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Use VariantContext and Genotype accessor methods for attributes that will return null for unparseable data 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4699 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2010-11-17 18:19:56 +00:00
parent 2f3578182a
commit 367cc9135f
3 changed files with 15 additions and 70 deletions
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74
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
View File

@ -824,9 +824,7 @@ public class VariantContextUtils {
String mergedName = VariantContextUtils.mergeVariantContextNames(vc1.getSource(), vc2.getSource());
double mergedNegLog10PError = Math.max(vc1.getNegLog10PError(), vc2.getNegLog10PError());
Set<String> mergedFilters = new HashSet<String>(); // Since vc1 and vc2 were unfiltered, the merged record remains unfiltered
Map<String, Object> mergedAttribs = VariantContextUtils.mergeVariantContextAttributes(vc1.getAttributes(), vc2.getAttributes());
if (mergedAttribs == null)
return null;
Map<String, Object> mergedAttribs = VariantContextUtils.mergeVariantContextAttributes(vc1, vc2);
VariantContext mergedVc = new VariantContext(mergedName, vc1.getChr(), vc1.getStart(), vc2.getEnd(), mergeData.getAllMergedAlleles(), mergedGenotypes, mergedNegLog10PError, mergedFilters, mergedAttribs);
@ -906,18 +904,18 @@ public class VariantContextUtils {
return name1 + "_" + name2;
}
private static Map<String, Object> mergeVariantContextAttributes(Map<String, Object> attribs1, Map<String, Object> attribs2) {
private static Map<String, Object> mergeVariantContextAttributes(VariantContext vc1, VariantContext vc2) {
Map<String, Object> mergedAttribs = new HashMap<String, Object>();
List<Map<String, Object>> attribsList = new LinkedList<Map<String, Object>>();
attribsList.add(attribs1);
attribsList.add(attribs2);
List<VariantContext> vcList = new LinkedList<VariantContext>();
vcList.add(vc1);
vcList.add(vc2);
String[] MERGE_OR_ATTRIBS = {VCFConstants.DBSNP_KEY};
for (String orAttrib : MERGE_OR_ATTRIBS) {
boolean attribVal = false;
for (Map<String, Object> attribs : attribsList) {
Boolean val = getBooleanAttribute(attribs, orAttrib);
for (VariantContext vc : vcList) {
Boolean val = vc.getAttributeAsBooleanNoException(orAttrib);
if (val != null)
attribVal = (attribVal || val);
if (attribVal) // already true, so no reason to continue:
@ -928,8 +926,8 @@ public class VariantContextUtils {
// Merge ID fields:
String iDVal = null;
for (Map<String, Object> attribs : attribsList) {
String val = getStringAttribute(attribs, VariantContext.ID_KEY);
for (VariantContext vc : vcList) {
String val = vc.getAttributeAsStringNoException(VariantContext.ID_KEY);
if (val != null && !val.equals(VCFConstants.EMPTY_ID_FIELD)) {
if (iDVal == null)
iDVal = val;
@ -943,58 +941,6 @@ public class VariantContextUtils {
return mergedAttribs;
}
public static Boolean getBooleanAttribute(Map<String, Object> attribs, String attribName) {
Object val = attribs.get(attribName);
if (val == null || val.equals(VCFConstants.MISSING_VALUE_v4))
return null;
try {
return new Boolean(val.toString());
}
catch (Exception e) {// IGNORE unparseable data
return null;
}
}
public static String getStringAttribute(Map<String, Object> attribs, String attribName) {
Object val = attribs.get(attribName);
if (val == null || val.equals(VCFConstants.MISSING_VALUE_v4))
return null;
try {
return val.toString();
}
catch (Exception e) {// IGNORE unparseable data
return null;
}
}
public static Double getDoubleAttribute(Map<String, Object> attribs, String attribName) {
Object val = attribs.get(attribName);
if (val == null || val.equals(VCFConstants.MISSING_VALUE_v4))
return null;
try {
return new Double(val.toString());
}
catch (Exception e) {// IGNORE unparseable data
return null;
}
}
public static Integer getIntegerAttribute(Map<String, Object> attribs, String attribName) {
Object val = attribs.get(attribName);
if (val == null || val.equals(VCFConstants.MISSING_VALUE_v4))
return null;
try {
return new Integer(val.toString());
}
catch (Exception e) {// IGNORE unparseable data
return null;
}
}
private static boolean mergeIntoMNPvalidationCheck(GenomeLocParser genomeLocParser,VariantContext vc1, VariantContext vc2) {
GenomeLoc loc1 = VariantContextUtils.getLocation(genomeLocParser,vc1);
GenomeLoc loc2 = VariantContextUtils.getLocation(genomeLocParser,vc2);
@ -1061,7 +1007,7 @@ public class VariantContextUtils {
public PhaseAndQuality(Genotype gt) {
this.isPhased = gt.genotypesArePhased();
if (this.isPhased)
this.PQ = VariantContextUtils.getDoubleAttribute(gt.getAttributes(), ReadBackedPhasingWalker.PQ_KEY);
this.PQ = gt.getAttributeAsDoubleNoException(ReadBackedPhasingWalker.PQ_KEY);
}
}

9
java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java
View File

@ -462,25 +462,24 @@ class RefSeqData {
private static String CODON_KEY = REFSEQ_PREFIX + "codonCoord";
private static Map<String, String> getRefSeqEntriesToNames(VariantContext vc, boolean getName2) {
Map<String, Object> vcAttribs = vc.getAttributes();
Map<String, String> entriesToNames = new HashMap<String, String>();
Integer numRecords = VariantContextUtils.getIntegerAttribute(vcAttribs, NUM_RECORDS_KEY);
Integer numRecords = vc.getAttributeAsIntegerNoException(NUM_RECORDS_KEY);
if (numRecords != null) {
for (int i = 1; i <= numRecords; i++) {
String key = NAME_KEY + "_" + i;
String name = VariantContextUtils.getStringAttribute(vcAttribs, key);
String name = vc.getAttributeAsStringNoException(key);
if (name != null)
entriesToNames.put(key, name);
}
}
else {
String name = VariantContextUtils.getStringAttribute(vcAttribs, NAME_KEY);
String name = vc.getAttributeAsStringNoException(NAME_KEY);
if (name != null) {
entriesToNames.put(NAME_KEY, name);
}
else { // Check all INFO fields for a match:
for (Map.Entry<String, Object> entry : vcAttribs.entrySet()) {
for (Map.Entry<String, Object> entry : vc.getAttributes().entrySet()) {
String key = entry.getKey();
if (getName2 && key.startsWith(NAME2_KEY))
entriesToNames.put(key, entry.getValue().toString());

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
View File

@ -207,7 +207,7 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
}
public static Double getPQ(Genotype gt) {
return VariantContextUtils.getDoubleAttribute(gt.getAttributes(), ReadBackedPhasingWalker.PQ_KEY);
return gt.getAttributeAsDoubleNoException(ReadBackedPhasingWalker.PQ_KEY);
}
public boolean topMatchesTop(AllelePair b1, AllelePair b2) {