/*
* 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.MergingSamRecordIterator;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFileWriter;
import htsjdk.samtools.SAMFileWriterFactory;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SamFileHeaderMerger;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
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.Log;
import htsjdk.samtools.util.ProgressLogger;
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.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Reads a SAM or BAM file and combines the output to one file
*
* @author Tim Fennell
*/
@CommandLineProgramProperties(
usage = MergeSamFiles.USAGE_SUMMARY + MergeSamFiles.USAGE_DETAILS,
usageShort = MergeSamFiles.USAGE_SUMMARY,
programGroup = SamOrBam.class
)
public class MergeSamFiles extends CommandLineProgram {
private static final Log log = Log.getInstance(MergeSamFiles.class);
static final String USAGE_SUMMARY = "Merges multiple SAM and/or BAM files into a single file. ";
static final String USAGE_DETAILS = "This tool is used for combining SAM and/or BAM files from different runs or read groups, similarly " +
"to the \"merge\" function of Samtools (http://www.htslib.org/doc/samtools.html). " +
"<br /><br />Note that to prevent errors in downstream processing, it is critical to identify/label read groups appropriately. " +
"If different samples contain identical read group IDs, this tool will avoid collisions by modifying the read group IDs to be " +
"unique. For more information about read groups, see the " +
"<a href='https://www.broadinstitute.org/gatk/guide/article?id=6472'>GATK Dictionary entry.</a> <br /><br />" +
"<br />" +
"<h4>Usage example:</h4>" +
"<pre>" +
"java -jar picard.jar MergeSamFiles \\<br />" +
" I=input_1.bam \\<br />" +
" I=input_2.bam \\<br />" +
" O=merged_files.bam" +
"</pre>" +
"<hr />"
;
@Option(shortName = "I", doc = "SAM or BAM input file", minElements = 1)
public List<File> INPUT = new ArrayList<File>();
@Option(shortName = "O", doc = "SAM or BAM file to write merged result to")
public File OUTPUT;
@Option(shortName = StandardOptionDefinitions.SORT_ORDER_SHORT_NAME, doc = "Sort order of output file", optional = true)
public SAMFileHeader.SortOrder SORT_ORDER = SAMFileHeader.SortOrder.coordinate;
@Option(doc = "If true, assume that the input files are in the same sort order as the requested output sort order, even if their headers say otherwise.",
shortName = StandardOptionDefinitions.ASSUME_SORTED_SHORT_NAME)
public boolean ASSUME_SORTED = false;
@Option(shortName = "MSD", doc = "Merge the sequence dictionaries", optional = true)
public boolean MERGE_SEQUENCE_DICTIONARIES = false;
@Option(doc = "Option to create a background thread to encode, " +
"compress and write to disk the output file. The threaded version uses about 20% more CPU and decreases " +
"runtime by ~20% when writing out a compressed BAM file.")
public boolean USE_THREADING = false;
@Option(doc = "Comment(s) to include in the merged output file's header.", optional = true, shortName = "CO")
public List<String> COMMENT = new ArrayList<String>();
@Option(shortName = "RGN", doc = "An interval list file that contains the locations of the positions to merge. "+
"Assume bam are sorted and indexed. "+
"The resulting file will contain alignments that may overlap with genomic regions outside the requested region. "+
"Unmapped reads are discarded.",
optional = true)
public File INTERVALS = null;
private static final int PROGRESS_INTERVAL = 1000000;
/** Required main method implementation. */
public static void main(final String[] argv) {
System.exit(new MergeSamFiles().instanceMain(argv));
}
/** Combines multiple SAM/BAM files into one. */
@Override
protected int doWork() {
boolean matchedSortOrders = true;
// read interval list if it is defined
final List<Interval> intervalList = (INTERVALS == null ? null : IntervalList.fromFile(INTERVALS).uniqued().getIntervals() );
// map reader->iterator used if INTERVALS is defined
final Map<SamReader, CloseableIterator<SAMRecord> > samReaderToIterator = new HashMap<SamReader, CloseableIterator<SAMRecord> >(INPUT.size());
// Open the files for reading and writing
final List<SamReader> readers = new ArrayList<SamReader>();
final List<SAMFileHeader> headers = new ArrayList<SAMFileHeader>();
{
SAMSequenceDictionary dict = null; // Used to try and reduce redundant SDs in memory
for (final File inFile : INPUT) {
IOUtil.assertFileIsReadable(inFile);
final SamReader in = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(inFile);
if ( INTERVALS != null ) {
if( ! in.hasIndex() ) throw new PicardException("Merging with interval but Bam file is not indexed "+ inFile);
final CloseableIterator<SAMRecord> samIterator = new SamRecordIntervalIteratorFactory().makeSamRecordIntervalIterator(in, intervalList, true);
samReaderToIterator.put(in, samIterator);
}
readers.add(in);
headers.add(in.getFileHeader());
// A slightly hackish attempt to keep memory consumption down when merging multiple files with
// large sequence dictionaries (10,000s of sequences). If the dictionaries are identical, then
// replace the duplicate copies with a single dictionary to reduce the memory footprint.
if (dict == null) {
dict = in.getFileHeader().getSequenceDictionary();
} else if (dict.equals(in.getFileHeader().getSequenceDictionary())) {
in.getFileHeader().setSequenceDictionary(dict);
}
matchedSortOrders = matchedSortOrders && in.getFileHeader().getSortOrder() == SORT_ORDER;
}
}
// If all the input sort orders match the output sort order then just merge them and
// write on the fly, otherwise setup to merge and sort before writing out the final file
IOUtil.assertFileIsWritable(OUTPUT);
final boolean presorted;
final SAMFileHeader.SortOrder headerMergerSortOrder;
final boolean mergingSamRecordIteratorAssumeSorted;
if (matchedSortOrders || SORT_ORDER == SAMFileHeader.SortOrder.unsorted || ASSUME_SORTED || INTERVALS != null ) {
log.info("Input files are in same order as output so sorting to temp directory is not needed.");
headerMergerSortOrder = SORT_ORDER;
mergingSamRecordIteratorAssumeSorted = ASSUME_SORTED;
presorted = true;
} else {
log.info("Sorting input files using temp directory " + TMP_DIR);
headerMergerSortOrder = SAMFileHeader.SortOrder.unsorted;
mergingSamRecordIteratorAssumeSorted = false;
presorted = false;
}
final SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(headerMergerSortOrder, headers, MERGE_SEQUENCE_DICTIONARIES);
final MergingSamRecordIterator iterator;
// no interval defined, get an iterator for the whole bam
if( intervalList == null) {
iterator = new MergingSamRecordIterator(headerMerger, readers, mergingSamRecordIteratorAssumeSorted);
}
else {
// show warning related to https://github.com/broadinstitute/picard/pull/314/files
log.info("Warning: merged bams from different interval lists may contain the same read in both files");
iterator = new MergingSamRecordIterator(headerMerger, samReaderToIterator, true);
}
final SAMFileHeader header = headerMerger.getMergedHeader();
for (final String comment : COMMENT) {
header.addComment(comment);
}
header.setSortOrder(SORT_ORDER);
final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
if (USE_THREADING) {
samFileWriterFactory.setUseAsyncIo(true);
}
final SAMFileWriter out = samFileWriterFactory.makeSAMOrBAMWriter(header, presorted, OUTPUT);
// Lastly loop through and write out the records
final ProgressLogger progress = new ProgressLogger(log, PROGRESS_INTERVAL);
while (iterator.hasNext()) {
final SAMRecord record = iterator.next();
out.addAlignment(record);
progress.record(record);
}
log.info("Finished reading inputs.");
for(final CloseableIterator<SAMRecord> iter : samReaderToIterator.values()) CloserUtil.close(iter);
CloserUtil.close(readers);
out.close();
return 0;
}
@Override
protected String[] customCommandLineValidation() {
if (CREATE_INDEX && SORT_ORDER != SAMFileHeader.SortOrder.coordinate) {
return new String[]{"Can't CREATE_INDEX unless SORT_ORDER is coordinate"};
}
return null;
}
}