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VariantsToTable now blows up by default if you ask for a field that isn't present in a record. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5636 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-04-14 14:42:43 +00:00
parent b3cd14d10a
commit 8ed9c0f518
2 changed files with 25 additions and 12 deletions
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15
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
View File

@ -58,8 +58,11 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
public int MAX_RECORDS = -1;
int nRecords = 0;
@Argument(fullName="ignoreMultiAllelic", shortName="IMA", doc="If provided, we will not require the site to be biallelic", required=false)
public boolean ignoreMultiAllelic = false;
@Argument(fullName="keepMultiAllelic", shortName="KMA", doc="If provided, we will not require the site to be biallelic", required=false)
public boolean keepMultiAllelic = false;
@Argument(fullName="allowMissingData", shortName="AMD", doc="If provided, we will not require every record to contain every field", required=false)
public boolean ALLOW_MISSING_DATA = false;
public void initialize() {
out.println(Utils.join("\t", fieldsToTake));
@ -119,8 +122,8 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
for ( VariantContext vc : vcs) {
if ( (! ignoreMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {
List<String> vals = extractFields(vc, fieldsToTake);
if ( (keepMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {
List<String> vals = extractFields(vc, fieldsToTake, ALLOW_MISSING_DATA);
out.println(Utils.join("\t", vals));
}
}
@ -139,7 +142,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
return s.endsWith("*");
}
public static List<String> extractFields(VariantContext vc, List<String> fields) {
public static List<String> extractFields(VariantContext vc, List<String> fields, boolean allowMissingData) {
List<String> vals = new ArrayList<String>();
for ( String field : fields ) {
@ -162,6 +165,8 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
Collections.sort(toVal);
val = Utils.join(",", toVal);
}
} else if ( ! allowMissingData ) {
throw new UserException(String.format("Missing field %s in vc %s at %s", field, vc.getSource(), vc));
}
vals.add(val);

22
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java
View File

@ -33,16 +33,24 @@ import java.util.*;
import java.io.File;
public class VariantsToTableIntegrationTest extends WalkerTest {
private String variantsToTableCmd(String moreArgs) {
return "-R " + hg18Reference +
" -B:eval,vcf " + validationDataLocation + "/soap_gatk_annotated.vcf" +
" -T VariantsToTable" +
" -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F FILTER -F TRANSITION -F DP -F SB -F set -F RankSumP -F refseq.functionalClass*" +
" -L chr1 -KMA -o %s" + moreArgs;
}
@Test(enabled = true)
public void testComplexVariantsToTable() {
// functional class is a wild card operator
WalkerTestSpec spec = new WalkerTestSpec(
"-R " + hg18Reference +
" -B:eval,vcf " + validationDataLocation + "/soap_gatk_annotated.vcf" +
" -T VariantsToTable" +
" -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F FILTER -F TRANSITION -F DP -F SB -F set -F RankSumP -F refseq.functionalClass*" +
" -L chr1 -o %s",
WalkerTestSpec spec = new WalkerTestSpec(variantsToTableCmd(" -AMD"),
Arrays.asList("b2a3712c1bfad8f1383ffada8b5017ba"));
executeTest("testComplexVariantsToTable", spec).getFirst();
}
@Test(enabled = true)
public void testComplexVariantsToTableFail() {
WalkerTestSpec spec = new WalkerTestSpec(variantsToTableCmd(""), 1, UserException.class);
executeTest("testComplexVariantsToTable-FAIL", spec);
}
}