build.xml

 <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" />

debian/changelog

+trimmomatic (0.39+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper 12
+  * Standards-Version: 4.3.0
+  * Secure URI in copyright format
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/copyright
+
+ -- Andreas Tille <tille@debian.org>  Wed, 03 Jul 2019 08:56:09 +0200
+
 trimmomatic (0.38+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-11
+12

debian/control

@@ -4,12 +4,12 @@ Uploaders: Andreas Tille <tille@debian.org>,
            Steffen Moeller <moeller@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
                default-jdk | openjdk-7-jdk,
                javahelper,
                ant,
                libjbzip2-java
-Standards-Version: 4.1.4
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/trimmomatic
 Vcs-Git: https://salsa.debian.org/med-team/trimmomatic.git
 Homepage: http://www.usadellab.org/cms/index.php?page=trimmomatic

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: Trimmomatic
 Upstream-Contact: Federico Giorgi <federico.giorgi@gmail.com>,
                   Anthony Bolger <bolger@mpimp-golm.mpg.de>

debian/patches/buildxmlJbzip2.patch

@@ -4,7 +4,7 @@ Description: Use Debian packaged bzip2 library
 --- a/build.xml
 +++ b/build.xml
 @@ -2,7 +2,7 @@
- 	<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

@@ -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

@@ -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();