-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
-i, --input <ClcObjectUrl> |
Input data on server |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--lower-threshold <Double> |
Include parts of the graph with a counts greater than or equal to this number (default: 0.0) |
--masking-mode <[NO_REGION, EXCLUDE, INCLUDE]> |
With exclude masking, reads are not mapped to annotated regions. With include masking, reads are mapped to annotated regions only (default: NO_REGION) |
--region-track <ClcObjectUrl> |
Annotation track used for masking parts of the reference |
--upper-threshold <Double> |
Include parts of the graph with a counts less than or equal to this number (default: 1000.0) |
--use-lower-threshold <Boolean> |
Use a lower threshold (default: true) |
--use-upper-threshold <Boolean> |
Use an upper threshold (default: true) |
--window-size |
|
Integer: 1 <= x <= 1000000 |
A window size of 1 checks if individual positions are within the threshold. A window size of 5 checks if the average value of all neighbouring 5-tuples are within the threshold. Increasing the window size can help you prevent jumps in the data messing up the output intervals, or detect regions that are only different when looked at as an interval. (default: 1) |
