Detects the quality encoding format for all kind of sources for ReadTools.
Description
Detects the quality encoding for a SAM/BAM/CRAM/FASTQ files, output to the STDOUT the quality encoding.
Arguments
Required Arguments
| Argument name(s) | Type | Description |
|---|---|---|
--input-I |
String | Reads input. |
Optional Arguments
| Argument name(s) | Type | Default value(s) | Description |
|---|---|---|---|
--arguments_file |
List[File] | [] | read one or more arguments files and add them to the command line |
--gcs_max_retries-gcs_retries |
int | 20 | If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection |
--help-h |
boolean | false | display the help message |
--maximumReads-maximumReads |
Long | 1000000 | Maximum number of reads to use for detect the quality encoding. |
--version |
boolean | false | display the version number for this tool |
Optional Common Arguments
| Argument name(s) | Type | Default value(s) | Description |
|---|---|---|---|
--QUIET |
Boolean | false | Whether to suppress job-summary info on System.err. |
--readValidationStringency-VS |
ValidationStringency | SILENT | Validation stringency for all SAM/BAM/CRAM files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. Possible values: STRICT, LENIENT, SILENT |
--TMP_DIR |
List[File] | [] | Undocumented option |
--use_jdk_deflater-jdk_deflater |
boolean | false | Whether to use the JdkDeflater (as opposed to IntelDeflater) |
--use_jdk_inflater-jdk_inflater |
boolean | false | Whether to use the JdkInflater (as opposed to IntelInflater) |
--verbosity-verbosity |
LogLevel | INFO | Control verbosity of logging. Possible values: ERROR, WARNING, INFO, DEBUG |
Advanced Arguments
| Argument name(s) | Type | Default value(s) | Description |
|---|---|---|---|
--showHidden-showHidden |
boolean | false | display hidden arguments |