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Viewing changes to src/org/usadellab/trimmomatic/trim/LeadingTrimmer.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/trim/LeadingTrimmer.java
 
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package org.usadellab.trimmomatic.trim;
 
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import org.usadellab.trimmomatic.fastq.FastqRecord;
 
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public class LeadingTrimmer extends AbstractSingleRecordTrimmer
 
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{
 
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    private int qual;
 
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    public LeadingTrimmer(String args)
 
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    {
 
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            qual=Integer.parseInt(args);
 
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    }
 
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    public LeadingTrimmer(int qual) {
 
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        this.qual = qual;
 
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    }
 
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    @Override
 
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    public FastqRecord processRecord(FastqRecord in)
 
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    {
 
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            String seq=in.getSequence();
 
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            int quals[]=in.getQualityAsInteger(true);
 
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            for(int i=0;i<seq.length();i++)
 
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                    {
 
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                    if(quals[i]>=qual)
 
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                            return new FastqRecord(in,i,seq.length()-i);
 
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                    }
 
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            return null;
 
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    }
 
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}