public class Defaults
extends java.lang.Object
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
Compression 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 |
DEFAULT_SAM_EXTENSION
The extension to assume a sam file has when the actual file doesn't have an extension, useful
for when outputing to /dev/stdout, for example.
|
static java.lang.String |
DEFAULT_VCF_EXTENSION
The extension to assume a vcf has when the actual file doesn't have an extension, useful
for when outputing to /dev/stdout, for example.
|
static boolean |
DISABLE_SNAPPY_COMPRESSOR
Disable use of the Snappy compressor.
|
static java.lang.String |
DISABLE_SNAPPY_PROPERTY_NAME
The name of the system property that disables snappy.
|
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 java.lang.String |
SAMJDK_PREFIX |
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 and Description |
---|
Defaults() |
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.
|
public static final boolean CREATE_INDEX
public static final boolean CREATE_MD5
public static final boolean USE_ASYNC_IO_READ_FOR_SAMTOOLS
public static final boolean USE_ASYNC_IO_WRITE_FOR_SAMTOOLS
public static final boolean USE_ASYNC_IO_WRITE_FOR_TRIBBLE
public static final int COMPRESSION_LEVEL
public static final int BUFFER_SIZE
public static final SamFlagField SAM_FLAG_FIELD_FORMAT
public static final java.lang.String DEFAULT_SAM_EXTENSION
public static final java.lang.String DEFAULT_VCF_EXTENSION
public static final int NON_ZERO_BUFFER_SIZE
public static final java.io.File REFERENCE_FASTA
public static final java.lang.String CUSTOM_READER_FACTORY
public static final boolean USE_CRAM_REF_DOWNLOAD
public static final java.lang.String EBI_REFERENCE_SERVICE_URL_MASK
public static final boolean SRA_LIBRARIES_DOWNLOAD
public static final java.lang.String DISABLE_SNAPPY_PROPERTY_NAME
public static final boolean DISABLE_SNAPPY_COMPRESSOR
public static final java.lang.String SAMJDK_PREFIX