org.mulinlab.varnote.cmdline.txtreader.run

Class AnnoRunReader<T>

java.lang.Object

org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader<T>

org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader<T>

org.mulinlab.varnote.cmdline.txtreader.run.FileQueryReader<T>

org.mulinlab.varnote.cmdline.txtreader.run.AnnoRunReader<T>

All Implemented Interfaces:

RunReaderInterface<T>

public final class AnnoRunReader<T>
extends FileQueryReader<T>

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ANNO_CONFIG
static java.lang.String	ANNO_FORMAT
static java.lang.String	FORCE_OVERLAP
static java.lang.String	VCF_HEADER_PATH_FOR_BED

Fields inherited from class org.mulinlab.varnote.cmdline.txtreader.run.FileQueryReader

format, queryFileParam, runParam

Fields inherited from class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

ALLOW_LARGE_VARIANTS, COMMNT_INDICATOR, DB_BEGIN, DB_INDEX_TYPE, DB_LABEL, DB_MODE, DB_PATH, dbParams, HAS_HEADER, HEADER, HEADER_PATH, ISZIP, LOJ, MAX_VARIANT_LENGTH, MODE, OUTPUT_MODE, OUTPUT_PATH, QUERY, QUERY_ALT, QUERY_BEGIN, QUERY_CHROM, QUERY_END, QUERY_FORMAT, QUERY_REF, REMOVE_COMMENT, THREAD, USE_JDK_INFLATER, VERBOSE, ZERO_BASED

Fields inherited from class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

COMMENT_LINE, END, OVERLAP_EQUAL, OVERLAP_NOTE, valueHash

Constructor Summary

Constructors

Constructor and Description
AnnoRunReader()

Method Summary

Modifier and Type	Method and Description
T	doEnd()

Methods inherited from class org.mulinlab.varnote.cmdline.txtreader.run.FileQueryReader

processLine

Methods inherited from class org.mulinlab.varnote.cmdline.txtreader.abs.QueryReader

checkDB, doInit, filterLine, read, setDB, setformat, setformatHeader, setOutParam

Methods inherited from class org.mulinlab.varnote.cmdline.txtreader.abs.AbstractQueryReader

isBreak, putValue, splitLine

Methods inherited from class java.lang.Object

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

Field Detail

ANNO_CONFIG

public static final java.lang.String ANNO_CONFIG

See Also:

Constant Field Values

VCF_HEADER_PATH_FOR_BED

public static final java.lang.String VCF_HEADER_PATH_FOR_BED

See Also:

Constant Field Values

FORCE_OVERLAP

public static final java.lang.String FORCE_OVERLAP

See Also:

Constant Field Values

ANNO_FORMAT

public static final java.lang.String ANNO_FORMAT

See Also:

Constant Field Values

Constructor Detail

AnnoRunReader

public AnnoRunReader()

Method Detail

doEnd

public T doEnd()

Specified by:

doEnd in interface RunReaderInterface<T>

Overrides:

doEnd in class FileQueryReader<T>