Commit 38d18d35 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.39+dfsg

parent d2edfdea

build.xml

+1 −1
Original line number Diff line number Diff line 
<project name="Trimmomatic" default="dist" basedir=".">

	<property name="version" value="0.38"/>

	<property name="version" value="0.39"/>

	

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

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

src/org/usadellab/trimmomatic/trim/HeadCropTrimmer.java

+69 −7
Original line number Diff line number Diff line
@@ -2,24 +2,86 @@ package org.usadellab.trimmomatic.trim; 


import org.usadellab.trimmomatic.fastq.FastqRecord;



public class HeadCropTrimmer extends AbstractSingleRecordTrimmer

public class HeadCropTrimmer implements Trimmer

{

	private int bases;

	private int maxLength=Integer.MAX_VALUE/2;

	private int firstBases;

	private int midBases;

	private int lastBases;

	

	private int firstMaxLength=Integer.MAX_VALUE/2;

	private int midMaxLength=Integer.MAX_VALUE/2;

	private int lastMaxLength=Integer.MAX_VALUE/2;



	public HeadCropTrimmer(String args)

	{

		String arg[]=args.split(":");

	

		bases=Integer.parseInt(arg[0]);

		switch(arg.length)

			{

			case 1:

				firstBases=midBases=lastBases=Integer.parseInt(arg[0]);

				break;

				

			case 2:

				firstBases=midBases=lastBases=Integer.parseInt(arg[0]);

				firstMaxLength=midMaxLength=lastMaxLength=Integer.parseInt(arg[1]);

				break;

				

			case 4:

				firstBases=midBases=Integer.parseInt(arg[0]);

				firstMaxLength=midMaxLength=Integer.parseInt(arg[1]);

				lastBases=Integer.parseInt(arg[2]);

				lastMaxLength=Integer.parseInt(arg[3]);

				break;

				

			case 6:

				firstBases=Integer.parseInt(arg[0]);

				firstMaxLength=Integer.parseInt(arg[1]);

				midBases=Integer.parseInt(arg[2]);

				midMaxLength=Integer.parseInt(arg[3]);

				lastBases=Integer.parseInt(arg[4]);

				lastMaxLength=Integer.parseInt(arg[5]);

				break;



			default:

				

			}

		

		if(arg.length>1)

			maxLength=Integer.parseInt(arg[1]);

			

	}



	@Override

	public FastqRecord processRecord(FastqRecord in)

	public FastqRecord[] processRecords(FastqRecord[] in) {

		

		if(in==null)

			return null; 



		FastqRecord out[]=new FastqRecord[in.length];

		

		int lastRecord=in.length-1;

		

		if(in.length>0)

			{

			if(in[0]!=null)

				out[0]=processRecord(in[0], firstBases, firstMaxLength);

			}	

		

		for(int i=1;i<lastRecord;i++)

			{

			if(in[i]!=null)

				out[i]=processRecord(in[i], midBases, midMaxLength);

			}

		

		if(lastRecord>0)

			{

			if(in[lastRecord]!=null)

				out[lastRecord]=processRecord(in[lastRecord], lastBases, lastMaxLength);

			}

			

		return out;

	}



	private FastqRecord processRecord(FastqRecord in, int bases, int maxLength)

	{

		int len=in.getSequence().length();

src/org/usadellab/trimmomatic/trim/TailCropTrimmer.java

+61 −20
Original line number Diff line number Diff line
@@ -2,44 +2,85 @@ package org.usadellab.trimmomatic.trim; 


import org.usadellab.trimmomatic.fastq.FastqRecord;



public class TailCropTrimmer extends AbstractSingleRecordTrimmer

public class TailCropTrimmer implements Trimmer

{

	private int bases;

	private int maxLength=Integer.MAX_VALUE/2;

	private int firstBases;

	private int midBases;

	private int lastBases;

	

	private int firstMaxLength=Integer.MAX_VALUE/2;

	private int midMaxLength=Integer.MAX_VALUE/2;

	private int lastMaxLength=Integer.MAX_VALUE/2;

	

	public TailCropTrimmer(String args)

	{

		String arg[]=args.split(":");

		

		bases=Integer.parseInt(arg[0]);

		switch(arg.length)

			{

			case 1:

				firstBases=midBases=lastBases=Integer.parseInt(arg[0]);

				break;

				

			case 2:

				firstBases=midBases=lastBases=Integer.parseInt(arg[0]);

				firstMaxLength=midMaxLength=lastMaxLength=Integer.parseInt(arg[1]);

				break;

				

			case 4:

				firstBases=midBases=Integer.parseInt(arg[0]);

				firstMaxLength=midMaxLength=Integer.parseInt(arg[1]);

				lastBases=Integer.parseInt(arg[2]);

				lastMaxLength=Integer.parseInt(arg[3]);

				break;

				

			case 6:

				firstBases=Integer.parseInt(arg[0]);

				firstMaxLength=Integer.parseInt(arg[1]);

				midBases=Integer.parseInt(arg[2]);

				midMaxLength=Integer.parseInt(arg[3]);

				lastBases=Integer.parseInt(arg[4]);

				lastMaxLength=Integer.parseInt(arg[5]);

				break;



			default:

				

		if(arg.length>1)

			maxLength=Integer.parseInt(arg[1]);

			}

	}

    

        

/*

	@Override

	public FastqRecord[] processRecords(FastqRecord[] in)

	{

	public FastqRecord[] processRecords(FastqRecord[] in) {

		

		if(in==null)

			return null; 



		FastqRecord out[]=new FastqRecord[in.length];

		

		for(int i=0;i<in.length;i++)

		int lastRecord=in.length-1;

		

		if(in.length>0)

			{

			if(in[0]!=null)

				out[0]=processRecord(in[0], firstBases, firstMaxLength);

			}	

		

		for(int i=1;i<lastRecord;i++)

			{

			if(in[i]!=null)

				out[i]=processRecord(in[i]);

				out[i]=processRecord(in[i], midBases, midMaxLength);

			}

		

		return out;

		if(lastRecord>0)

			{

                        if(in[lastRecord]!=null)

				out[lastRecord]=processRecord(in[lastRecord], lastBases, lastMaxLength);

			}	

 */

			

		return out;

	}



	@Override

	public FastqRecord processRecord(FastqRecord in)

	private FastqRecord processRecord(FastqRecord in, int bases, int maxLength)

	{

		int len=in.getSequence().length();