public class Defaults extends Object
Modifier and Type | Field | 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 String |
CUSTOM_READER_FACTORY |
Custom reader factory able to handle URL based resources like ga4gh.
|
static boolean |
DISABLE_SNAPPY_COMPRESSOR |
Disable use of the Snappy compressor
|
static String |
DISABLE_SNAPPY_PROPERTY_NAME |
the name of the system property that disables snappy
|
static 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 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 | Description |
---|---|
Defaults() |
Modifier and Type | Method | Description |
---|---|---|
static SortedMap<String,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 int NON_ZERO_BUFFER_SIZE
public static final File REFERENCE_FASTA
public static final String CUSTOM_READER_FACTORY
public static final boolean USE_CRAM_REF_DOWNLOAD
public static final String EBI_REFERENCE_SERVICE_URL_MASK
public static final boolean SRA_LIBRARIES_DOWNLOAD
public static final String DISABLE_SNAPPY_PROPERTY_NAME
public static final boolean DISABLE_SNAPPY_COMPRESSOR