--auto-detect-paired-distances <Boolean> |
Determine appropriate paired distance limits automatically by sampling each paired read list. Applies to base-space mapping only. For color space alignment - or if deselected - the distance setting on paired read lists is used. (default: true) |
--collect-unmapped <Boolean> |
Collect reads that were not mapped to any reference sequence (default: false) |
--color-error-cost |
|
Integer: 1 <= x <= 3 |
Cost of creating a color error (1, 2, or 3) (default: 3) |
--color-space <Boolean> |
Perform color space alignment for relevant data sets (default: true) |
--contigs <ClcObjectUrl> |
Contig sequences or genome track |
--create-report <Boolean> |
Create a summary report with mapping statistics (default: false) |
-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--deletion-cost |
|
Integer: 1 <= x <= 3 |
Cost of creating a deletion (1, 2, or 3) (default: 3) |
--global-alignment <Boolean> |
When selected, end gaps are treated as mismatches. Otherwise, end gaps have no cost. (default: false) |
-i, --input <ClcObjectUrl> |
Input data on server |
--insertion-cost |
|
Integer: 1 <= x <= 3 |
Cost of creating an insertion (1, 2, or 3) (default: 3) |
--length-fraction |
|
Double: 0.0 < x <= 1.0 |
Minimum length fraction of a read that must match the reference sequence (default: 0.5) |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--masking-mode |
|
<[NO_MASKING, EXCLUDE,INCLUDE]> |
With exclude masking, reads are not mapped to annotated regions. With include masking, reads are mapped to annotated regions only (default: NO_MASKING) |
--masking-track <ClcObjectUrl> |
Annotation track used for masking parts of the contigs |
--mismatch-cost |
|
Integer: 1 <= x <= 3 |
Cost of creating a mismatch (1, 2, or 3) (default: 2) |
--non-specific-match-handling |
|
<[RANDOMIGNORE]> |
, Reads with more than one match may be assigned randomly or ignored (default: RANDOM) |
--output-mode <[TRACK, CLUSTER]> |
Output may be given as a single reads track, or as a set of stand-alone read mapping objects with reference and consensus sequences (default: TRACK) |
--similarity-fraction |
|
Double: 0.0 < x <= 1.0 |
Minimum fraction of similarity between read and reference sequence (default: 0.8) |
--update-contigs <Boolean> |
The contigs will be adjusted by the mapped reads. (default: false) |