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Ran the rod on a binary plink file with indels and it just worked. Love it when that happens! Unit test to ensure this behaviour is maintained. 

****** PLINK ROD IS NOW READY TO GO ********




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2670 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-01-23 18:13:05 +00:00
parent ae22d35212
commit ac983e7a0b
1 changed files with 37 additions and 0 deletions
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37
java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodTest.java
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@ -203,4 +203,41 @@ public class PlinkRodTest extends BaseTest {
snpNo++;
}
}
@Test
public void testIndelBinary() {
PlinkRodWithGenomeLoc rod = new PlinkRodWithGenomeLoc("binaryTest2");
try {
rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/binary_indel_test.bed"));
} catch (FileNotFoundException e) {
throw new StingException("Test file for testBinaryPedFileNoIndels() could not be found",e);
}
ArrayList<ArrayList<Genotype>> genotypesInRod = new ArrayList<ArrayList<Genotype>>();
do {
genotypesInRod.add(rod.getGenotypes());
} while ( rod.parseLine(null,null) );
List<String> expecAlleles = Arrays.asList("ACCA","","ACCAACCA","GGGG","GG","","AA","TA","00","","CCTCCT","CCT",
"TC","CC","TT","GG","GG","AG","","CTTGCTTG","CTTG","TG","GG","GG");
List<Boolean> expecDeletion = Arrays.asList(false,false,false,false,false,false,false,false,false,true,false,true,
false,false,false,false,false,false,true,false,true,false,false,false);
List<Boolean> expecInsertion = Arrays.asList(true,false,true,true,true,false,false,false,false,false,false,false,
false,false,false,false,false,false,false,false,false,false,false,false);
int al = 0;
for ( ArrayList<Genotype> snp : genotypesInRod ) {
for ( Genotype gen : snp ) {
String alStr = gen.getAlleles().get(0).getBases()+gen.getAlleles().get(1).getBases();
Allele firstAl = gen.getAlleles().get(0);
Allele secondAl = gen.getAlleles().get(1);
boolean isInsertion = ( firstAl.getType() == Allele.AlleleType.INSERTION || secondAl.getType() == Allele.AlleleType.INSERTION );
boolean isDeletion = ( firstAl.getType() == Allele.AlleleType.DELETION || secondAl.getType() == Allele.AlleleType.DELETION );
Assert.assertEquals("That the indel file has the correct alleles for genotype "+al,expecAlleles.get(al), alStr);
Assert.assertEquals("That the insertion property of genotype "+al+" is correct",expecInsertion.get(al),isInsertion);
Assert.assertEquals("That the deletion property of genotype "+al+" is correct", expecDeletion.get(al), isDeletion);
al++;
}
}
}
}