CRAM WIP: expand ReferenceContext to include Alignment Start and Span - Githubissues

samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

http://samtools.github.io/htsjdk/

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CRAM WIP: expand ReferenceContext to include Alignment Start and Span #1349

Closed jmthibault79 closed 5 years ago

jmthibault79 commented 5 years ago

Description

ReferenceContext often travels with Alignment Start and Span. Let's combine them.

Added new AlignmentContext to Slice, Container, and CRAIEntry.

Also adds ReferenceContext to CramIterator.

TODO:

AlignmentSpan
CramCompressionRecord (see #1332)
CRAMContainerStreamWriter (see #1333)
Maybe: BAMIndexer, BAMIndexMetadata, CRAMBAIIndexer, CRAMCRAIIndexer, CramIterator

Checklist

[x] Code compiles correctly
[x] New tests covering changes and new functionality
[x] All tests passing
[x] Extended the README / documentation, if necessary
[ ] Is not backward compatible (breaks binary or source compatibility)

cmnbroad commented 5 years ago

Closing in favor of pending refactoring branch.