ( recordRef.length > ref.length ) {

            filter = true;

        } else {

            for (int i = 0; i < recordRef.length && i < MAX_VARIANT_SIZE; i++) {

                if ( recordRef[i] != ref[i] ) {

                    filter = true;

                    break;

                }

            }

        }

        if ( filter )

            failedLocs++;

        else

            writer.add(vc);

        return !filter;

    }

    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {

        if ( tracker == null )

            return 0;

        final Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());

        for ( final VariantContext vc : VCs )

            filterOrWrite(ref.getBases(), vc);

        return 0;

    }

    public Integer reduceInit() { return 0; }

    public Integer reduce(Integer value, Integer sum) { return 0; }

    public void onTraversalDone(Integer result) {

        System.out.println("Filtered " + failedLocs + " records out of " + totalLocs + " total records.");

    }

}