picard.illumina.parser.PerTilePerCycleFileUtil Maven / Gradle / Ivy
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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
package picard.illumina.parser;
import htsjdk.samtools.util.IOUtil;
import picard.PicardException;
import picard.illumina.parser.fakers.FileFaker;
import picard.illumina.parser.readers.BclReader;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
import java.util.regex.Matcher;
public class PerTilePerCycleFileUtil extends ParameterizedFileUtil {
private final CycleIlluminaFileMap cycleFileMap;
private final Set detectedCycles = new TreeSet();
public PerTilePerCycleFileUtil(final String extension,
final File base, final FileFaker faker, final int lane) {
super(true, extension, base, faker, lane);
//sideEffect, assigned to numCycles
this.cycleFileMap = getPerTilePerCycleFiles();
}
/**
* For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through
* all the files for these tiles in expectedBase
* Side Effect: Assigns numCycles
*
* @return A CycleIlluminaFileMap with the listed (or all) tiles for at least expectedCycles number of cycles(or total available
* cycles if expectedCycles is null)
*/
protected CycleIlluminaFileMap getPerTilePerCycleFiles() {
final CycleIlluminaFileMap cycledMap = new CycleIlluminaFileMap();
final File laneDir = base;
final File[] tempCycleDirs;
tempCycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN);
if (tempCycleDirs == null || tempCycleDirs.length == 0) {
return cycledMap;
}
for (final File tempCycleDir : tempCycleDirs) {
detectedCycles.add(getCycleFromDir(tempCycleDir));
}
final Set uniqueTiles = new HashSet();
for (final File cycleDir : tempCycleDirs) {
final IlluminaFileMap fileMap = getTiledFiles(cycleDir, matchPattern);
uniqueTiles.addAll(fileMap.keySet());
cycledMap.put(getCycleFromDir(cycleDir), fileMap);
}
this.tiles = new ArrayList<>(uniqueTiles);
return cycledMap;
}
public CycleIlluminaFileMap getFiles() {
return cycleFileMap;
}
public CycleIlluminaFileMap getFiles(final List tiles) {
return cycleFileMap.keep(tiles, detectedCycles);
}
/**
* Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in. Any cycles that are missing
* cycle files or directories will be removed from the cycle list that is kept.
*
* @param cycles Cycles that should be present in the output CycleIlluminaFileMap
* @return A CycleIlluminaFileMap with all available tiles but at most the cycles passed in by the cycles parameter
*/
public CycleIlluminaFileMap getFiles(final int[] cycles) {
//Remove any cycles that were discovered to be NON-EXISTENT when this util was instantiated
final Set filteredCycles = removeNonExistentCycles(cycles);
return cycleFileMap.keep(tiles, filteredCycles);
}
/**
* Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the original CycleIlluminaFileMap, created
* on util instantiation, doesn't contain any of these tiles/cycles).
*
* @param cycles Cycles that should be present in the output CycleIlluminaFileMap
* @return A CycleIlluminaFileMap with at most the tiles/cycles listed in the parameters
*/
public CycleIlluminaFileMap getFiles(final List tiles, final int[] cycles) {
//Remove any cycles that were discovered to be NON-EXISTENT when this util was instantiated
final Set filteredCycles = removeNonExistentCycles(cycles);
return cycleFileMap.keep(tiles, filteredCycles);
}
private Set removeNonExistentCycles(final int[] cycles) {
final TreeSet inputCyclesSet = new TreeSet();
for (final Integer inputCycle : cycles) {
inputCyclesSet.add(inputCycle);
}
inputCyclesSet.retainAll(detectedCycles);
return inputCyclesSet;
}
public Set getDetectedCycles() {
return detectedCycles;
}
/**
* Discover all files of this type in expectedBase that match pattern and construct a list of tiles
* available based on these files. The same number of tiles is expected in each cycle dir.
*
* @return A list of tile integers for all tiles available
*/
public List getTiles() {
return tiles;
}
public boolean filesAvailable() {
boolean filesAvailable = false;
for (final IlluminaFileMap fileMap : cycleFileMap.values()) {
if (!fileMap.isEmpty()) {
filesAvailable = true;
break;
}
}
return filesAvailable;
}
@Override
public List verify(final List expectedTiles, final int[] expectedCycles) {
final List failures = new LinkedList();
final Map tileToFileLengthMap = new HashMap();
if (!base.exists()) {
failures.add("Base directory(" + base.getAbsolutePath() + ") does not exist!");
} else {
final CycleIlluminaFileMap cfm = getFiles(expectedTiles, expectedCycles);
for (final int currentCycle : expectedCycles) {
final IlluminaFileMap fileMap = cfm.get(currentCycle);
if (fileMap != null) {
for (final int tile : expectedTiles) {
final File cycleFile = fileMap.get(tile);
if (cycleFile != null) {
if (tileToFileLengthMap.get(tile) == null) {
tileToFileLengthMap.put(tile, cycleFile.length());
} else if (!extension.equals(".bcl.gz") && tileToFileLengthMap.get(tile) != cycleFile.length()) {
// TODO: The gzip bcl files might not be the same length despite having the same content,
// for now we're punting on this but this should be looked into at some point
failures.add("File type " + extension
+ " has cycles files of different length. Current cycle ("
+ currentCycle + ") " +
"Length of first non-empty file (" + tileToFileLengthMap.get(tile)
+ ") length of current cycle (" + cycleFile.length() + ")"
+ " File(" + cycleFile.getAbsolutePath() + ")");
}
} else {
failures.add("File type " + extension + " is missing a file for cycle " + currentCycle + " and tile " + tile);
}
}
} else {
failures.add("Missing file for cycle " + currentCycle + " in directory " + base.getAbsolutePath()
+ " for file type " + extension);
}
}
}
return failures;
}
@Override
public List fakeFiles(final List expectedTiles, final int[] expectedCycles,
final IlluminaFileUtil.SupportedIlluminaFormat format) {
final List failures = new LinkedList();
if (!base.exists()) {
base.mkdirs();
}
final Set missingCycleSet = new TreeSet();
for (final Integer cycle : expectedCycles) {
missingCycleSet.add(cycle);
}
missingCycleSet.removeAll(detectedCycles);
for (final Integer cycle : missingCycleSet) {
final File cycleDirectory = new File(base, "C" + cycle + ".1");
if (cycleDirectory.mkdirs()) {
detectedCycles.add(cycle);
}
}
final CycleIlluminaFileMap cfm = getPerTilePerCycleFiles();
final Map tileToSizeMap = new HashMap();
for (final int currentCycle : expectedCycles) {
final IlluminaFileMap fileMap = cfm.get(currentCycle);
if (fileMap == null) {
for (final Integer tile : expectedTiles) {
final File fileToFake = new File(base + File.separator + getFileForCycle(currentCycle, tile));
try {
if (tileToSizeMap.containsKey(tile)) {
faker.fakeFile(fileToFake, tileToSizeMap.get(tile));
}
else{
faker.fakeFile(fileToFake, 1);
}
} catch (final IOException e) {
failures.add("Could not create fake file: " + e.getMessage());
}
}
} else {
for (final int tile : expectedTiles) {
final File cycleFile = fileMap.get(tile);
if (cycleFile != null && !tileToSizeMap.containsKey(tile)) {
tileToSizeMap.put(tile, (int) BclReader.getNumberOfClusters(cycleFile));
}
try {
if (cycleFile == null) {
final File fileToFake = new File(base + File.separator + getFileForCycle(currentCycle, tile));
if (tileToSizeMap.containsKey(tile)) {
faker.fakeFile(fileToFake, tileToSizeMap.get(tile));
} else {
faker.fakeFile(fileToFake, 1);
}
}
} catch (final IOException e) {
failures.add("Could not create fake file: " + e.getMessage());
}
}
}
}
for (final Integer cycle : missingCycleSet) {
failures.add("Missing cycle directory " + cycle + " in directory " + base.getAbsolutePath()
+ " for file type " + extension);
}
return failures;
}
private String getFileForCycle(final int currentCycle, final int tile) {
return "C" + currentCycle + ".1" + File.separator + "s_" + lane + "_" + tile + extension;
}
public static int getCycleFromDir(final File tempCycleDir) {
final String fileName = tempCycleDir.getName();
final Matcher matcher = IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN.matcher(fileName);
if (!matcher.matches()) {
throw new PicardException("Invalid cycle directory name " + tempCycleDir.getName());
}
return Integer.parseInt(matcher.group(1));
}
}