Class SortingVariantContextWriter
- java.lang.Object
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- htsjdk.variant.variantcontext.writer.SortingVariantContextWriter
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- All Implemented Interfaces:
VariantContextWriter
,Closeable
,AutoCloseable
@Deprecated public class SortingVariantContextWriter extends Object
Deprecated.9/2017, this class is completely untested and unsupported, there is no replacement at this time if you use this class please file an issue on github or it will be removed at some point in the futurethis class writes VCF files, allowing records to be passed in unsorted (up to a certain genomic distance away)
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Field Summary
Fields Modifier and Type Field Description protected static int
BEFORE_MOST_UPSTREAM_LOC
Deprecated.protected Integer
mostUpstreamWritableLoc
Deprecated.
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Constructor Summary
Constructors Constructor Description SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance)
Deprecated.SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance, boolean takeOwnershipOfInner)
Deprecated.create a local-sorting VCF writer, given an inner VCF writer to write to
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description void
add(VariantContext vc)
Deprecated.add a record to the fileboolean
checkError()
Deprecated.void
close()
Deprecated.attempt to close the VCF file; we need to flush the queue firstprotected void
emitSafeRecords()
Deprecated.protected void
noteCurrentRecord(VariantContext vc)
Deprecated.void
setHeader(VCFHeader header)
Deprecated.Sets the VCF header so that data blocks can be written without writing the header Exactly one of writeHeader() or setHeader() should be called when using a writerString
toString()
Deprecated.Gets a string representation of this object.void
writeHeader(VCFHeader header)
Deprecated.Writes the header
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Field Detail
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mostUpstreamWritableLoc
protected Integer mostUpstreamWritableLoc
Deprecated.
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BEFORE_MOST_UPSTREAM_LOC
protected static final int BEFORE_MOST_UPSTREAM_LOC
Deprecated.- See Also:
- Constant Field Values
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Constructor Detail
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SortingVariantContextWriter
public SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance, boolean takeOwnershipOfInner)
Deprecated.create a local-sorting VCF writer, given an inner VCF writer to write to- Parameters:
innerWriter
- the VCFWriter to write tomaxCachingStartDistance
- the maximum start distance between records that we'll cachetakeOwnershipOfInner
- Should this Writer close innerWriter when it's done with it
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SortingVariantContextWriter
public SortingVariantContextWriter(VariantContextWriter innerWriter, int maxCachingStartDistance)
Deprecated.
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Method Detail
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noteCurrentRecord
protected void noteCurrentRecord(VariantContext vc)
Deprecated.
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checkError
public boolean checkError()
Deprecated.- Returns:
- true if the underlying stream is a java.io.PrintStream and its checkError returned true, used for pipelines
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writeHeader
public void writeHeader(VCFHeader header)
Deprecated.Description copied from interface:VariantContextWriter
Writes the header- Specified by:
writeHeader
in interfaceVariantContextWriter
- Parameters:
header
- header
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close
public void close()
Deprecated.attempt to close the VCF file; we need to flush the queue first- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
- Specified by:
close
in interfaceVariantContextWriter
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add
public void add(VariantContext vc)
Deprecated.add a record to the file- Specified by:
add
in interfaceVariantContextWriter
- Parameters:
vc
- the Variant Context object
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setHeader
public void setHeader(VCFHeader header)
Deprecated.Description copied from interface:VariantContextWriter
Sets the VCF header so that data blocks can be written without writing the header Exactly one of writeHeader() or setHeader() should be called when using a writer- Specified by:
setHeader
in interfaceVariantContextWriter
- Parameters:
header
- VCF header
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toString
public String toString()
Deprecated.Gets a string representation of this object.
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emitSafeRecords
protected void emitSafeRecords()
Deprecated.
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