org.mulinlab.varnote.config.anno.query

Class QueryVCFParser

java.lang.Object

org.mulinlab.varnote.config.anno.query.AbstractQueryParser

org.mulinlab.varnote.config.anno.query.QueryVCFParser

public final class QueryVCFParser
extends AbstractQueryParser

Field Summary

Fields inherited from class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

BED_FIELD, format, INFO_COL, INFO_FIELD_SEPARATOR, logger, NULLVALUE, TAB, VCF_FIELD, VCF_HEADER_INDICATOR, VCF_INFO_EQUAL

Constructor Summary

Constructors

Constructor and Description
QueryVCFParser(Format format, VCFParser vcfParser)

Method Summary

Modifier and Type	Method and Description
htsjdk.variant.vcf.VCFHeader	getVCFHeader()
java.lang.String	toBEDHeader(java.util.StringJoiner dbHeader)
java.lang.String	toBEDRecord(LocFeature query, java.util.StringJoiner dbjoiner)
java.lang.String	toVCFHeader()
java.lang.String	toVCFRecord(LocFeature query, java.util.StringJoiner dbjoiner)

Methods inherited from class org.mulinlab.varnote.config.anno.query.AbstractQueryParser

getBEDDataStart, getBEDHeaderStart

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

QueryVCFParser

public QueryVCFParser(Format format,
                      VCFParser vcfParser)

Method Detail

toVCFHeader

public java.lang.String toVCFHeader()

Specified by:

toVCFHeader in class AbstractQueryParser

toBEDHeader

public java.lang.String toBEDHeader(java.util.StringJoiner dbHeader)

Specified by:

toBEDHeader in class AbstractQueryParser

toVCFRecord

public java.lang.String toVCFRecord(LocFeature query,
                                    java.util.StringJoiner dbjoiner)

Specified by:

toVCFRecord in class AbstractQueryParser

toBEDRecord

public java.lang.String toBEDRecord(LocFeature query,
                                    java.util.StringJoiner dbjoiner)

Specified by:

toBEDRecord in class AbstractQueryParser

getVCFHeader

public htsjdk.variant.vcf.VCFHeader getVCFHeader()

Specified by:

getVCFHeader in class AbstractQueryParser