htsjdk.samtools

Class Defaults

java.lang.Object

htsjdk.samtools.Defaults

public class Defaults
extends java.lang.Object

Embodies defaults for global values that affect how the SAM JDK operates. Defaults are encoded in the class and are also overridable using system properties.

Field Summary

Fields

Modifier and Type	Field and Description
static int	BUFFER_SIZE Buffer size, in bytes, used whenever reading/writing files or streams.
static int	COMPRESSION_LEVEL Compresion level to be used for writing BAM and other block-compressed outputs.
static boolean	CREATE_INDEX Should BAM index files be created when writing out coordinate sorted BAM files? Default = false.
static boolean	CREATE_MD5 Should MD5 files be created when writing out SAM and BAM files? Default = false.
static java.lang.String	CUSTOM_READER_FACTORY Custom reader factory able to handle URL based resources like ga4gh.
static java.lang.String	EBI_REFERENCE_SERVICE_URL_MASK A mask (pattern) to use when building EBI reference service URL for a given MD5 checksum.
static int	NON_ZERO_BUFFER_SIZE Even if BUFFER_SIZE is 0, this is guaranteed to be non-zero.
static java.io.File	REFERENCE_FASTA The reference FASTA file.
static SamFlagField	SAM_FLAG_FIELD_FORMAT The output format of the flag field when writing SAM text.
static boolean	SRA_LIBRARIES_DOWNLOAD Boolean describing whether downloading of SRA native libraries is allowed, in case such native libraries are not found locally
static boolean	USE_ASYNC_IO_READ_FOR_SAMTOOLS Should asynchronous read I/O be used where supported by the samtools package (one thread per file).
static boolean	USE_ASYNC_IO_WRITE_FOR_SAMTOOLS Should asynchronous write I/O be used where supported by the samtools package (one thread per file).
static boolean	USE_ASYNC_IO_WRITE_FOR_TRIBBLE Should asynchronous write I/O be used where supported by the tribble package (one thread per file).
static boolean	USE_CRAM_REF_DOWNLOAD Boolean describing whether downloading a reference file is allowed (for CRAM files), in case the reference file is not specified by the user Enabling this is not necessarily a good idea, since this process often fails

Constructor Summary

Constructors

Constructor and Description
Defaults()

Method Summary

Modifier and Type	Method and Description
static java.util.SortedMap<java.lang.String,java.lang.Object>	allDefaults() Returns a map of all default values (keys are names), lexicographically sorted by keys.

Methods inherited from class java.lang.Object

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

Field Detail

CREATE_INDEX

public static final boolean CREATE_INDEX

Should BAM index files be created when writing out coordinate sorted BAM files? Default = false.

CREATE_MD5

public static final boolean CREATE_MD5

Should MD5 files be created when writing out SAM and BAM files? Default = false.

USE_ASYNC_IO_READ_FOR_SAMTOOLS

public static final boolean USE_ASYNC_IO_READ_FOR_SAMTOOLS

Should asynchronous read I/O be used where supported by the samtools package (one thread per file). Default = false.

USE_ASYNC_IO_WRITE_FOR_SAMTOOLS

public static final boolean USE_ASYNC_IO_WRITE_FOR_SAMTOOLS

Should asynchronous write I/O be used where supported by the samtools package (one thread per file). Default = false.

USE_ASYNC_IO_WRITE_FOR_TRIBBLE

public static final boolean USE_ASYNC_IO_WRITE_FOR_TRIBBLE

Should asynchronous write I/O be used where supported by the tribble package (one thread per file). Default = false.

COMPRESSION_LEVEL

public static final int COMPRESSION_LEVEL

Compresion level to be used for writing BAM and other block-compressed outputs. Default = 5.

BUFFER_SIZE

public static final int BUFFER_SIZE

Buffer size, in bytes, used whenever reading/writing files or streams. Default = 128k.

SAM_FLAG_FIELD_FORMAT

public static final SamFlagField SAM_FLAG_FIELD_FORMAT

The output format of the flag field when writing SAM text. Ignored for reading SAM text.

NON_ZERO_BUFFER_SIZE

public static final int NON_ZERO_BUFFER_SIZE

Even if BUFFER_SIZE is 0, this is guaranteed to be non-zero. If BUFFER_SIZE is non-zero, this == BUFFER_SIZE

REFERENCE_FASTA

public static final java.io.File REFERENCE_FASTA

The reference FASTA file. If this is not set, the file is null. This file may be required for reading writing SAM files (ex. CRAM).

CUSTOM_READER_FACTORY

public static final java.lang.String CUSTOM_READER_FACTORY

Custom reader factory able to handle URL based resources like ga4gh. Expected format: ,[,] E.g. https://www.googleapis.com/genomics/v1beta/reads/,com.google.genomics.ReaderFactory OR https://www.googleapis.com/genomics/v1beta/reads/,com.google.genomics.ReaderFactory,/tmp/genomics.jar

USE_CRAM_REF_DOWNLOAD

public static final boolean USE_CRAM_REF_DOWNLOAD

Boolean describing whether downloading a reference file is allowed (for CRAM files), in case the reference file is not specified by the user Enabling this is not necessarily a good idea, since this process often fails

EBI_REFERENCE_SERVICE_URL_MASK

public static final java.lang.String EBI_REFERENCE_SERVICE_URL_MASK

A mask (pattern) to use when building EBI reference service URL for a given MD5 checksum. Must contain one and only one string placeholder.

SRA_LIBRARIES_DOWNLOAD

public static final boolean SRA_LIBRARIES_DOWNLOAD

Boolean describing whether downloading of SRA native libraries is allowed, in case such native libraries are not found locally

Constructor Detail

Defaults

public Defaults()

Method Detail

allDefaults

public static java.util.SortedMap<java.lang.String,java.lang.Object> allDefaults()

Returns a map of all default values (keys are names), lexicographically sorted by keys. The returned map is unmodifiable. This function is useful for example when logging all defaults.