appendix c: QueryVPIndex options
| option | meaning | default value |
value in dna/build.sh |
|---|---|---|---|
| -d | location of "mobiosData" directory | current directory |
../ |
| -i | index filename | n/a |
dna_18_100000 |
| -q | query filename | n/a |
query.fasta |
| -r | search radius | 0 |
1 |
| -pl | length of the path distance list | 0 |
|
| -v | 1: verify results against linear scan; 0: do not verify results | 0 |
|
| -o | results filename, optional | do not save results |
query.fasta.res |
| -g | debug level | 0 |
see mobios-v0.9-examples/dna/query.sh for an example of how to call QueryVPIndex.
advanced options
The advanced options allow the user to query only a section of the query file, and to make a series of radius searches.
| option | meaning |
|---|---|
| -f | offset of first query to be used in the query file, start from 0, inclusive |
| -l | offset of last query to be used in the query file, exclusive |
| -minr | minimum search radius |
| -maxr | maximum search radius |
| -st | step size for search radii |
