Package gov.nih.nlm.ncbi.ngs

# Class NGS

java.lang.Object
gov.nih.nlm.ncbi.ngs.NGS

public class NGS extends Object

## Constructor Summary

Constructors
Constructor
Description
`NGS()`

## Method Summary

Modifier and Type
Method
Description
`static ExceptionInInitializerError`
`getInitializationError()`
Returns exception which occurred during initialization If the exception is a subclass of LibraryLoadError, then there was a problem with loading native libraries
`static boolean`
`isSupported()`
Check to see if NGS SDK is supported by current environment
`static boolean`
`isValid(String spec)`
Check to see if spec string represents an SRA archive
`static void`
`main(String[] args)`
`static ReadCollection`
`openReadCollection(String spec)`
Create an object representing a named collection of reads
`static ReferenceSequence`
`openReferenceSequence(String spec)`
Create an object representing a named reference sequence
`static void`
`setAppVersionString(String app_version)`
Updates User-Agent header in HTTP communications

### Methods inherited from class java.lang.Object

`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

## Constructor Details

### NGS

public NGS()

## Method Details

### isSupported

public static boolean isSupported()
Check to see if NGS SDK is supported by current environment

Returns:
  true if NGS SDK is supported

### getInitializationError

public static ExceptionInInitializerError getInitializationError()
Returns exception which occurred during initialization If the exception is a subclass of LibraryLoadError, then there was a problem with loading native libraries

Returns:
  initialization error or null

### setAppVersionString

public static void setAppVersionString(String app_version)
Updates User-Agent header in HTTP communications

Parameters:
  `app_version` - gives app name and version, e.g. "pileup-stats.1.0.0"

### openReadCollection

public static ReadCollection openReadCollection(String spec) throws ErrorMsg
Create an object representing a named collection of reads

Parameters:
  `spec` - may be a path to an object or may be an id, accession, or URL
Returns:
  the requested read-collection
Throws:
  `ErrorMsg` - if object cannot be located
  `ErrorMsg` - if object cannot be converted to a ReadCollection
  `ErrorMsg` - if an error occurs during construction

### openReferenceSequence

public static ReferenceSequence openReferenceSequence(String spec) throws ErrorMsg
Create an object representing a named reference sequence

Parameters:
  `spec` - may be a path to an object or may be an id, accession, or URL
Returns:
  the requested reference
Throws:
  `ErrorMsg` - if object cannot be located
  `ErrorMsg` - if object cannot be converted to a ReadCollection
  `ErrorMsg` - if an error occurs during construction

### isValid

public static boolean isValid(String spec)
Check to see if spec string represents an SRA archive

Parameters:
  `spec` - may be a path to an object or may be an id, accession, or URL
Returns:
  true spec represents an SRA archive

### main

public static void main(String[] args)