Controlling How HTSJDK Operates Through System Properties

Various system properties can be specified to control how HTSJDK operates (see Source). Each property described below should be prefixed with samjdk (ex. -Dsamdjk.create_index=true on the command line).

Property	Type	Default	Description
create_index	boolean	false	Create the index when writing a coordinate sorted BAM
create_md5	boolean	false	Create MD5 files when writing SAM/BAM/CRAM files
use_async_io_read_for_samtools	boolean	false	Use asynchronous I/O (one thread per file) when reading (samtools package only) (ex. SAM/BAM/CRAM files)
use_async_io_write_for_samtools	boolean	false	Use asynchronous I/O (one thread per file) when writing (samtools package only) (ex. SAM/BAM/CRAM files)
use_async_io_write_for_tribble	boolean	false	Use asynchronous I/O (one thread per file) when writing (tribble package only)
compression_level	int	5	Compression level to be used for writing BAM and other block-compressed outputs
buffer_size	int	128k	Buffer size, in bytes, used whenever reading/writing files or streams
sam_flag_field_format	samflagfield	DECIMAL	The output format of the flag field when writing SAM text. Ignored for reading SAM text
non_zero_buffer_size	int	128k	The buffer size when buffer_size is zero (when a non-zero buffer size must be guaranteed)
reference_fasta	file	null	The reference FASTA file. Typically required when reading or writing CRAM files
custom_reader_factory	string	<empty string>	The custom reader factory able to handle URL based resources like ga4gh. Expected format: <url prefix>,<fully qualified factory class name>[,<jar file name>]. 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	boolean	false	True to allow reference files to be downloaed for CRAM, 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	string	"https://www.ebi.ac.uk/ena/cram/md5/%s"	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	boolean	false	Boolean describing whether downloading of SRA native libraries is allowed, in case such native libraries are not found locally
disable_snappy_property_name	string	"snappy.disable"	The name of the system property that disables snappy
disable_snappy_compressor	boolean	false	Disable use of the Snappy compressor