New upstream version 0.38+dfsg (d2edfdea) · Commits · Debian Med / trimmomatic

build.xml

+1 −1

Original line number	Diff line number	Diff line
		<project name="Trimmomatic" default="dist" basedir=".">
		<property name="version" value="0.36"/>
		<property name="version" value="0.38"/>

		<property name="src" location="src" />
		<property name="lib" location="lib" />

src/org/usadellab/trimmomatic/TrimStats.java

+59 −34

Original line number	Diff line number	Diff line
		package org.usadellab.trimmomatic;

		import java.io.File;
		import java.io.IOException;
		import java.io.PrintStream;
		import java.text.DecimalFormat;

		import org.usadellab.trimmomatic.fastq.FastqRecord;
		@@ -8,25 +11,25 @@ public class TrimStats
		{
		private static DecimalFormat formatter=new DecimalFormat("0.00");

		private int input;
		private int survivingBoth;
		private int survivingForward;
		private int survivingReverse;
		private long readsInput;
		private long readsSurvivingBoth;
		private long readsSurvivingForward;
		private long readsSurvivingReverse;

		public TrimStats()
		{
		input=0;
		survivingBoth=0;
		survivingForward=0;
		survivingReverse=0;
		readsInput=0;
		readsSurvivingBoth=0;
		readsSurvivingForward=0;
		readsSurvivingReverse=0;
		}

		public void merge(TrimStats other)
		{
		input+=other.input;
		survivingBoth+=other.survivingBoth;
		survivingForward+=other.survivingForward;
		survivingReverse+=other.survivingReverse;
		readsInput+=other.readsInput;
		readsSurvivingBoth+=other.readsSurvivingBoth;
		readsSurvivingForward+=other.readsSurvivingForward;
		readsSurvivingReverse+=other.readsSurvivingReverse;
		}


		@@ -36,57 +39,79 @@ public class TrimStats
		{
		if(originalRecs[0]!=null)
		{
		input++;
		readsInput++;

		if(recs[0]!=null)
		survivingForward++;
		readsSurvivingForward++;
		}
		}
		else
		{
		if(originalRecs[0]!=null && originalRecs[1]!=null)
		{
		input++;
		readsInput++;

		if(recs[0]!=null)
		{
		if(recs[1]!=null)
		survivingBoth++;
		readsSurvivingBoth++;
		else
		survivingForward++;
		readsSurvivingForward++;
		}
		else if(recs[1]!=null)
		survivingReverse++;
		readsSurvivingReverse++;
		}

		}
		}

		public String getStatsSE()
		public String processStatsSE(PrintStream statsSummaryStream)
		{
		int dropped=input-survivingForward;
		long dropped=readsInput-readsSurvivingForward;

		double survivingForwardPercent=(100.0*survivingForward)/input;
		double droppedPercent=(100.0*dropped)/input;
		double survivingForwardPercent=(100.0*readsSurvivingForward)/readsInput;
		double droppedPercent=(100.0*dropped)/readsInput;

		return "Input Reads: "+input+
		" Surviving: "+survivingForward+" ("+formatter.format(survivingForwardPercent)+
		if(statsSummaryStream!=null)
		{
		statsSummaryStream.println("Input Reads: "+readsInput);
		statsSummaryStream.println("Surviving Reads: "+readsSurvivingForward);
		statsSummaryStream.println("Surviving Read Percent: "+formatter.format(survivingForwardPercent));
		statsSummaryStream.println("Dropped Reads: "+dropped);
		statsSummaryStream.println("Dropped Read Percent: "+formatter.format(droppedPercent));
		}

		return "Input Reads: "+readsInput+
		" Surviving: "+readsSurvivingForward+" ("+formatter.format(survivingForwardPercent)+
		"%) Dropped: "+dropped+" ("+formatter.format(droppedPercent)+"%)";
		}

		public String getStatsPE()
		public String processStatsPE(PrintStream statsSummaryStream)
		{
		int dropped=input-survivingBoth-survivingForward-survivingReverse;
		long dropped=readsInput-readsSurvivingBoth-readsSurvivingForward-readsSurvivingReverse;

		double survivingBothPercent=(100.0*survivingBoth)/input;
		double survivingForwardPercent=(100.0*survivingForward)/input;
		double survivingReversePercent=(100.0*survivingReverse)/input;
		double droppedPercent=(100.0*dropped)/input;
		double survivingBothPercent=(100.0*readsSurvivingBoth)/readsInput;
		double survivingForwardPercent=(100.0*readsSurvivingForward)/readsInput;
		double survivingReversePercent=(100.0*readsSurvivingReverse)/readsInput;
		double droppedPercent=(100.0*dropped)/readsInput;

		if(statsSummaryStream!=null)
		{
		statsSummaryStream.println("Input Read Pairs: "+readsInput);
		statsSummaryStream.println("Both Surviving Reads: "+readsSurvivingBoth);
		statsSummaryStream.println("Both Surviving Read Percent: "+formatter.format(survivingBothPercent));
		statsSummaryStream.println("Forward Only Surviving Reads: "+readsSurvivingForward);
		statsSummaryStream.println("Forward Only Surviving Read Percent: "+formatter.format(survivingForwardPercent));
		statsSummaryStream.println("Reverse Only Surviving Reads: "+readsSurvivingReverse);
		statsSummaryStream.println("Reverse Only Surviving Read Percent: "+formatter.format(survivingReversePercent));
		statsSummaryStream.println("Dropped Reads: "+dropped);
		statsSummaryStream.println("Dropped Read Percent: "+formatter.format(droppedPercent));
		}

		return "Input Read Pairs: "+input+
		" Both Surviving: "+survivingBoth+" ("+formatter.format(survivingBothPercent)+
		"%) Forward Only Surviving: "+survivingForward+" ("+formatter.format(survivingForwardPercent)+
		"%) Reverse Only Surviving: "+survivingReverse+" ("+formatter.format(survivingReversePercent)+
		return "Input Read Pairs: "+readsInput+
		" Both Surviving: "+readsSurvivingBoth+" ("+formatter.format(survivingBothPercent)+
		"%) Forward Only Surviving: "+readsSurvivingForward+" ("+formatter.format(survivingForwardPercent)+
		"%) Reverse Only Surviving: "+readsSurvivingReverse+" ("+formatter.format(survivingReversePercent)+
		"%) Dropped: "+dropped+" ("+formatter.format(droppedPercent)+"%)";

		}

src/org/usadellab/trimmomatic/Trimmomatic.java

+2 −2

Original line number	Diff line number	Diff line
		@@ -95,9 +95,9 @@ public class Trimmomatic
		if(showUsage)
		{
		System.err.println("Usage: ");
		System.err.println(" PE [-version] [-threads <threads>] [-phred33\|-phred64] [-trimlog <trimLogFile>] [-quiet] [-validatePairs] [-basein <inputBase> \| <inputFile1> <inputFile2>] [-baseout <outputBase> \| <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...");
		System.err.println(" PE [-version] [-threads <threads>] [-phred33\|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> \| <inputFile1> <inputFile2>] [-baseout <outputBase> \| <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...");
		System.err.println(" or: ");
		System.err.println(" SE [-version] [-threads <threads>] [-phred33\|-phred64] [-trimlog <trimLogFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...");
		System.err.println(" SE [-version] [-threads <threads>] [-phred33\|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...");
		System.err.println(" or: ");
		System.err.println(" -version");
		System.exit(1);

src/org/usadellab/trimmomatic/TrimmomaticPE.java

+26 −10

Original line number	Diff line number	Diff line
		@@ -50,7 +50,7 @@ public class TrimmomaticPE extends Trimmomatic

		public void processSingleThreaded(FastqParser parser1, FastqParser parser2, FastqSerializer serializer1P,
		FastqSerializer serializer1U, FastqSerializer serializer2P, FastqSerializer serializer2U,
		Trimmer trimmers[], PrintStream trimLogStream, PairingValidator pairingValidator) throws IOException
		Trimmer trimmers[], PrintStream trimLogStream, PrintStream statsSummaryStream, PairingValidator pairingValidator) throws IOException
		{
		TrimStats stats = new TrimStats();

		@@ -115,12 +115,13 @@ public class TrimmomaticPE extends Trimmomatic
		}
		}

		logger.infoln(stats.getStatsPE());
		logger.infoln(stats.processStatsPE(statsSummaryStream));
		}

		public void processMultiThreaded(FastqParser parser1, FastqParser parser2, FastqSerializer serializer1P,
		FastqSerializer serializer1U, FastqSerializer serializer2P, FastqSerializer serializer2U,
		Trimmer trimmers[], PrintStream trimLogStream, PairingValidator pairingValidator, int threads) throws IOException
		Trimmer trimmers[], PrintStream trimLogStream, PrintStream statsSummaryStream,
		PairingValidator pairingValidator, int threads) throws IOException
		{
		ArrayBlockingQueue<List<FastqRecord>> parser1Queue = new ArrayBlockingQueue<List<FastqRecord>>(threads);
		ArrayBlockingQueue<List<FastqRecord>> parser2Queue = new ArrayBlockingQueue<List<FastqRecord>>(threads);
		@@ -249,7 +250,7 @@ public class TrimmomaticPE extends Trimmomatic
		trimLogThread.join();

		statsThread.join();
		logger.infoln(statsWorker.getStats().getStatsPE());
		logger.infoln(statsWorker.getStats().processStatsPE(statsSummaryStream));
		}
		catch (InterruptedException e)
		{
		@@ -258,7 +259,7 @@ public class TrimmomaticPE extends Trimmomatic
		}

		public void process(File input1, File input2, File output1P, File output1U, File output2P, File output2U,
		Trimmer trimmers[], int phredOffset, File trimLog, boolean validatePairing, int threads) throws IOException
		Trimmer trimmers[], int phredOffset, File trimLog, File statsSummaryFile, boolean validatePairing, int threads) throws IOException
		{
		FastqParser parser1 = new FastqParser(phredOffset);
		parser1.parse(input1);
		@@ -302,6 +303,10 @@ public class TrimmomaticPE extends Trimmomatic
		// FileOutputStream(trimLog),1000000),false);
		trimLogStream = new PrintStream(trimLog);

		PrintStream statsSummaryStream = null;
		if(statsSummaryFile!=null)
		statsSummaryStream = new PrintStream(statsSummaryFile);

		PairingValidator pairingValidator=null;

		if(validatePairing)
		@@ -309,10 +314,10 @@ public class TrimmomaticPE extends Trimmomatic

		if (threads == 1)
		processSingleThreaded(parser1, parser2, serializer1P, serializer1U, serializer2P, serializer2U, trimmers,
		trimLogStream, pairingValidator);
		trimLogStream, statsSummaryStream, pairingValidator);
		else
		processMultiThreaded(parser1, parser2, serializer1P, serializer1U, serializer2P, serializer2U, trimmers,
		trimLogStream, pairingValidator, threads);
		trimLogStream, statsSummaryStream, pairingValidator, threads);

		serializer1P.close();
		serializer1U.close();
		@@ -321,6 +326,9 @@ public class TrimmomaticPE extends Trimmomatic

		if (trimLogStream != null)
		trimLogStream.close();

		if(statsSummaryStream != null)
		statsSummaryStream.close();
		}

		private static int getFileExtensionIndex(String str)
		@@ -414,6 +422,7 @@ public class TrimmomaticPE extends Trimmomatic
		boolean showVersion=false;

		File trimLog = null;
		File statsSummary = null;

		List<String> nonOptionArgs=new ArrayList<String>();

		@@ -436,6 +445,13 @@ public class TrimmomaticPE extends Trimmomatic
		else
		badOption = true;
		}
		else if (arg.equals("-summary"))
		{
		if (argIndex < args.length)
		statsSummary = new File(args[argIndex++]);
		else
		badOption = true;
		}
		else if (arg.equals("-basein"))
		{
		if (argIndex < args.length)
		@@ -536,7 +552,8 @@ public class TrimmomaticPE extends Trimmomatic
		Trimmer trimmers[]=createTrimmers(logger, nonOptionArgsIter);

		TrimmomaticPE tm = new TrimmomaticPE(logger);
		tm.process(inputs[0], inputs[1], outputs[0], outputs[1], outputs[2], outputs[3], trimmers, phredOffset, trimLog, validatePairs, threads);
		tm.process(inputs[0], inputs[1], outputs[0], outputs[1], outputs[2], outputs[3],
		trimmers, phredOffset, trimLog, statsSummary, validatePairs, threads);

		logger.infoln("TrimmomaticPE: Completed successfully");
		return true;
		@@ -546,8 +563,7 @@ public class TrimmomaticPE extends Trimmomatic
		{
		if (!run(args))
		{
		System.err
		.println("Usage: TrimmomaticPE [-threads <threads>] [-phred33\|-phred64] [-trimlog <trimLogFile>] [-quiet] [-validatePairs] [-basein <inputBase> \| <inputFile1> <inputFile2>] [-baseout <outputBase> \| <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...");
		System.err.println("Usage: [-version] [-threads <threads>] [-phred33\|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> \| <inputFile1> <inputFile2>] [-baseout <outputBase> \| <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...");
		System.exit(1);
		}
		}

src/org/usadellab/trimmomatic/TrimmomaticSE.java

+24 −9

Original line number	Diff line number	Diff line
		@@ -48,7 +48,7 @@ public class TrimmomaticSE extends Trimmomatic
		}

		public void processSingleThreaded(FastqParser parser, FastqSerializer serializer, Trimmer trimmers[],
		PrintStream trimLogStream) throws IOException
		PrintStream trimLogStream, PrintStream statsSummaryStream) throws IOException
		{
		TrimStats stats = new TrimStats();

		@@ -102,11 +102,11 @@ public class TrimmomaticSE extends Trimmomatic
		}
		}

		logger.infoln(stats.getStatsSE());
		logger.infoln(stats.processStatsSE(statsSummaryStream));
		}

		public void processMultiThreaded(FastqParser parser, FastqSerializer serializer, Trimmer trimmers[],
		PrintStream trimLogStream, int threads) throws IOException
		PrintStream trimLogStream, PrintStream statsSummaryStream, int threads) throws IOException
		{
		ArrayBlockingQueue<List<FastqRecord>> parserQueue = new ArrayBlockingQueue<List<FastqRecord>>(threads);
		ArrayBlockingQueue<Runnable> taskQueue = new ArrayBlockingQueue<Runnable>(threads * 2);
		@@ -181,7 +181,7 @@ public class TrimmomaticSE extends Trimmomatic
		trimLogThread.join();

		statsThread.join();
		logger.infoln(statsWorker.getStats().getStatsSE());
		logger.infoln(statsWorker.getStats().processStatsSE(statsSummaryStream));
		}
		catch (InterruptedException e)
		{
		@@ -190,7 +190,7 @@ public class TrimmomaticSE extends Trimmomatic

		}

		public void process(File input, File output, Trimmer trimmers[], int phredOffset, File trimLog, int threads)
		public void process(File input, File output, Trimmer trimmers[], int phredOffset, File trimLog, File statsSummaryFile, int threads)
		throws IOException
		{
		FastqParser parser = new FastqParser(phredOffset);
		@@ -218,15 +218,22 @@ public class TrimmomaticSE extends Trimmomatic
		if (trimLog != null)
		trimLogStream = new PrintStream(trimLog);

		PrintStream statsSummaryStream = null;
		if(statsSummaryFile!=null)
		statsSummaryStream = new PrintStream(statsSummaryFile);

		if (threads == 1)
		processSingleThreaded(parser, serializer, trimmers, trimLogStream);
		processSingleThreaded(parser, serializer, trimmers, trimLogStream, statsSummaryStream);
		else
		processMultiThreaded(parser, serializer, trimmers, trimLogStream, threads);
		processMultiThreaded(parser, serializer, trimmers, trimLogStream, statsSummaryStream, threads);

		serializer.close();

		if (trimLogStream != null)
		trimLogStream.close();

		if(statsSummaryStream != null)
		statsSummaryStream.close();
		}

		public static boolean run(String[] args) throws IOException
		@@ -238,6 +245,7 @@ public class TrimmomaticSE extends Trimmomatic
		boolean badOption = false;

		File trimLog = null;
		File statsSummary = null;
		boolean quiet=false;
		boolean showVersion=false;

		@@ -262,6 +270,13 @@ public class TrimmomaticSE extends Trimmomatic
		else
		badOption = true;
		}
		else if (arg.equals("-summary"))
		{
		if (argIndex < args.length)
		statsSummary = new File(args[argIndex++]);
		else
		badOption = true;
		}
		else if (arg.equals("-quiet"))
		quiet=true;
		else if (arg.equals("-version"))
		@@ -303,7 +318,7 @@ public class TrimmomaticSE extends Trimmomatic
		Trimmer trimmers[]=createTrimmers(logger, nonOptionArgsIter);

		TrimmomaticSE tm = new TrimmomaticSE(logger);
		tm.process(input, output, trimmers, phredOffset, trimLog, threads);
		tm.process(input, output, trimmers, phredOffset, trimLog, statsSummary, threads);

		logger.infoln("TrimmomaticSE: Completed successfully");
		return true;
		@@ -314,7 +329,7 @@ public class TrimmomaticSE extends Trimmomatic
		if(!run(args))
		{
		System.err
		.println("Usage: TrimmomaticSE [-threads <threads>] [-phred33\|-phred64] [-trimlog <trimLogFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...");
		.println("Usage: TrimmomaticSE [-version] [-threads <threads>] [-phred33\|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...");
		System.exit(1);
		}
		}