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 |