/*
* 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
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.illumina.parser;
import htsjdk.samtools.util.CollectionUtil;
import htsjdk.samtools.util.IterableAdapter;
import picard.PicardException;
import picard.illumina.parser.readers.TileMetricsOutReader;
import picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.Map;
import java.util.Set;
/**
* Utility for reading the tile data from an Illumina run directory's TileMetricsOut.bin file
*
* @author mccowan
*/
public class TileMetricsUtil {
/** The path to the directory containing the tile metrics file relative to the basecalling directory. */
public static String INTEROP_SUBDIRECTORY_NAME = "InterOp";
/** The expected name of the tile metrics output file. */
public static String TILE_METRICS_OUT_FILE_NAME = "TileMetricsOut.bin";
/** Returns the path to the TileMetrics file given the basecalling directory. */
public static File renderTileMetricsFileFromBasecallingDirectory(final File illuminaRunDirectory) {
return new File(new File(illuminaRunDirectory, INTEROP_SUBDIRECTORY_NAME), TILE_METRICS_OUT_FILE_NAME);
}
/**
* Returns an unmodifiable collection of tile data read from the provided file. For each tile we will extract:
* - lane number
* - tile number
* - density
* - cluster ID
* - Phasing & Prephasing for first template read (if available)
* - Phasing & Prephasing for second template read (if available)
*/
public static Collection<Tile> parseTileMetrics(final File tileMetricsOutFile, final ReadStructure readStructure) throws FileNotFoundException {
// Get the tile metrics lines from TileMetricsOut, keeping only the last value for any Lane/Tile/Code combination
final Collection<IlluminaTileMetrics> tileMetrics = determineLastValueForLaneTileMetricsCode(new TileMetricsOutReader
(tileMetricsOutFile));
// Collect the tiles by lane & tile, and then collect the metrics by lane
final Map<String, Collection<IlluminaTileMetrics>> locationToMetricsMap = partitionTileMetricsByLocation(tileMetrics);
final Collection<Tile> tiles = new LinkedList<Tile>();
for (final Map.Entry<String, Collection<IlluminaTileMetrics>> entry : locationToMetricsMap.entrySet()) {
final Collection<IlluminaTileMetrics> tileRecords = entry.getValue();
// Get a mapping from metric code number to the corresponding IlluminaTileMetrics
final Map<Integer, Collection<IlluminaTileMetrics>> codeMetricsMap = partitionTileMetricsByCode(tileRecords);
final Set<Integer> observedCodes = codeMetricsMap.keySet();
if (!(observedCodes.contains(IlluminaMetricsCode.DENSITY_ID.getMetricsCode()) && observedCodes.contains(IlluminaMetricsCode.CLUSTER_ID.getMetricsCode())))
throw new PicardException(String.format("Expected to find cluster and density record codes (%s and %s) in records read for tile location %s (lane:tile), but found only %s.",
IlluminaMetricsCode.CLUSTER_ID.getMetricsCode(), IlluminaMetricsCode.DENSITY_ID.getMetricsCode(), entry.getKey(), observedCodes));
final IlluminaTileMetrics densityRecord = CollectionUtil.getSoleElement(codeMetricsMap.get(IlluminaMetricsCode.DENSITY_ID.getMetricsCode()));
final IlluminaTileMetrics clusterRecord = CollectionUtil.getSoleElement(codeMetricsMap.get(IlluminaMetricsCode.CLUSTER_ID.getMetricsCode()));
// Snag the phasing data for each read in the read structure. For both types of phasing values, this is the median of all of the individual values seen
final Collection<TilePhasingValue> tilePhasingValues = getTilePhasingValues(codeMetricsMap, readStructure);
tiles.add(new Tile(densityRecord.getLaneNumber(), densityRecord.getTileNumber(), densityRecord.getMetricValue(), clusterRecord.getMetricValue(),
tilePhasingValues.toArray(new TilePhasingValue[tilePhasingValues.size()])));
}
return Collections.unmodifiableCollection(tiles);
}
/** Pulls out the phasing & prephasing value for the template reads and returns a collection of TilePhasingValues representing these */
private static Collection<TilePhasingValue> getTilePhasingValues(final Map<Integer, Collection<IlluminaTileMetrics>> codeMetricsMap, final ReadStructure readStructure) {
boolean isFirstRead = true;
final Collection<TilePhasingValue> tilePhasingValues = new ArrayList<TilePhasingValue>();
for (int descriptorIndex = 0; descriptorIndex < readStructure.descriptors.size(); descriptorIndex++) {
if (readStructure.descriptors.get(descriptorIndex).type == ReadType.Template) {
final TileTemplateRead tileTemplateRead = isFirstRead ? TileTemplateRead.FIRST : TileTemplateRead.SECOND;
// For both phasing & prephasing, pull out the value and create a TilePhasingValue for further processing
final int phasingCode = IlluminaMetricsCode.getPhasingCode(descriptorIndex, IlluminaMetricsCode.PHASING_BASE);
final int prePhasingCode = IlluminaMetricsCode.getPhasingCode(descriptorIndex, IlluminaMetricsCode.PREPHASING_BASE);
if (!(codeMetricsMap.containsKey(phasingCode) && codeMetricsMap.containsKey(prePhasingCode))) {
throw new PicardException("Don't have both phasing and prephasing values for tile");
}
tilePhasingValues.add(new TilePhasingValue(tileTemplateRead,
CollectionUtil.getSoleElement(codeMetricsMap.get(phasingCode)).getMetricValue(),
CollectionUtil.getSoleElement(codeMetricsMap.get(prePhasingCode)).getMetricValue()));
isFirstRead = false;
}
}
return tilePhasingValues;
}
/** According to Illumina, for every lane/tile/code combination they will only use the last value. Filter out the previous values */
private static Collection<IlluminaTileMetrics> determineLastValueForLaneTileMetricsCode(final Iterator<IlluminaTileMetrics>
tileMetricsIterator) {
final Map<TileMetricsOutReader.IlluminaLaneTileCode, IlluminaTileMetrics> filteredTileMetrics = new HashMap<TileMetricsOutReader.IlluminaLaneTileCode, IlluminaTileMetrics>();
for (final IlluminaTileMetrics illuminaTileMetrics : new IterableAdapter<IlluminaTileMetrics>(tileMetricsIterator)) {
filteredTileMetrics.put(illuminaTileMetrics.getLaneTileCode(), illuminaTileMetrics);
}
return filteredTileMetrics.values();
}
private static String renderMetricLocationKey(final IlluminaTileMetrics metric) {
return String.format("%s:%s", metric.getLaneNumber(), metric.getTileNumber());
}
// Wrapper around CollectionUtil.Partitioner, purely to de-bulk the actual methods
private static Map<Integer, Collection<IlluminaTileMetrics>> partitionTileMetricsByCode(final Collection<IlluminaTileMetrics> tileMetrics) {
return CollectionUtil.partition(tileMetrics, new CollectionUtil.Partitioner<IlluminaTileMetrics, Integer>() {
@Override
public Integer getPartition(final IlluminaTileMetrics metric) {
return metric.getMetricCode();
}
});
}
// Wrapper around CollectionUtil.Partitioner, purely to de-bulk the actual methods
private static Map<String, Collection<IlluminaTileMetrics>> partitionTileMetricsByLocation(final Collection<IlluminaTileMetrics> tileMetrics) {
return CollectionUtil.partition(tileMetrics, new CollectionUtil.Partitioner<IlluminaTileMetrics, String>() {
@Override
public String getPartition(final IlluminaTileMetrics metric) {
return renderMetricLocationKey(metric);
}
});
}
}