Package org.snpsift.gwasCatalog
Class GwasCatalog
- java.lang.Object
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- org.snpsift.gwasCatalog.GwasCatalog
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- All Implemented Interfaces:
java.lang.Iterable<GwasCatalogEntry>
public class GwasCatalog extends java.lang.Object implements java.lang.Iterable<GwasCatalogEntry>
GWAS catalog table. It is small enough to fit in memory Refernces: http://www.genome.gov/gwastudies/- Author:
- pablocingolani
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Constructor Summary
Constructors Constructor Description GwasCatalog(java.lang.String fileName)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.List<GwasCatalogEntry>
get(java.lang.String key)
java.util.List<GwasCatalogEntry>
get(java.lang.String chrName, int pos)
Get all entries at a given chromosome & position Note: Position is zero based.java.util.List<GwasCatalogEntry>
getByRs(java.lang.String rs)
Get an entry based on 'RS' numberjava.util.Iterator<GwasCatalogEntry>
iterator()
java.lang.String
key(java.lang.String chrName, int pos)
Create a 'key' stringjava.lang.String
key(GwasCatalogEntry ge)
Create a 'key' stringprotected void
load(java.lang.String fileName)
Load data from file
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Method Detail
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get
public java.util.List<GwasCatalogEntry> get(java.lang.String key)
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get
public java.util.List<GwasCatalogEntry> get(java.lang.String chrName, int pos)
Get all entries at a given chromosome & position Note: Position is zero based.
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getByRs
public java.util.List<GwasCatalogEntry> getByRs(java.lang.String rs)
Get an entry based on 'RS' number
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iterator
public java.util.Iterator<GwasCatalogEntry> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<GwasCatalogEntry>
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key
public java.lang.String key(GwasCatalogEntry ge)
Create a 'key' string
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key
public java.lang.String key(java.lang.String chrName, int pos)
Create a 'key' string
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load
protected void load(java.lang.String fileName)
Load data from file
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