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misc improvements 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2972 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-10 03:00:28 +00:00
parent 6e855809e1
commit 1a576525e9
2 changed files with 37 additions and 25 deletions
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58
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
View File

@ -42,8 +42,11 @@ public class SequenomValidationConverter extends RodWalker<VCFRecord,Integer> {
// max allowable indel size (based on ref window)
private static final int MAX_INDEL_SIZE = 40;
// the VCF writer
private VCFWriter vcfWriter = null;
// sample names
private TreeSet<String> sampleNames = null;
// vcf records
private ArrayList<VCFRecord> records = new ArrayList<VCFRecord>();
// statistics
private int numRecords = 0;
@ -83,18 +86,26 @@ public class SequenomValidationConverter extends RodWalker<VCFRecord,Integer> {
if ( plinkRod == null )
return null;
if ( vcfWriter == null )
initializeWriter(plinkRod);
if ( sampleNames == null )
sampleNames = new TreeSet<String>(plinkRod.getSampleNames());
return addVariantInformationToCall(ref, plinkRod);
}
private void initializeWriter(PlinkRod plinkRod) {
vcfWriter = new VCFWriter(vcfFile);
public Integer reduce(VCFRecord call, Integer numVariants) {
if ( call != null ) {
numVariants++;
records.add(call);
}
return numVariants;
}
public void onTraversalDone(Integer finalReduce) {
VCFWriter vcfWriter = new VCFWriter(vcfFile);
// set up the info and filter headers
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.add(new VCFHeaderLine("source", "PlinkToVCF"));
hInfo.add(new VCFHeaderLine("source", "SequenomValidationConverter"));
hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
hInfo.add(new VCFInfoHeaderLine("NoCallPct", 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Percent of no-calls"));
hInfo.add(new VCFInfoHeaderLine("HomRefPct", 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Percent of homozygous reference genotypes"));
@ -107,28 +118,29 @@ public class SequenomValidationConverter extends RodWalker<VCFRecord,Integer> {
hInfo.add(new VCFFilterHeaderLine("HighNoCallRate", "The validation no-call rate is too high"));
hInfo.add(new VCFFilterHeaderLine("TooManyHomVars", "The validation homozygous variant rate is too high"));
VCFHeader header = new VCFHeader(hInfo, new TreeSet<String>(plinkRod.getSampleNames()));
vcfWriter.writeHeader(header);
}
public Integer reduce(VCFRecord call, Integer numVariants) {
if ( call != null ) {
numVariants++;
vcfWriter.addRecord(call);
}
return numVariants;
}
public void onTraversalDone(Integer finalReduce) {
if ( vcfWriter != null )
vcfWriter.close();
// print out (and add to headers) the validation metrics
System.out.println(String.format("Total number of samples assayed:\t\t\t%d", sampleNames.size()));
hInfo.add(new VCFHeaderLine("ValidationMetrics_SamplesAssayed", String.format("%d", sampleNames.size())));
System.out.println(String.format("Total number of records processed:\t\t\t%d", numRecords));
hInfo.add(new VCFHeaderLine("ValidationMetrics_RecordsProcessed", String.format("%d", numRecords)));
System.out.println(String.format("Number of Hardy-Weinberg violations:\t\t\t%d (%d%%)", numHWViolations, 100*numHWViolations/numRecords));
hInfo.add(new VCFHeaderLine("ValidationMetrics_HardyWeinbergViolations", String.format("\"%d (%d%%)\"", numHWViolations, 100*numHWViolations/numRecords)));
System.out.println(String.format("Number of no-call violations:\t\t\t\t%d (%d%%)", numNoCallViolations, 100*numNoCallViolations/numRecords));
hInfo.add(new VCFHeaderLine("ValidationMetrics_NoCallViolations", String.format("\"%d (%d%%)\"", numNoCallViolations, 100*numNoCallViolations/numRecords)));
System.out.println(String.format("Number of homozygous variant violations:\t\t%d (%d%%)", numHomVarViolations, 100*numHomVarViolations/numRecords));
hInfo.add(new VCFHeaderLine("ValidationMetrics_HomVarViolations", String.format("\"%d (%d%%)\"", numHomVarViolations, 100*numHomVarViolations/numRecords)));
int goodRecords = numRecords - numHWViolations - numNoCallViolations - numHomVarViolations;
System.out.println(String.format("Number of records passing all filters:\t\t\t%d (%d%%)", goodRecords, 100*goodRecords/numRecords));
System.out.println(String.format("Number of passing records that validated as true:\t%d (%d%%)", numTrueVariants, 100*numTrueVariants/goodRecords));
hInfo.add(new VCFHeaderLine("ValidationMetrics_RecordsPassingFilters", String.format("\"%d (%d%%)\"", goodRecords, 100*goodRecords/numRecords)));
System.out.println(String.format("Number of passing records that are polymorphic:\t\t%d (%d%%)", numTrueVariants, 100*numTrueVariants/goodRecords));
hInfo.add(new VCFHeaderLine("ValidationMetrics_PolymorphicPassingRecords", String.format("\"%d (%d%%)\"", numTrueVariants, 100*numTrueVariants/goodRecords)));
VCFHeader header = new VCFHeader(hInfo, sampleNames);
vcfWriter.writeHeader(header);
for ( VCFRecord record : records )
vcfWriter.addRecord(record);
vcfWriter.close();
}

4
java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java
View File

@ -11,7 +11,7 @@ public class SequenomValidationConverterIntegrationTest extends WalkerTest {
String testPedFile = validationDataLocation + "Sequenom_Test_File.txt";
String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T SequenomValidationConverter -B input,Plink,"+testPedFile+" -vcf %s";
WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
Arrays.asList("02dcb683db503599efed0b76daa8fcba"));
Arrays.asList("d19f28fdbe3e731522a52c5329777a9f"));
executeTest("Test SNPs", spec);
}
@ -20,7 +20,7 @@ public class SequenomValidationConverterIntegrationTest extends WalkerTest {
String testPedFile = validationDataLocation + "pilot2_indel_validation.renamed.ped";
String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T SequenomValidationConverter -B input,Plink,"+testPedFile+" -vcf %s";
WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
Arrays.asList("e72c0ab95b279a4d39cc14d40770a801"));
Arrays.asList("257fcd5e345f2853813e37b88fbc707c"));
executeTest("Test Indels", spec);
}
}