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| DEFAULT_GENE_FLANK || If only a --refgene is given with no --flank, this variable sets the default flank that is used.
| DEFAULT_GENE_FLANK || If only a --refgene is given with no --flank, this variable sets the default flank that is used.
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=== LD cache ===
LocusZoom attempts to remember LD calculations that were made on previous runs of the program to avoid having to re-calculate the same regional LD for subsequent runs. The process works as follows:
* For a given reference SNP and chr/start/stop:
** If LD has not been previously computed, use new_fugue to compute LD with the reference SNP and all other SNPs in the region, and store this result to the LD cache
** Else, retrieve the previously stored LD results
The cache intelligently stores LD from separate sources (hapmap, 1000G), populations, builds, and even different versions of genotype files separately.
Upon running LocusZoom, a file called "ld_cache.db" will automatically be created in the current directory, and LD computations will be stored there. If you wish to change the location of the LD cache, use <code>--cache <file></code>. If you wish to disable LD caching, you can use <code>--cache None</code>.
''Python note:'' The ld_cache.db is actually a shelve, and you can explore its contents using:
<code><pre>
import shelve
d = shelve.open("ld_cache.db")
</pre></code>
== License ==
== License ==
[[Category:Software]]
[[Category:Software]]
