Package htsjdk.samtools.sra
Class SRAUtils
- java.lang.Object
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- htsjdk.samtools.sra.SRAUtils
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public class SRAUtils extends Object
Provides some functionality which can be used by other classes Created by andrii.nikitiuk on 10/28/15.
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Field Summary
Fields Modifier and Type Field 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).
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Constructor Summary
Constructors Constructor Description SRAUtils()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static long
getNumberOfReads(ngs.ReadCollection run)
Is used to build RecordRangeInfostatic List<Long>
getReferencesLengthsAligned(ngs.ReadCollection run)
Loads reference lengths from a read collection.
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Field Detail
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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
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Method Detail
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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
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getReferencesLengthsAligned
public static List<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
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