Package org.snpsift.annotate
Interface DbMarker<Q extends org.snpeff.interval.Marker,R extends org.snpeff.interval.Marker>
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- All Known Implementing Classes:
DbNsfp
,DbVcf
,DbVcfMem
,DbVcfSorted
,DbVcfTabix
public interface DbMarker<Q extends org.snpeff.interval.Marker,R extends org.snpeff.interval.Marker>
Use a file as a 'marker' database. E.g. A VCF file, dbNSFP file/s, GTF, etc. Basically any genomic data file format that could be queried by genomic interval (e.g. by using Tabix, CSI or some other index).- Author:
- pcingola
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
close()
Close database, free resourcesvoid
open()
Open database (load index in memory if required)java.util.Collection<R>
query(Q queryMarker)
Find matching entries in the databasevoid
setDebug(boolean debug)
void
setVerbose(boolean verbose)
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