/*
* The MIT License
*
* Copyright (c) 2014 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.markduplicates.util;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.util.Histogram;
import picard.sam.DuplicationMetrics;
import java.util.HashMap;
import java.util.Map;
/**
* A class to generate library Ids and keep duplication metrics by library IDs.
*
* @author nhomer
*/
public class LibraryIdGenerator {
private final SAMFileHeader header;
private final Map<String, Short> libraryIds = new HashMap<String, Short>(); // from library string to library id
private short nextLibraryId = 1;
private final Map<String, DuplicationMetrics> metricsByLibrary = new HashMap<String, DuplicationMetrics>();
private final Histogram<Short> opticalDuplicatesByLibraryId = new Histogram<Short>();
public LibraryIdGenerator(final SAMFileHeader header) {
this.header = header;
for (final SAMReadGroupRecord readGroup : header.getReadGroups()) {
final String library = readGroup.getLibrary();
DuplicationMetrics metrics = metricsByLibrary.get(library);
if (metrics == null) {
metrics = new DuplicationMetrics();
metrics.LIBRARY = library;
metricsByLibrary.put(library, metrics);
}
}
}
public Map<String, Short> getLibraryIdsMap() { return this.libraryIds; }
public Map<String, DuplicationMetrics> getMetricsByLibraryMap() { return this.metricsByLibrary; }
public Histogram<Short> getOpticalDuplicatesByLibraryIdMap() { return this.opticalDuplicatesByLibraryId; }
/**
* Gets the library name from the header for the record. If the RG tag is not present on
* the record, or the library isn't denoted on the read group, a constant string is
* returned.
*/
public static String getLibraryName(final SAMFileHeader header, final SAMRecord rec) {
final String readGroupId = (String) rec.getAttribute("RG");
if (readGroupId != null) {
final SAMReadGroupRecord rg = header.getReadGroup(readGroupId);
if (rg != null) {
final String libraryName = rg.getLibrary();
if (null != libraryName) return libraryName;
}
}
return "Unknown Library";
}
/** Get the library ID for the given SAM record. */
public short getLibraryId(final SAMRecord rec) {
final String library = getLibraryName(this.header, rec);
Short libraryId = this.libraryIds.get(library);
if (libraryId == null) {
libraryId = this.nextLibraryId++;
this.libraryIds.put(library, libraryId);
}
return libraryId;
}
public DuplicationMetrics getMetricsByLibrary(final String library) {
return this.metricsByLibrary.get(library);
}
public void addMetricsByLibrary(final String library, final DuplicationMetrics metrics) {
this.metricsByLibrary.put(library, metrics);
}
public long getNumberOfOpticalDuplicateClusters() {
return (long) this.opticalDuplicatesByLibraryId.getSumOfValues();
}
}