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Viewing changes to src/org/usadellab/trimmomatic/Trimmomatic.java

  • Committer: Package Import Robot
  • Author(s): Andreas Tille, Olivier Sallou
  • Date: 2013-08-07 12:14:33 UTC
  • mfrom: (1.1.1)
  • Revision ID: package-import@ubuntu.com-20130807121433-qxchmfrrodridtvz
Tags: 0.30+dfsg-1
http://bugs.debian.org/718850
* New upstream version
* debian/copyright:
   - DEP5
   - Add Files-Excluded to document what was removed from original source
* debian/watch: handle +dfsg suffix
* debian/get-orig-source: use new uscan if available
* debian/control:
   - cme fix dpkg-control
   - debhelper 9
   - use anonscm in Vcs fields
   - Build-Depends: default-jdk | ...
     Closes: #718850
[ Olivier Sallou]
    * Manage java libs with javahelper
    * Provide upstream missing MANIFEST.MF

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src/org/usadellab/trimmomatic/Trimmomatic.java
 
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package org.usadellab.trimmomatic;
 
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import java.io.IOException;
 
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import java.util.Arrays;
 
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public class Trimmomatic
 
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{
 
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        /**
 
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         * @param args
 
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         */
 
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        public static void main(String[] args) throws IOException
 
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        {
 
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                boolean showUsage=true;
 
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                if(args.length>1)
 
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                        {
 
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                        String mode=args[0];
 
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                        String restOfArgs[]=Arrays.copyOfRange(args, 1, args.length);
 
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                        if(mode.equals("PE"))
 
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                                {
 
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                                if(TrimmomaticPE.run(restOfArgs))
 
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                                        showUsage=false;
 
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                                }
 
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                        else if(mode.equals("SE"))
 
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                                {
 
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                                if(TrimmomaticSE.run(restOfArgs))
 
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                                        showUsage=false;
 
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                                }
 
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                        }
 
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                if(showUsage)
 
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                        {
 
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                        System.err.println("Usage: ");
 
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                        System.err.println("       PE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile1> <inputFile2> <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U> <trimmer1>...");
 
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                        System.err.println("   or: ");
 
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                        System.err.println("       SE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile> <outputFile> <trimmer1>...");
 
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                        System.exit(1);
 
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                        }
 
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        }
 
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}