htsjdk.samtools.cram.structure

Class AlignmentContext

java.lang.Object

htsjdk.samtools.cram.structure.AlignmentContext

public class AlignmentContext
extends java.lang.Object

An AlignmentContext represents mapping information related to a collection of reads, or a single CRAMCompressionRecord, Slice, or Container. It contains a ReferenceContext, and if that context is of type SINGLE_REFERENCE_TYPE then it also contains Alignment Start and Alignment Span values.

Field Summary

Fields

Modifier and Type	Field and Description
static AlignmentContext	EOF_CONTAINER_CONTEXT
static AlignmentContext	MULTIPLE_REFERENCE_CONTEXT
static int	NO_ALIGNMENT_END
static int	NO_ALIGNMENT_SPAN
static int	NO_ALIGNMENT_START
static AlignmentContext	UNMAPPED_UNPLACED_CONTEXT

Constructor Summary

Constructors

Constructor and Description
AlignmentContext(ReferenceContext referenceContext, int alignmentStart, int alignmentSpan) Create an AlignmentContext from a reference context, start, and span.

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o)
int	getAlignmentSpan()
int	getAlignmentStart()
ReferenceContext	getReferenceContext()
int	hashCode()
java.lang.String	toString()
static void	validateAlignmentContext(boolean isStrict, ReferenceContext referenceContext, int alignmentStart, int alignmentSpan) Determine if the provided values would result in a valid alignment context.

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

NO_ALIGNMENT_START

public static final int NO_ALIGNMENT_START

See Also:

Constant Field Values

NO_ALIGNMENT_SPAN

public static final int NO_ALIGNMENT_SPAN

See Also:

Constant Field Values

NO_ALIGNMENT_END

public static final int NO_ALIGNMENT_END

See Also:

Constant Field Values

MULTIPLE_REFERENCE_CONTEXT

public static final AlignmentContext MULTIPLE_REFERENCE_CONTEXT

UNMAPPED_UNPLACED_CONTEXT

public static final AlignmentContext UNMAPPED_UNPLACED_CONTEXT

EOF_CONTAINER_CONTEXT

public static final AlignmentContext EOF_CONTAINER_CONTEXT

Constructor Detail

AlignmentContext

public AlignmentContext(ReferenceContext referenceContext,
                        int alignmentStart,
                        int alignmentSpan)

Create an AlignmentContext from a reference context, start, and span. Unfortunately, this can't enforce that the values are valid alignment values, or even warn about such values here, because there are too many cases where the spec doesn't or didn't originally prescribe valid values for cases like MULTIPLE_REF containers/slices, or unmapped slices, or SAMFileHeader containers. As a result, there are many files floating around that use various out-of-spec values that were created with old htsjdk or other implementations that were based based on older spec versions.

Parameters:

referenceContext - the reference context for this alignment context

alignmentStart - the 1-based alignment start

alignmentSpan - the alignment span

Method Detail

getReferenceContext

public ReferenceContext getReferenceContext()

getAlignmentStart

public int getAlignmentStart()

getAlignmentSpan

public int getAlignmentSpan()

validateAlignmentContext

public static void validateAlignmentContext(boolean isStrict,
                                            ReferenceContext referenceContext,
                                            int alignmentStart,
                                            int alignmentSpan)

Determine if the provided values would result in a valid alignment context. Note: The spec does not prescribe what the alignment start/span for a SAMFileHeader container should be, and only recently prescribed what they should be for multi-ref slices, so there are many files out their with various out-of-band values in those cases, so we can't validate or throw in the general case.

Parameters:

isStrict - throw if the values do not represent a valid alignmentContext

referenceContext - reference context to validate

alignmentStart - alignment start to validate

alignmentSpan - alignment span to validate

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object