Commands
Required commands
Use the following commands to decompress the files:
orad FILE [args]
or orad [args] FILE
A folder that contains FASTQ.ORA files can also be provided for batch decompression of FASTQ.ORA files at top level directory:
orad ./pathtofolder/ [args]
On Windows, replace orad
with orad.exe
.
orad.exe FILE [args]
.
To decompress FASTQ.ORA compressed with a reference other than the default human reference, ensure the specific reference is available locally.
No change applies in the command line. The decompression software automatically detects which species/model is used.
Command Line Options
Command | Description |
---|---|
-C --check | Checks the integrity of the specified ORA file. This option decompresses the file in memory and verifies that the checksum of the decompressed data and the checksum of the original data are identical. The decompressed file is not saved. |
--raw | Decompresses the ORA file into an uncompressed FASTQ file. By default, the DRAGEN ORA Decompression Software decompresses to gzip format. |
--rm | Deletes the input file after successful execution. By default, the input file is not deleted. This option is not supported for files in AWS S3 or Azure Blob Storage. |
-t --threads | Sets the maximum number of threads allowed by the system. The default value is 8. |
-f --force | Overwrites the output file without prompting. By default, if the output file exists, the software exits without overwriting. |
-h --help | Prints help and exits. |
-v --version | Prints software version. |
-i --info | Prints information about the compressed ORA file. The following information is included:
This option is not supported for files in AWS S3 or Azure Blob Storage. Although the ORA file format supports concatenation of fastq.ora files, using this command on a concatenated fastq.ora file prints erroneous information. |
-c --stdout | Prints the decompressed file to the default standard output stdout. This is useful to share the results with another application without writing the decompressed file to disk. |
- | Reads an input fastq.ora file from the default standard input stdin. This option is not supported for Windows OS. |
-P --path | Sets the path location of the output file. The default file name is used. If a path is not specified, the file is created in the same location as the input file.This option overwrites the path if it is used with the -o option. |
-o --out | Sets the name of the output file and the path when used with -P. The default is the name of the input fastq.ora file. |
-N --name | Restores the original name saved in the fastq.ora file, at the time it was compressed to a fastq.ora file. |
-I --interleave | Decompresses the output file into a single interleaved file. By default, when the input is a single interleaved fastq.ora file, the decompression automatically decompresses into two separate paired read files. If the interleaved fastq.ora file was generated with DRAGEN ORA Decompression v.4.0 or later, |
--ora-reference | Changes the directory of the ORA reference file
If you specified a location in the environment variable, the software also looks in the location |
--check-ora-reference-path | Verifies if the ORA reference file |
--quiet | Sets decompression to quiet mode. In quiet mode, nothing is written to the standard output and standard error. This mode is ignored when used with |
--empty-third-line | Outputs the third line in the FASTQ format, (which is, the line that starts with +) as an empty line. By default this line is preserved. |
-r --repeat-header | Adds the read header to the third line in the FASTQ format, (which is, the line that starts with +). |
Command Examples
Using Windows, replace orad
with orad.exe
. Example is: orad.exe myfile.fastq.ora --check
Command | Description |
---|---|
| Checks the integrity of an ora file. |
| Decompresses |
| Prints information summary of an ora file. |
| Prints the first lines of the corresponding .FASTQ file in the terminal. |
| Verifies the accessibility of the ora reference file and print its path. |
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