LeadingTrimmerReadFilterTest.java

package fr.ens.biologie.genomique.eoulsan.bio.readsfilters;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;

import org.junit.Test;

import fr.ens.biologie.genomique.eoulsan.EoulsanException;
import fr.ens.biologie.genomique.eoulsan.bio.ReadSequence;

public class LeadingTrimmerReadFilterTest {
  @Test
  public void LeadingTirmmertest() throws EoulsanException {
  ReadFilter filter = new LeadingTrimmerReadFilter();

  filter.setParameter("arguments", "33");
  filter.init();

  ReadSequence read =
      new ReadSequence(0, "read1", "AGG", "ABC");
  assertTrue(filter.accept(read));
  assertEquals("read1", read.getName());
  assertEquals("GG", read.getSequence());
  assertEquals("BC", read.getQuality());
  assertFalse(filter.accept(null));
  
  filter = new LeadingTrimmerReadFilter();
  filter.setParameter("arguments", "34");
  filter.init();
  assertTrue(filter.accept(read));
  assertEquals("read1", read.getName());
  assertEquals("G", read.getSequence());
  assertEquals("C", read.getQuality());
  assertFalse(filter.accept(null));
  
  filter = new LeadingTrimmerReadFilter();
  filter.setParameter("arguments", "35");
  filter.init();
  assertFalse(filter.accept(read));
  assertEquals("read1", read.getName());
  assertEquals("G", read.getSequence());
  assertEquals("C", read.getQuality());
  assertFalse(filter.accept(null));

  filter = new LeadingTrimmerReadFilter();
  filter.setParameter("arguments", "34");
  filter.init();
  read = new ReadSequence(0,"read2","AGAGTTA","CABABAA");
  assertTrue(filter.accept(read));
  assertEquals("read2", read.getName());
  assertEquals("AGAGTTA", read.getSequence());
  assertEquals("CABABAA", read.getQuality());
  
  read = new ReadSequence(0,"read3","AGAGT","ABABC");
  assertTrue(filter.accept(read));
  assertEquals("read3", read.getName());
  assertEquals("T", read.getSequence());
  assertEquals("C", read.getQuality());
  

  
  

  }
}