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Added integration test for beagle and verbose output in UG. 

Minor cleanup of VCFRecord code.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2570 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-01-13 03:55:24 +00:00
parent 02e23e2d9c
commit f99586f91b
2 changed files with 41 additions and 16 deletions
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32
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
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@ -36,6 +36,7 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
public static final String PASSES_FILTERS = "0"; public static final String PASSES_FILTERS = "0";
public static final String EMPTY_INFO_FIELD = "."; public static final String EMPTY_INFO_FIELD = ".";
public static final String EMPTY_ID_FIELD = "."; public static final String EMPTY_ID_FIELD = ".";
public static final String EMPTY_ALLELE_FIELD = ".";
public static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f"; public static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f";
// the reference base // the reference base
@ -75,13 +76,13 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
* given the values for each of the columns, create a VCF record. * given the values for each of the columns, create a VCF record.
* *
* @param columnValues a mapping of header strings to values * @param columnValues a mapping of header strings to values
* @param formatString the format string for the genotype records * @param genotypeFormatString the format string for the genotype records
* @param genotypeRecords the genotype records * @param genotypeRecords the genotype records
*/ */
public VCFRecord(Map<VCFHeader.HEADER_FIELDS, String> columnValues, String formatString, List<VCFGenotypeRecord> genotypeRecords) { public VCFRecord(Map<VCFHeader.HEADER_FIELDS, String> columnValues, String genotypeFormatString, List<VCFGenotypeRecord> genotypeRecords) {
extractFields(columnValues); extractFields(columnValues);
mGenotypeRecords.addAll(genotypeRecords); mGenotypeRecords.addAll(genotypeRecords);
mGenotypeFormatString = formatString; mGenotypeFormatString = genotypeFormatString;
} }
/** /**
@ -385,14 +386,6 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
return mInfoFields; return mInfoFields;
} }
/**
* @return the number of columnsof data we're storing
*/
public int getColumnCount() {
if (hasGenotypeData()) return mGenotypeRecords.size() + VCFHeader.HEADER_FIELDS.values().length;
return VCFHeader.HEADER_FIELDS.values().length;
}
public List<VCFGenotypeRecord> getVCFGenotypeRecords() { public List<VCFGenotypeRecord> getVCFGenotypeRecords() {
ArrayList<VCFGenotypeRecord> list = new ArrayList<VCFGenotypeRecord>(); ArrayList<VCFGenotypeRecord> list = new ArrayList<VCFGenotypeRecord>();
for ( Genotype g : mGenotypeRecords ) for ( Genotype g : mGenotypeRecords )
@ -450,8 +443,7 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
}// the formatting string for our genotype records }// the formatting string for our genotype records
public void setReferenceBase(char referenceBase) { public void setReferenceBase(char referenceBase) {
// upppercase the character referenceBase = Character.toUpperCase(referenceBase);
referenceBase = (char) ((referenceBase > 96) ? referenceBase - 32 : referenceBase);
if (referenceBase != 'A' && referenceBase != 'C' && referenceBase != 'T' && referenceBase != 'G' && referenceBase != 'N') if (referenceBase != 'A' && referenceBase != 'C' && referenceBase != 'T' && referenceBase != 'G' && referenceBase != 'N')
throw new IllegalArgumentException("Reference base must be one of A,C,G,T,N, we saw: " + referenceBase); throw new IllegalArgumentException("Reference base must be one of A,C,G,T,N, we saw: " + referenceBase);
mReferenceBase = referenceBase; mReferenceBase = referenceBase;
@ -558,9 +550,17 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
builder.append(FIELD_SEPERATOR); builder.append(FIELD_SEPERATOR);
builder.append(getReferenceBase()); builder.append(getReferenceBase());
builder.append(FIELD_SEPERATOR); builder.append(FIELD_SEPERATOR);
String alts = ""; List<VCFGenotypeEncoding> alts = getAlternateAlleles();
for (VCFGenotypeEncoding str : getAlternateAlleles()) alts += str.toString() + ","; if ( alts.size() > 0 ) {
builder.append((alts.length() > 0) ? alts.substring(0, alts.length() - 1) + FIELD_SEPERATOR : "." + FIELD_SEPERATOR); builder.append(alts.get(0));
for ( int i = 1; i < alts.size(); i++ ) {
builder.append(",");
builder.append(alts.get(i));
}
} else {
builder.append(EMPTY_ALLELE_FIELD);
}
builder.append(FIELD_SEPERATOR);
builder.append(String.format(DOUBLE_PRECISION_FORMAT_STRING, getQual())); builder.append(String.format(DOUBLE_PRECISION_FORMAT_STRING, getQual()));
builder.append(FIELD_SEPERATOR); builder.append(FIELD_SEPERATOR);
builder.append(Utils.join(FILTER_CODE_SEPERATOR, getFilteringCodes())); builder.append(Utils.join(FILTER_CODE_SEPERATOR, getFilteringCodes()));

25
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -204,4 +204,29 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
executeTest(String.format("testMultiTechnologies"), spec); executeTest(String.format("testMultiTechnologies"), spec);
} }
// --------------------------------------------------------------------------------------------------------------
//
// testing verbose and beagle output
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testOtherOutput() {
String[] md5s = {"a5dce541f00d3fe364d110f1cae53538", "677963a26f867fbbd5f030cc3df55075", "cea954546a304aa98fc3a18d4305090a"};
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper" +
" -R " + oneKGLocation + "reference/human_b36_both.fasta" +
" -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam" +
" -varout %s" +
" -verbose %s" +
" -beagle %s" +
" -L 1:10,023,400-10,024,000" +
" -bm empirical" +
" -gm JOINT_ESTIMATE" +
" -vf GELI",
3,
Arrays.asList(md5s));
executeTest(String.format("testOtherOutput"), spec);
}
} }