Class Defaults

java.lang.Object
htsjdk.samtools.Defaults

public class Defaults extends 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 Details

    • 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
      Compression 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. Default = DECIMAL
    • DEFAULT_SAM_EXTENSION

      public static final 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.
    • DEFAULT_VCF_EXTENSION

      public static final 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.
    • OPTIMISTIC_VCF_4_4

      public static final boolean OPTIMISTIC_VCF_4_4
    • 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 (Default = 128k).
    • REFERENCE_FASTA

      public static final 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). Default = null.
    • CUSTOM_READER_FACTORY

      public static final 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 Default = "".
    • 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. Default = false.
    • EBI_REFERENCE_SERVICE_URL_MASK

      public static final 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. Default = "https://www.ebi.ac.uk/ena/cram/md5/%s".
    • 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. Default = false.
    • DISABLE_SNAPPY_PROPERTY_NAME

      public static final String DISABLE_SNAPPY_PROPERTY_NAME
      The name of the system property that disables snappy. Default = "snappy.disable".
      See Also:
    • OPTIMISTIC_VCF_4_4_PROPERTY

      public static final String OPTIMISTIC_VCF_4_4_PROPERTY
      See Also:
    • DISABLE_SNAPPY_COMPRESSOR

      public static final boolean DISABLE_SNAPPY_COMPRESSOR
      Disable use of the Snappy compressor. Default = false.
    • SAMJDK_PREFIX

      public static final String SAMJDK_PREFIX
      See Also:
  • Constructor Details

    • Defaults

      public Defaults()
  • Method Details

    • allDefaults

      public static SortedMap<String,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.