| Value | Meaning |
|---|---|
| verbose"-v" | |
| strongCompositionalBias"-b" | If the -b option is set, then the daligner assumes the data has a strong compositional bias (e.g. >65% AT rich). |
| asymmetric"-A" | If the -A option is set (“A” for “asymmetric”) then just overlaps where the a-read is in block X and the b-read is in block Y are reported, and if X = Y then it further reports only those overlaps where the a-read index is less than the b-read index. |
| identity"-I" | If the -I option is set (“I” for “identity”) then when X = Y, overlaps between different portions of the same read will also be found and reported. |
| kMerSize"-k" | Search code looks for a pair of diagonal bands of width 2^^w (default 26 = 64) that contain a collection of exact matching k-mers (default 14) between the two reads, such that the total number of bases covered by the k-mer hits is h (default 35). |
| bandWidth"-w" | ditto |
| hitBaseCoverage"-h" | ditto |
| maxKmerOccurence"-t" | Suppresses the use of any k-mer that occurs more than t times in either the subject or target block. |
| maxKmerMemory"-M" | Let the program automatically select a value of t that meets a given memory usage limit specified (in Gb) by the -M parameter. |
| tempDir"-P" | |
| minAlignmentLength"-l" | Searching for local alignments involving at least -l base pairs (default 1000) or more, that have an average correlation rate of -e (default 70%). |
| averageCorrelationRate"-e" | ditto |
| tracePointDistance"-s" | The local alignments found will be output in a sparse encoding where a trace point on the alignment is recorded every -s base pairs of the a-read (default 100bp). |
| minAReadLength"-H" | By setting the -H parameter to say N, one alters daligner so that it only reports overlaps where the a-read is over N base-pairs long. |
| numThreads"-T" | The program runs with 4 threads by default, but this may be set to any power of 2 with the -T option. |
| masks"-m" | If there are one or more interval tracks specified with the -m option (m for mask), then the reads of the DB or DB’s to which the track applies are soft masked with the union of the intervals of all the interval tracks that apply, that is any k-mers that contain any bases in any of the masked intervals are ignored for the purposes of seeding a match. |
Options for daligner.