Package htsjdk.samtools.cram.structure
Class AlignmentSpan
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- htsjdk.samtools.cram.structure.AlignmentSpan
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public class AlignmentSpan extends Object
A span of over a single reference. Immutable. Holds alignment start and span values as well as counts of how many are mapped vs. unmapped vs unmapped-unplaced.
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Constructor Summary
Constructors Constructor Description AlignmentSpan(int alignmentStart, int alignmentSpan, int mappedCount, int unmappedCount, int unmappedUnplacedCount)
Create a new span with a multiple reads in it.AlignmentSpan(AlignmentContext alignmentContext, int mappedCount, int unmappedCount, int unmappedUnplacedCount)
This does not retain the alignmentContext referenceContext state (its just a shorthand for passing the rest of the alignmentContext values in).
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static AlignmentSpan
combine(AlignmentSpan a, AlignmentSpan b)
Combine two AlignmentSpansboolean
equals(Object o)
int
getAlignmentSpan()
int
getAlignmentStart()
int
getMappedCount()
int
getUnmappedCount()
int
getUnmappedUnplacedCount()
int
hashCode()
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Constructor Detail
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AlignmentSpan
public AlignmentSpan(AlignmentContext alignmentContext, int mappedCount, int unmappedCount, int unmappedUnplacedCount)
This does not retain the alignmentContext referenceContext state (its just a shorthand for passing the rest of the alignmentContext values in).- Parameters:
alignmentContext
-mappedCount
-unmappedCount
-unmappedUnplacedCount
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AlignmentSpan
public AlignmentSpan(int alignmentStart, int alignmentSpan, int mappedCount, int unmappedCount, int unmappedUnplacedCount)
Create a new span with a multiple reads in it.- Parameters:
alignmentStart
- minimum alignment start of the reads represented by this span, using a 1-based coordinate systemalignmentSpan
- span from minimum alignment start to maximum alignment end of the reads represented by this span span = max(end) - min(start) + 1mappedCount
- number of mapped reads in the spanunmappedCount
- number of unmapped reads in the span
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Method Detail
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combine
public static AlignmentSpan combine(AlignmentSpan a, AlignmentSpan b)
Combine two AlignmentSpans- Parameters:
a
- the first AlignmentSpan to combineb
- the second AlignmentSpan to combine- Returns:
- the new combined AlignmentSpan
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getAlignmentStart
public int getAlignmentStart()
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getAlignmentSpan
public int getAlignmentSpan()
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getMappedCount
public int getMappedCount()
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getUnmappedCount
public int getUnmappedCount()
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getUnmappedUnplacedCount
public int getUnmappedUnplacedCount()
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