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

 

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table of contents

tutorial

appendix a: data formats accepted by MoBIoS
appendix b : BuildVPIndex options
appendix c: (this page)
appendix d
: sample annotated output