Converts a GEM-mappability file into a BED-graph format
Warning: This a EXPERIMENTAL tool and should not be used for production
Description
Converts a GEM-mappability ( Derrien et al. 2012) file into a BED-graph format.
The GEM-mappability format is a FASTA-like file with:
- Header including information for the algorithm applied (e.g., k-mer size).
- Sequences in FASTA-like format: sequence name preceded by ~ and a character per-base encoded in the header. Each character encodes a different range of values, which represent the number of mappings of the reads starting at that position.
This tool parses the GEM-mappability file and outputs a per-position BED-graph format. For each position, different scoring systems could be use (see arguments for more information).
Arguments
Required Arguments
| Argument name(s) | Type | Description |
|---|---|---|
--input-I |
String | GEM-mappability file (FASTA-like) to parse |
--output-O |
String | Bed-graph output with the number of mappings as score. If it contains a block-compressed extension (e.g., .bgz), it will be compressed. |
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 |
--score-method |
GemScoreMethod | MID | Method to convert number of mappings within a range into the reported score Possible values: MIN (Minimum of the range of mappings.), MAX (Maximum of the range of mappings.), MID (Middle point of the range of mappings.) |
--version |
boolean | false | display the version number for this tool |
Optional Common Arguments
| Argument name(s) | Type | Default value(s) | Description |
|---|---|---|---|
--forceOverwrite-forceOverwrite |
Boolean | false | Force output overwriting if it exists |
--QUIET |
Boolean | false | Whether to suppress job-summary info on System.err. |
--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 |