Uses of Class
htsjdk.samtools.cram.structure.AlignmentSpan

Packages that use AlignmentSpan

Package	Description
htsjdk.samtools.cram.build
htsjdk.samtools.cram.encoding.reader
htsjdk.samtools.cram.structure

Uses of AlignmentSpan in htsjdk.samtools.cram.build

Methods in htsjdk.samtools.cram.build that return types with arguments of type AlignmentSpan

Modifier and Type	Method and Description
java.util.Map<java.lang.Integer,AlignmentSpan>	ContainerParser.getReferences(Container container, ValidationStringency validationStringency)

Uses of AlignmentSpan in htsjdk.samtools.cram.encoding.reader

Methods in htsjdk.samtools.cram.encoding.reader that return types with arguments of type AlignmentSpan

Modifier and Type	Method and Description
java.util.Map<java.lang.Integer,AlignmentSpan>	RefSeqIdReader.getReferenceSpans()

Uses of AlignmentSpan in htsjdk.samtools.cram.structure

Fields in htsjdk.samtools.cram.structure declared as AlignmentSpan

Modifier and Type	Field and Description
static AlignmentSpan	AlignmentSpan.UNMAPPED_SPAN A constant to represent an unmapped span.