/*
 * The MIT License
 *
 * Copyright (c) 2012 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package picard.vcf;

import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.MergingIterator;
import htsjdk.samtools.util.ProgressLogger;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextComparator;
import htsjdk.variant.variantcontext.writer.Options;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
import htsjdk.variant.vcf.VCFFileReader;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFUtils;
import picard.PicardException;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.VcfOrBcf;

import java.io.File;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;

/**
 * Combines multiple VCF files into a single file. Input files must be sorted by their contigs
 * and, within contigs, by start position. Throws IllegalArgumentException if the contig lists
 * are not present in the input files, are not identical or if the sample lists are not the
 * same; this class uses the GATK to merge headers, which may throw exceptions if the headers
 * cannot be merged. See VCFUtils.smartMergeHeaders for details.
 * <p/>
 * An index file is created for the output file by default. Using an output file name with a
 * ".gz" extension will create gzip-compressed output.
 */
@CommandLineProgramProperties(
        usage = "Merges multiple VCF or BCF files into one VCF file. Input files must be sorted by their contigs " +
                "and, within contigs, by start position. The input files must have the same sample and " +
                "contig lists. An index file is created and a sequence dictionary is required by default.",
        usageShort = "Merges multiple VCF or BCF files into one VCF file or BCF",
        programGroup = VcfOrBcf.class
)
public class MergeVcfs extends CommandLineProgram {

    @Option(shortName= StandardOptionDefinitions.INPUT_SHORT_NAME, doc="VCF or BCF input files File format is determined by file extension.", minElements=1)
    public List<File> INPUT;

    @Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "The merged VCF or BCF file. File format is determined by file extension.")
    public File OUTPUT;

    @Option(shortName = "D", doc = "The index sequence dictionary to use instead of the sequence dictionary in the input file", optional = true)
    public File SEQUENCE_DICTIONARY;

    private final Log log = Log.getInstance(MergeVcfs.class);

    public static void main(final String[] argv) {
        new MergeVcfs().instanceMainWithExit(argv);
    }

    public MergeVcfs() {
        this.CREATE_INDEX = true;
    }

    @Override
    protected int doWork() {
        final ProgressLogger progress = new ProgressLogger(log, 10000);
        final List<String> sampleList = new ArrayList<String>();
        final Collection<CloseableIterator<VariantContext>> iteratorCollection = new ArrayList<CloseableIterator<VariantContext>>(INPUT.size());
        final Collection<VCFHeader> headers = new HashSet<VCFHeader>(INPUT.size());

        VariantContextComparator variantContextComparator = null;
        SAMSequenceDictionary sequenceDictionary = null;

        if (SEQUENCE_DICTIONARY != null) {
            sequenceDictionary = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(SEQUENCE_DICTIONARY).getFileHeader().getSequenceDictionary();
        }

        for (final File file : INPUT) {
            IOUtil.assertFileIsReadable(file);
            final VCFFileReader fileReader = new VCFFileReader(file, false);
            final VCFHeader fileHeader = fileReader.getFileHeader();

            if (variantContextComparator == null) {
                variantContextComparator = fileHeader.getVCFRecordComparator();
            } else {
                if (!variantContextComparator.isCompatible(fileHeader.getContigLines())) {
                    throw new IllegalArgumentException(
                            "The contig entries in input file " + file.getAbsolutePath() + " are not compatible with the others.");
                }
            }

            if (sequenceDictionary == null) sequenceDictionary = fileHeader.getSequenceDictionary();

            if (sampleList.isEmpty()) {
                sampleList.addAll(fileHeader.getSampleNamesInOrder());
            } else {
                if (!sampleList.equals(fileHeader.getSampleNamesInOrder())) {
                    throw new IllegalArgumentException("Input file " + file.getAbsolutePath() + " has sample entries that don't match the other files.");
                }
            }

            headers.add(fileHeader);
            iteratorCollection.add(fileReader.iterator());
        }

        if (CREATE_INDEX && sequenceDictionary == null) {
            throw new PicardException("A sequence dictionary must be available (either through the input file or by setting it explicitly) when creating indexed output.");
        }

        final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
                .setOutputFile(OUTPUT)
                .setReferenceDictionary(sequenceDictionary);
        if (CREATE_INDEX) {
            builder.setOption(Options.INDEX_ON_THE_FLY);
        }
        final VariantContextWriter writer = builder.build();

        writer.writeHeader(new VCFHeader(VCFUtils.smartMergeHeaders(headers, false), sampleList));

        final MergingIterator<VariantContext> mergingIterator = new MergingIterator<VariantContext>(variantContextComparator, iteratorCollection);
        while (mergingIterator.hasNext()) {
            final VariantContext context = mergingIterator.next();
            writer.add(context);
            progress.record(context.getContig(), context.getStart());
        }

        CloserUtil.close(mergingIterator);
        writer.close();
        return 0;
    }
}

@@ -3531,16 +3531,17 @@
 t files 
+(
 File for
@@ -3575,16 +3575,85 @@
 xtension
+), or a file having a '.list' suffix containing the path to the files
 .%22, minE
@@ -4467,24 +4467,90 @@
 %3CString%3E();%0A
+        INPUT = IOUtil.unrollFiles(INPUT, IOUtil.VCF_EXTENSIONS);%0A
         fina

add IOUtil.unrollFiles(INPUT, IOUtil.VCF_EXTENSIONS); to MergeVcfs (#729)