GwasCatalog (SnpSift 5.2 API)

java.lang.Object

org.snpsift.gwasCatalog.GwasCatalog

All Implemented Interfaces:: Iterable<GwasCatalogEntry>

public class GwasCatalog extends Object implements Iterable<GwasCatalogEntry>

GWAS catalog table. It is small enough to fit in memory Refernces: http://www.genome.gov/gwastudies/

Author:: pablocingolani

Constructor Summary

Constructors

Constructor

Description

GwasCatalog(String fileName)
Method Summary

Modifier and Type

Method

Description

List<GwasCatalogEntry>

get(String key)

List<GwasCatalogEntry>

get(String chrName, int pos)

Get all entries at a given chromosome invalid input: '&' position Note: Position is zero based.

List<GwasCatalogEntry>

getByRs(String rs)

Get an entry based on 'RS' number

Iterator<GwasCatalogEntry>

iterator()

String

key(String chrName, int pos)

Create a 'key' string

String

key(GwasCatalogEntry ge)

Create a 'key' string

protected void

load(String fileName)

Load data from file

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Constructor Details
- GwasCatalog
  
  public GwasCatalog(String fileName)
Method Details
- get
  
  public List<GwasCatalogEntry> get(String key)
- get
  
  public List<GwasCatalogEntry> get(String chrName, int pos)
  
  Get all entries at a given chromosome invalid input: '&' position Note: Position is zero based.
- getByRs
  
  public List<GwasCatalogEntry> getByRs(String rs)
  
  Get an entry based on 'RS' number
- iterator
  
  public Iterator<GwasCatalogEntry> iterator()
  
  Specified by:
  
  iterator in interface Iterable<GwasCatalogEntry>
- key
  
  public String key(GwasCatalogEntry ge)
  
  Create a 'key' string
- key
  
  public String key(String chrName, int pos)
  
  Create a 'key' string
- load
  
  protected void load(String fileName)
  
  Load data from file