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Refactored some of the small utility methods 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3475 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-06-02 16:26:00 +00:00
parent 898a78e97d
commit e14ae471a0
1 changed files with 43 additions and 58 deletions
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101
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotation.java
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@ -26,7 +26,6 @@
package org.broadinstitute.sting.playground.gatk.walkers.annotator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
@ -60,31 +59,39 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
public static final String HAPLOTYPE_ALTERNATE_COLUMN = "haplotypeAlternate";
public static final String HAPLOTYPE_STRAND_COLUMN = "haplotypeStrand";
public static final String NUM_MATCHES_SPECIAL_INFO_FIELD = "numMatchingRecords";
/** Characters that aren't allowed within VCF info field key-value pairs */
public static final char[] ILLEGAL_INFO_FIELD_VALUES = { ' ', '=', ';' };
/** Replacement for each character in ILLEGAL_INFO_FIELD_VALUES */
public static final char[] ILLEGAL_INFO_FIELD_VALUE_SUBSTITUTES = { '_', '-', '!' };
/**
* For each ROD (aka. record) which overlaps the current locus, generates a
* For each -B input file, for each record which overlaps the current locus, generates a
* set of annotations of the form:
*
* thisRodName.fieldName1=fieldValue, thisRodName.fieldName1=fieldValue
* bindingName.columnName1=columnValue, bindingName.columnName2=columnValue2, etc.
*
* Examples of generated annotations are: dbSNP.avHet=0.7, dbSNP.ref_allele=A, etc.
* For example: dbSNP.avHet=0.7, dbSNP.ref_allele=A, etc.
*
* @return The following is an explanation of this method's return value:
* The annotations (aka. columnName=fieldValue pairs) from a matching record in a particular file are stored in a Map<String, String>.
*
* The annotations from a matching in a particular file are stored in a Map<String, String>
* where the key is bindingName.columnName and the value is the columnValue.
* Since a single input file can have multiple records that overlap the current
* locus (eg. dbSNP can have multiple entries for the same location), a different
* locus (eg. dbSNP can have multiple entries for the same genomic position), a different
* Map<String, String> is created for each matching record in a particular file.
* The list of matching records for each file is then represented as a List<Map<String, String>>
* The set of matching records for each file is then represented as a List<Map<String, String>>
*
* The return value of this method is a Map<String, Object> of the form:
* rodName1 -> List<Map<String, String>>
* rodName2 -> List<Map<String, String>>
* rodName3 -> List<Map<String, String>>
* ...
* Where the rodNames are the -B binding names for each file that were specified on the command line.
* Where the rodNames are the -B binding names for each file that were specified on the command line (eg. -B bindingName,AnnotatorInputTable,/path/to/file).
*
* NOTE: The lists (List<Map<String, String>>) are guaranteed to have size > 0.
* The reason is that a rodName -> List<Map<String, String>> entry will only
* NOTE: The lists (List<Map<String, String>>) are guaranteed to have size > 0
* because a rodName -> List<Map<String, String>> entry will only
* be created in Map<String, Object> if the List has at least one element.
*/
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
@ -106,7 +113,7 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
continue; //GenericAnnotation only works with TabularRODs because it needs to be able to select individual columns.
}
final Map<String, String> annotationsForRecord = convertRecordToAnnotations( gatkFeature );
final Map<String, String> annotationsForRecord = convertRecordToAnnotations( gatkFeature.getName(), ((AnnotatorInputTableFeature) gatkFeature.getUnderlyingObject()).getColumnValues());
//If this record contains the HAPLOTYPE_REFERENCE_COLUMN and/or HAPLOTYPE_ALTERNATE_COLUMN, check whether the
//alleles specified match the the variant's reference allele and alternate allele.
@ -202,77 +209,55 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
/**
* Converts the ROD to a set of key-value pairs of the form:
* thisRodName.fieldName1=fieldValue, thisRodName.fieldName1=fieldValue
* Converts the given record to a set of key-value pairs of the form:
* bindingName.columnName1=column1Value, bindingName.columnName2=column2Value
* (eg. dbSNP.avHet=0.7, dbSNP.ref_allele=A)
*
* @param annotatorInputTableFeature AnnotatorInputTableFeature corresponding to one record in one input file.
* @param annotatorInputTableFeature AnnotatorInputTableFeature corresponding to one record in one -B input file.
* @param name The binding name of the given AnnotatorInputTableFeature.
* @return The map of column-name -> value pairs.
* @return The map of columnName -> columnValue pairs.
*/
private Map<String, String> convertRecordToAnnotations( final GATKFeature feature) {
public static Map<String, String> convertRecordToAnnotations( String bindingName, Map<String, String> record) {
final Map<String, String> result = new HashMap<String, String>();
for(final Entry<String, String> entry : ((AnnotatorInputTableFeature) feature.getUnderlyingObject()).getEntrySet()) {
for(final Entry<String, String> entry : record.entrySet()) {
final String value = entry.getValue();
if(!value.trim().isEmpty()) {
result.put( generateInfoFieldKey(feature.getName(), entry.getKey()), entry.getValue());
result.put( generateInfoFieldKey(bindingName, entry.getKey()), scrubInfoFieldValue(entry.getValue()));
}
}
return result;
}
/**
* Combines the 2 values into a full key.
* @param rodBindingName
* @param columnName
* @return
*/
public static String generateInfoFieldKey(String rodBindingName, String columnName ) {
return rodBindingName + "." + columnName;
return rodBindingName + '.' + columnName;
}
/**
* Parses the columns arg and returns a Map of columns hashed by their binding name.
* For example:
* The command line:
* -s dbSnp.valid,dbsnp.avHet -s refGene.txStart,refGene.txEnd
* Replaces any characters that are not allowed in the info field of a VCF file.
*
* will be passed to this method as:
* ["dbSnp.valid,dbsnp.avHet", "refGene.txStart,refGene.txEnd"]
*
* resulting in a return value of:
* {
* "dbSnp" -> "dbSnp.valid" ,
* "dbSnp" -> "dbsnp.avHet" ,
* "refGene" -> "refGene.txStart",
* "refGene" -> "refGene.txEnd"
* }
*
* @param columnsArg The -s command line arg value.
*
* @return Map representing a parsed version of this arg - see above.
* @param value
* @return the value with any illegal characters replaced by legal ones.
*/
public static Map<String, Set<String>> parseColumnsArg(String[] columnsArg) {
Map<String, Set<String>> result = new HashMap<String, Set<String>>();
for(String s : columnsArg) {
for(String columnSpecifier : s.split(",") ) {
String[] rodNameColumnName = columnSpecifier.split("\\.");
if(rodNameColumnName.length != 2) {
throw new IllegalArgumentException("The following column specifier in the -s arg is invalid: [" + columnSpecifier + "]. It must be of the form 'bindingName.columnName'.");
}
String rodName = rodNameColumnName[0];
//String columnName = rodNameColumnName[1];
Set<String> requestedColumns = result.get(rodName);
if(requestedColumns == null) {
requestedColumns = new HashSet<String>();
result.put(rodName, requestedColumns);
}
requestedColumns.add(columnSpecifier);
}
private static String scrubInfoFieldValue(String value) {
for(int i = 0; i < GenomicAnnotation.ILLEGAL_INFO_FIELD_VALUES.length; i++) {
value = value.replace(GenomicAnnotation.ILLEGAL_INFO_FIELD_VALUES[i], GenomicAnnotation.ILLEGAL_INFO_FIELD_VALUE_SUBSTITUTES[i]);
}
return result;
return value;
}
public VCFInfoHeaderLine getDescription() {
return new VCFInfoHeaderLine("GenericAnnotation", 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position. ");
}