Package org.snpsift.annotate
Interface DbMarker<Q extends org.snpeff.interval.Marker,R extends org.snpeff.interval.Marker>
- 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
-
Method Summary
Modifier and TypeMethodDescriptionvoid
close()
Close database, free resourcesvoid
open()
Open database (load index in memory if required)Find matching entries in the databasevoid
setDebug
(boolean debug) void
setVerbose
(boolean verbose)
-
Method Details
-
close
void close()Close database, free resources -
open
void open()Open database (load index in memory if required) -
query
Find matching entries in the database -
setDebug
void setDebug(boolean debug) -
setVerbose
void setVerbose(boolean verbose)
-