package picard.sam;

import htsjdk.samtools.BamFileIoUtils;

import htsjdk.samtools.SAMFileHeader;

import htsjdk.samtools.SAMFileWriter;

import htsjdk.samtools.SAMFileWriterFactory;

import htsjdk.samtools.SAMRecord;

import htsjdk.samtools.SamReader;

import htsjdk.samtools.SamReaderFactory;

import htsjdk.samtools.util.CloserUtil;

import htsjdk.samtools.util.IOUtil;

import htsjdk.samtools.util.Log;

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.util.List;

/**

* Program to perform a rapid "gather" operation on BAM files after a scatter operations where

* the same process has been performed on different regions of a BAM file creating many smaller

* BAM files that now need to be concatenated back together.

*

* @author Tim Fennell

*/

@CommandLineProgramProperties(

usage = GatherBamFiles.USAGE_SUMMARY + GatherBamFiles.USAGE_DETAILS,

usageShort = GatherBamFiles.USAGE_SUMMARY,

programGroup = SamOrBam.class

)

public class GatherBamFiles extends CommandLineProgram {

static final String USAGE_SUMMARY = "Concatenate one or more BAM files as efficiently as possible";

static final String USAGE_DETAILS = "This tool performs a rapid \"gather\" operation on BAM files after scatter" +

" operations where the same process has been performed on different regions of a BAM file creating many " +

"smaller BAM files that now need to be concatenated (reassembled) back together." +

"<br /><br />" +

"Assumes that the list of BAM files provided as INPUT are in the order that they should be concatenated and" +

" simply concatenates the bodies of the BAM files while retaining the header from the first file. " +

"Operates via copying of the gzip blocks directly for speed but also supports generation of an MD5 on the" +

" output and indexing of the output BAM file. Only supports BAM files, does not support SAM files." +

"<h4>Usage example:</h4>" +

"<pre>" +

"java -jar picard.jar GatherBamFiles \\<br /> " +

" I=input1.bam \\ <br /> " +

" I=input2.bam \\ <br /> " +

" O=gathered_files.bam" +

"</pre> " +

"<hr />";

@Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME,

doc = "Two or more BAM files or text files containing lists of BAM files (one per line).")

public List<File> INPUT;

@Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "The output BAM file to write.")

public File OUTPUT;

private static final Log log = Log.getInstance(GatherBamFiles.class);

// Stock main method.

public static void main(final String[] args) {

final GatherBamFiles gatherer = new GatherBamFiles();

gatherer.CREATE_INDEX = true;

gatherer.instanceMainWithExit(args);

}

@Override

protected int doWork() {

final List<File> inputs = IOUtil.unrollFiles(INPUT, BamFileIoUtils.BAM_FILE_EXTENSION, ".sam");

for (final File f : inputs) IOUtil.assertFileIsReadable(f);

IOUtil.assertFileIsWritable(OUTPUT);

if (determineBlockCopyingStatus(inputs)) {

BamFileIoUtils.gatherWithBlockCopying(inputs, OUTPUT, CREATE_INDEX, CREATE_MD5_FILE);

} else {

gatherNormally(inputs, OUTPUT, CREATE_INDEX, CREATE_MD5_FILE, REFERENCE_SEQUENCE);

}

return 0;

}

private boolean determineBlockCopyingStatus(final List<File> inputs) {

boolean useBlockCopying = true;

for (final File f : inputs) {

if (!BamFileIoUtils.isBamFile(f)) {

useBlockCopying = false;

}

}

return useBlockCopying;

}

/**

* Simple implementation of a gather operations that uses SAMFileReaders and Writers in order to concatenate

* multiple BAM files.

*/

private static void gatherNormally(final List<File> inputs, final File output, final boolean createIndex, final boolean createMd5,

final File referenceFasta) {

final SAMFileHeader header;

{

header = SamReaderFactory.makeDefault().referenceSequence(referenceFasta).getFileHeader(inputs.get(0));

}

final SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(createIndex).setCreateMd5File(createMd5).makeSAMOrBAMWriter(header, true, output);

for (final File f : inputs) {

log.info("Gathering " + f.getAbsolutePath());

final SamReader in = SamReaderFactory.makeDefault().referenceSequence(referenceFasta).open(f);

for (final SAMRecord rec : in) out.addAlignment(rec);

CloserUtil.close(in);

}

out.close();

}

}