/*
 * The MIT License
 *
 * Copyright (c) 2009 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.sam;

import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMTextHeaderCodec;
import htsjdk.samtools.SamInputResource;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.util.AsciiWriter;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.IntervalList;
import htsjdk.samtools.util.SamRecordIntervalIteratorFactory;
import picard.PicardException;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.SamOrBam;

import java.io.File;
import java.io.IOException;
import java.io.PrintStream;
import java.util.List;

/**
 * Very simple command that just reads a SAM or BAM file and writes out the header
 * and each records to standard out.  When an (optional) intervals file is specified, 
 * only records overlapping those intervals will be output.
 *
 * @author tfennell@broad.mit.edu
 */
@CommandLineProgramProperties(
        usage = "Prints a SAM or BAM file to the screen.",
        usageShort = "Prints a SAM or BAM file to the screen",
        programGroup = SamOrBam.class
)
public class ViewSam extends CommandLineProgram {
    public static enum AlignmentStatus {Aligned, Unaligned, All}

    public static enum PfStatus {PF, NonPF, All}

    public final String USAGE = getStandardUsagePreamble() + "Prints a SAM or BAM file to the screen.";
    @Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "The SAM or BAM file or GA4GH url to view.")
    public String INPUT;

    @Option(doc = "Print out all reads, just the aligned reads or just the unaligned reads.")
    public AlignmentStatus ALIGNMENT_STATUS = AlignmentStatus.All;

    @Option(doc = "Print out all reads, just the PF reads or just the non-PF reads.")
    public PfStatus PF_STATUS = PfStatus.All;

    @Option(doc="Print the SAM header only.", optional = true)
    public boolean HEADER_ONLY = false;

    @Option(doc="Print the alignment records only.", optional = true)
    public boolean RECORDS_ONLY = false;

    @Option(doc = "An intervals file used to restrict what records are output.", optional = true)
    public File INTERVAL_LIST;

    public static void main(final String[] args) {
        new ViewSam().instanceMain(args);
    }

    @Override
    protected int doWork() {
        return writeSamText(System.out);
    }

    @Override
    protected String[] customCommandLineValidation() {
        if (HEADER_ONLY && RECORDS_ONLY) {
            return new String[]{"Cannot specify both HEADER_ONLY=true and RECORDS_ONLY=true."};
        }
        return super.customCommandLineValidation();
    }


    /**
     * This is factored out of doWork only for unit testing.
     */
    int writeSamText(PrintStream printStream) {
        try {
            final CloseableIterator<SAMRecord> samRecordsIterator;
            final SamReader samReader = SamReaderFactory.makeDefault()
                    .referenceSequence(REFERENCE_SEQUENCE)
                    .open(SamInputResource.of(INPUT));

            // if we are only using the header or we aren't using intervals, then use the reader as the iterator.
            // otherwise use the SamRecordIntervalIteratorFactory to make an interval-ed iterator
            if (HEADER_ONLY || INTERVAL_LIST == null) {
                samRecordsIterator = samReader.iterator();
            } else {
                IOUtil.assertFileIsReadable(INTERVAL_LIST);

                final List<Interval> intervals = IntervalList.fromFile(INTERVAL_LIST).uniqued().getIntervals();
                samRecordsIterator = new SamRecordIntervalIteratorFactory().makeSamRecordIntervalIterator(samReader, intervals, samReader.hasIndex());
            }
            final AsciiWriter writer = new AsciiWriter(printStream);
            final SAMFileHeader header = samReader.getFileHeader();
            if (!RECORDS_ONLY) {
                if (header.getTextHeader() != null) {
                    writer.write(header.getTextHeader());
                } else {
                    // Headers that are too large are not retained as text, so need to regenerate text
                    new SAMTextHeaderCodec().encode(writer, header, true);
                }
            }
            if (!HEADER_ONLY) {
                while (samRecordsIterator.hasNext()) {
                    final SAMRecord rec = samRecordsIterator.next();

                    if (printStream.checkError()) {
                        return 1;
                    }

                    if (this.ALIGNMENT_STATUS == AlignmentStatus.Aligned && rec.getReadUnmappedFlag()) continue;
                    if (this.ALIGNMENT_STATUS == AlignmentStatus.Unaligned && !rec.getReadUnmappedFlag()) continue;

                    if (this.PF_STATUS == PfStatus.PF && rec.getReadFailsVendorQualityCheckFlag()) continue;
                    if (this.PF_STATUS == PfStatus.NonPF && !rec.getReadFailsVendorQualityCheckFlag()) continue;
                    writer.write(rec.getSAMString());
                }
            }
            writer.flush();
            if (printStream.checkError()) {
                return 1;
            }
            CloserUtil.close(writer);
            CloserUtil.close(samRecordsIterator);
            return 0;
        } catch (IOException e) {
            throw new PicardException("Exception writing SAM text", e);
        }
    }
}

@@ -2226,9 +2226,8 @@
 ied,
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 %0A * 

remove funky character