contig_read_mapping

--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)