1 package org.broadinstitute.hellbender.transformers;
2 
3 import org.broadinstitute.hellbender.utils.read.GATKRead;
4 
5 /**
6  * A read transformer to modify the mapping quality of reads with MQ=255 to reads with MQ=60
7  *
8  *
9  */
10 public class MappingQualityReadTransformer implements ReadTransformer {
11     private static final long serialVersionUID = 1L;
12 
13     private int fromQuality = 255;
14     private int toQuality = 60;
15 
MappingQualityReadTransformer(final int fromQuality, final int toQuality)16     public MappingQualityReadTransformer(final int fromQuality, final int toQuality) {
17         this.fromQuality = fromQuality;
18         this.toQuality = toQuality;
19     }
20 
21     @Override
apply(final GATKRead read)22     public GATKRead apply(final GATKRead read) {
23         if (read.getMappingQuality() == fromQuality) {
24             read.setMappingQuality(toQuality);
25         }
26         return read;
27     }
28 }
29