com.intel.genomicsdb

Class GenomicsDBConfiguration

java.lang.Object

org.apache.hadoop.conf.Configuration

com.intel.genomicsdb.GenomicsDBConfiguration

All Implemented Interfaces:

Serializable, Iterable<Map.Entry<String,String>>, org.apache.hadoop.io.Writable

public class GenomicsDBConfiguration
extends org.apache.hadoop.conf.Configuration
implements Serializable

The configuration class enables users to use Java/Scala to populate the input parameters of GenomicsDB. The first version of the input format are JSON files. Through this class, we provide a programmable interface. Note, that once fully coded, this configuration object can be directly passed from GATK4.0

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.apache.hadoop.conf.Configuration

org.apache.hadoop.conf.Configuration.IntegerRanges

Field Summary

Fields

Modifier and Type	Field and Description
private ArrayList<String>	hosts
static String	LOADERJSON
static String	MPIHOSTFILE
private Integer	nCellsPerTile
static String	PARTITION_STRATEGY
private LinkedList<GenomicsDBPartitionInfo>	partitionInfoList
private Boolean	produceCombinedVCF
private Boolean	produceTileDBArray
static String	QUERYJSON
private Integer	segmentSize

Constructor Summary

Constructors

Constructor and Description
GenomicsDBConfiguration(org.apache.hadoop.conf.Configuration configuration)
GenomicsDBConfiguration(org.apache.hadoop.conf.Configuration configuration, List<GenomicsDBPartitionInfo> list) Constructor with partition information

Method Summary

Modifier and Type	Method and Description
private void	addPartitions(GenomicsDBPartitionInfo genomicsDBPartitionInfo)
(package private) List<String>	getHosts()
GenomicsDBConfiguration	setHostFile(String path) Host file contains the hosts where GenomicsDB instances reside.
GenomicsDBConfiguration	setLoaderJsonFile(String path)
(package private) void	setPartitionStrategy(Boolean isRowPartitioned) Set the partition strategy for underlying TileDB storage manager
(package private) void	setPartitionStrategy(String partitionStrategy) Set the partition strategy for underlying TileDB storage manager
GenomicsDBConfiguration	setQueryJsonFile(String path)

Methods inherited from class org.apache.hadoop.conf.Configuration

addDefaultResource, addDeprecation, addDeprecation, addDeprecation, addDeprecation, addResource, addResource, addResource, addResource, addResource, clear, dumpConfiguration, dumpDeprecatedKeys, get, get, getBoolean, getClass, getClass, getClassByName, getClassByNameOrNull, getClasses, getClassLoader, getConfResourceAsInputStream, getConfResourceAsReader, getDouble, getEnum, getFile, getFloat, getInstances, getInt, getInts, getLocalPath, getLong, getLongBytes, getPattern, getPropertySources, getProps, getRange, getRaw, getResource, getSocketAddr, getStringCollection, getStrings, getStrings, getTimeDuration, getTrimmed, getTrimmed, getTrimmedStringCollection, getTrimmedStrings, getTrimmedStrings, getValByRegex, isDeprecated, iterator, main, readFields, reloadConfiguration, set, set, setBoolean, setBooleanIfUnset, setClass, setClassLoader, setDouble, setEnum, setFloat, setIfUnset, setInt, setLong, setPattern, setQuietMode, setSocketAddr, setStrings, setTimeDuration, size, toString, unset, updateConnectAddr, write, writeXml, writeXml

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

LOADERJSON

public static final String LOADERJSON

See Also:

Constant Field Values

QUERYJSON

public static final String QUERYJSON

See Also:

Constant Field Values

MPIHOSTFILE

public static final String MPIHOSTFILE

See Also:

Constant Field Values

PARTITION_STRATEGY

public static final String PARTITION_STRATEGY

See Also:

Constant Field Values

produceCombinedVCF

private Boolean produceCombinedVCF

produceTileDBArray

private Boolean produceTileDBArray

segmentSize

private Integer segmentSize

nCellsPerTile

private Integer nCellsPerTile

partitionInfoList

private LinkedList<GenomicsDBPartitionInfo> partitionInfoList

hosts

private ArrayList<String> hosts

Constructor Detail

GenomicsDBConfiguration

public GenomicsDBConfiguration(org.apache.hadoop.conf.Configuration configuration)
                        throws FileNotFoundException

Throws:

FileNotFoundException

GenomicsDBConfiguration

public GenomicsDBConfiguration(org.apache.hadoop.conf.Configuration configuration,
                               List<GenomicsDBPartitionInfo> list)
                        throws FileNotFoundException

Constructor with partition information

Parameters:

configuration - Existing configuration object (can contain Hadoop config values)

list - Contains partition information

Throws:

FileNotFoundException - thrown when loader file not found

Method Detail

setLoaderJsonFile

public GenomicsDBConfiguration setLoaderJsonFile(String path)

setQueryJsonFile

public GenomicsDBConfiguration setQueryJsonFile(String path)

setHostFile

public GenomicsDBConfiguration setHostFile(String path)
                                    throws FileNotFoundException

Host file contains the hosts where GenomicsDB instances reside. This file can be a replica of the slaves file. For now, we have kept it separate, can be merged later

Parameters:

path - Full path of the host file

Returns:

GenomicsDBConfiguration object

Throws:

FileNotFoundException - If file not found, throw exception

getHosts

List<String> getHosts()

setPartitionStrategy

void setPartitionStrategy(Boolean isRowPartitioned)

Set the partition strategy for underlying TileDB storage manager

Parameters:

isRowPartitioned - If true, data is partitioned as row major (ROW_MAJOR), COL_MAJOR otherwise

setPartitionStrategy

void setPartitionStrategy(String partitionStrategy)

Set the partition strategy for underlying TileDB storage manager

Parameters:

partitionStrategy - Partition strategy can be either column major (COL_MAJOR) or row major (ROW_MAJOR)

addPartitions

private void addPartitions(GenomicsDBPartitionInfo genomicsDBPartitionInfo)