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Viewing changes to src/org/usadellab/trimmomatic/fastq/trim/BarcodeSplitter.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/fastq/trim/BarcodeSplitter.java
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/*
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 * To change this template, choose Tools | Templates
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 * and open the template in the editor.
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 */
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package org.usadellab.trimmomatic.fastq.trim;
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import java.io.File;
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import java.io.IOException;
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import java.util.HashMap;
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import org.usadellab.trimmomatic.fastq.FastqRecord;
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/**
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 *
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 * @author marc
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 */
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public class BarcodeSplitter extends AbstractSingleRecordTrimmer {
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    private HashMap<String, String> barcodes;
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    private int maxMisMatch = 0;
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    private boolean clipOffBarcodes = true;    
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    public BarcodeSplitter(HashMap<String, String> barcodes, int mism, boolean clip) {
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        this.barcodes = barcodes;
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        this.maxMisMatch = mism;
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        this.clipOffBarcodes = clip;
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    }
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    public HashMap<String, String> getBarcodeMap() {
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        return barcodes;
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    }
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    @Override
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    public FastqRecord processRecord(FastqRecord entry) {
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        String seq = entry.getSequence();
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        for (String label : barcodes.keySet()) {
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            int codeLength = barcodes.get(label).length();
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            if (maxMisMatch == 0) {
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                if (entry.getSequence().startsWith(barcodes.get(label))) {
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                    if (clipOffBarcodes) {
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                    FastqRecord outentry = new FastqRecord(entry, codeLength, seq.length() - codeLength);
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                        outentry.setBarcodeLabel(label);                    
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                        return outentry;
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                    } else {
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                        entry.setBarcodeLabel(label);                    
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                        return entry;
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                    }
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                }
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            } else {
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                if (getMisMatches(barcodes.get(label), entry.getSequence(), barcodes.get(label).length()) <= maxMisMatch) {
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                    if (clipOffBarcodes) {
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                    FastqRecord outentry = new FastqRecord(entry, codeLength, seq.length() - codeLength);
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                        outentry.setBarcodeLabel(label);                    
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                        return outentry;
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                    } else {
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                        entry.setBarcodeLabel(label);                    
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                        return entry;
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                    }
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                }
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            }
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        }        
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        // entry did not match any barcodes - write to UNKNOWN
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        entry.setBarcodeLabel("UNKNOWN");
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        return entry;
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    }
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    private int getMisMatches(String a, String b, int range) {
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        int mismatch = 0;
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        for (int i = 0; i < range; i++) {
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            mismatch += (a.charAt(i) == b.charAt(i)) ? 0 : 1;
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        }
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        return mismatch;
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    }
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}