--auto-detect-paired-distances <Boolean> |
Determine appropriate paired distance limits automatically by sampling each paired read list. 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) |
--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) |
--deletion-extend-cost |
|
Integer: 1 <= x <= 3 |
Cost of extending a deletion (1, 2, or 3) (default: 1) |
--deletion-open-cost |
|
Integer: 1 <= x <= 10 |
Cost of starting a deletion (1-10) (default: 6) |
--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 |
--indel-mode <[LINEAR, AFFINE]> |
Insertion and deletions can either have linear or affine gap costs (default: LINEAR) |
--insertion-cost |
|
Integer: 1 <= x <= 3 |
Cost of creating an insertion (1, 2, or 3) (default: 3) |
--insertion-extend-cost |
|
Integer: 1 <= x <= 3 |
Cost of extending an insertion (1, 2, or 3) (default: 1) |
--insertion-open-cost |
|
Integer: 1 <= x <= 10 |
Cost of starting an insertion (1-10) (default: 6) |
--length-fraction |
|
Double: 1.0E-5 <= x <= 1.0 |
The minimum fraction of the total alignment length 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 reference |
--match-cost |
|
Integer: 1 <= x <= 10 |
Score of a match (1-10) (default: 1) |
--mismatch-cost |
|
Integer: 1 <= x <= 10 |
Cost of creating a mismatch (1-10) (default: 2) |
--non-specific-match-handling <[RANDOM, IGNORE]> |
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) |
--references <ClcObjectUrl> |
Reference sequences or genome track |
--similarity-fraction |
|
Double: 1.0E-5 <= x <= 1.0 |
The minimum identity fraction between the aligned region of the read and the reference sequence (default: 0.8) |
