htsjdk.samtools.sra

Class SRAUtils

java.lang.Object

htsjdk.samtools.sra.SRAUtils

public class SRAUtils
extends java.lang.Object

Provides some functionality which can be used by other classes Created by andrii.nikitiuk on 10/28/15.

Field Summary

Fields

Modifier and Type	Field and Description
static int	REFERENCE_ALIGNMENT References are stored in SRA table in chunks of 5k bases per row, while last chunk of a reference is less or equal than 5k bases in size (even if the next reference follows).

Constructor Summary

Constructors

Constructor and Description
SRAUtils()

Method Summary

Modifier and Type	Method and Description
static long	getNumberOfReads(ngs.ReadCollection run) Is used to build RecordRangeInfo
static java.util.List<java.lang.Long>	getReferencesLengthsAligned(ngs.ReadCollection run) Loads reference lengths from a read collection.

Methods inherited from class java.lang.Object

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

Field Detail

REFERENCE_ALIGNMENT

public static final int REFERENCE_ALIGNMENT

References are stored in SRA table in chunks of 5k bases per row, while last chunk of a reference is less or equal than 5k bases in size (even if the next reference follows). So, it will be optimal if we align reference sizes to 5k bases to read by reference rows.

See Also:

Constant Field Values

Constructor Detail

SRAUtils

public SRAUtils()

Method Detail

getNumberOfReads

public static long getNumberOfReads(ngs.ReadCollection run)
                             throws ngs.ErrorMsg

Is used to build RecordRangeInfo

Parameters:

run - open read collection

Returns:

total number of reads (both aligned and unaligned) in SRA archive

Throws:

ngs.ErrorMsg

getReferencesLengthsAligned

public static java.util.List<java.lang.Long> getReferencesLengthsAligned(ngs.ReadCollection run)
                                                                  throws ngs.ErrorMsg

Loads reference lengths from a read collection. Aligns reference lengths by REFERENCE_ALIGNMENT bases for optimal loads of alignments (references are stored in REFERENCE_ALIGNMENT bases chunks in SRA table) Is used to build RecordRangeInfo

Parameters:

run - single opened read collection

Returns:

list with references lengths

Throws:

ngs.ErrorMsg