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Changes to MVC to make the the header of its output VCF compliant with spec (give expected # of values for info field annotations) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3660 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-06-28 18:33:23 +00:00
parent c047232b18
commit 20f5fdbcf7
1 changed files with 17 additions and 15 deletions
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32
java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
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@ -307,34 +307,36 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
} }
public enum MendelianInfoKey { public enum MendelianInfoKey {
ViolationType("MVT","String","\"The Mendelian violation type\""), ViolationType("MVT","String",1,"\"The Mendelian violation type\""),
ParentalDeletion("deletedParent","String","\"The parent from whom the child (putatively) inherited a deletion at opposite homozygous sites\""), ParentalDeletion("deletedParent","String",1,"\"The parent from whom the child (putatively) inherited a deletion at opposite homozygous sites\""),
TriAllelicQuality("TriAlQ","Integer","\"The variant quality of the third allele at putative tri-allelic sites\""), TriAllelicQuality("TriAlQ","Integer",1,"\"The variant quality of the third allele at putative tri-allelic sites\""),
TriAllelicBase("TriAlB","String","\"The third allele at putative tri-allelic sites\""), TriAllelicBase("TriAlB","String",1,"\"The third allele at putative tri-allelic sites\""),
MotherHomozygosityRegion("MHR","String","\"An identifier for the mother's homozygosity region where the violation is located\""), MotherHomozygosityRegion("MHR","String",1,"\"An identifier for the mother's homozygosity region where the violation is located\""),
FatherHomozygosityRegion("FHR","String","\"An identifier for the father's homozygosity region where the violation is located\""), FatherHomozygosityRegion("FHR","String",1,"\"An identifier for the father's homozygosity region where the violation is located\""),
ChildHomozygosityRegion("CHR","Integer","\"An identifier for the child's homozygosity region where the violation is located\""), ChildHomozygosityRegion("CHR","Integer",1,"\"An identifier for the child's homozygosity region where the violation is located\""),
ProportionOfParentAllele("PropParent","Double","\"The proportion of bases in the child that were the parent allele at deNovo SNP sites\""), ProportionOfParentAllele("PropParent","Float",1,"\"The proportion of bases in the child that were the parent allele at deNovo SNP sites\""),
/* ***************************************** UNUSED ************************************************ */ /* ***************************************** UNUSED ************************************************ */
NumCallsInRegion("REGION_NCALLS","Integer","\"The number of unfiltered SNP calls found in the homozygosity region\""), NumCallsInRegion("REGION_NCALLS","Integer",1,"\"The number of unfiltered SNP calls found in the homozygosity region\""),
ChildHomozygosityRegionSize("CHRS","Integer","\"The size of the region of homozygosity in the child in which the opposite homozygote is located\""), ChildHomozygosityRegionSize("CHRS","Integer",1,"\"The size of the region of homozygosity in the child in which the opposite homozygote is located\""),
OppositeHomozygotesInRegion("CHROH","Integer","\"The number of opposite-homozygotes located in the region of homozygosity\""), OppositeHomozygotesInRegion("CHROH","Integer",1,"\"The number of opposite-homozygotes located in the region of homozygosity\""),
ParentHomozygosityRegionSize("PHRS","Integer","\"The size of the parental homozygosity region where the deNovo SNP is located\""), ParentHomozygosityRegionSize("PHRS","Integer",1,"\"The size of the parental homozygosity region where the deNovo SNP is located\""),
DeNovoSNPsInRegion("PHRDN","Integer","\"The number of deNovo SNP events located in the same region of parental homozygosity where the deNovo SNP is located\""); DeNovoSNPsInRegion("PHRDN","Integer",1,"\"The number of deNovo SNP events located in the same region of parental homozygosity where the deNovo SNP is located\"");
String keyName; String keyName;
String valueType; String valueType;
String valueDescription; String valueDescription;
int numFields;
MendelianInfoKey(String keyStr,String infoType,String description) { MendelianInfoKey(String keyStr,String infoType, int fields, String description) {
keyName = keyStr; keyName = keyStr;
valueType = infoType; valueType = infoType;
valueDescription = description; valueDescription = description;
numFields = fields;
} }
public String toString() { public String toString() {
return String.format("%s,%s,%s",keyName,valueType,valueDescription); return String.format("%s,%s,%d,%s",keyName,valueType,numFields,valueDescription);
} }
public String getKey() { public String getKey() {