Package htsjdk.samtools
Enum SamIndexes
- java.lang.Object
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- java.lang.Enum<SamIndexes>
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- htsjdk.samtools.SamIndexes
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- All Implemented Interfaces:
Serializable
,Comparable<SamIndexes>
public enum SamIndexes extends Enum<SamIndexes>
A helper class to read BAI and CRAI indexes. Main goal is to provide BAI stream as a sort of common API for all index types. Created by vadim on 14/08/2015.
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Field Summary
Fields Modifier and Type Field Description String
fileNameSuffix
byte[]
magic
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static SeekableStream
asBaiSeekableStreamOrNull(SeekableStream inputStream, SAMSequenceDictionary dictionary)
static InputStream
asBaiStreamOrNull(InputStream inputStream, SAMSequenceDictionary dictionary)
static InputStream
openIndexFileAsBaiOrNull(File file, SAMSequenceDictionary dictionary)
static InputStream
openIndexUrlAsBaiOrNull(URL url, SAMSequenceDictionary dictionary)
static SamIndexes
valueOf(String name)
Returns the enum constant of this type with the specified name.static SamIndexes[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
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Enum Constant Detail
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BAI
public static final SamIndexes BAI
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CRAI
public static final SamIndexes CRAI
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CSI
public static final SamIndexes CSI
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Field Detail
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fileNameSuffix
public final String fileNameSuffix
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magic
public final byte[] magic
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Method Detail
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values
public static SamIndexes[] values()
Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:for (SamIndexes c : SamIndexes.values()) System.out.println(c);
- Returns:
- an array containing the constants of this enum type, in the order they are declared
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valueOf
public static SamIndexes valueOf(String name)
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)- Parameters:
name
- the name of the enum constant to be returned.- Returns:
- the enum constant with the specified name
- Throws:
IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is null
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openIndexFileAsBaiOrNull
public static InputStream openIndexFileAsBaiOrNull(File file, SAMSequenceDictionary dictionary) throws IOException
- Throws:
IOException
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openIndexUrlAsBaiOrNull
public static InputStream openIndexUrlAsBaiOrNull(URL url, SAMSequenceDictionary dictionary) throws IOException
- Throws:
IOException
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asBaiStreamOrNull
public static InputStream asBaiStreamOrNull(InputStream inputStream, SAMSequenceDictionary dictionary) throws IOException
- Throws:
IOException
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asBaiSeekableStreamOrNull
public static SeekableStream asBaiSeekableStreamOrNull(SeekableStream inputStream, SAMSequenceDictionary dictionary) throws IOException
- Throws:
IOException
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