Add Range codec (Update CRAM Codecs to CRAM 3.1)

samtools / htsjdk

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

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

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Add Range codec (Update CRAM Codecs to CRAM 3.1) #1644

Open yash-puligundla opened 1 year ago

yash-puligundla commented 1 year ago

NOTE: This PR is in draft as it is dependent on RANS NX16 PR

Description This PR is part of an effort to upgrade CRAM to v3.1. It adds the Range Codec implementation.

List of Changes:

Add Range Codec Add RangeTest to unittest the Range Codec implementation Add RangeInteropTest to test the Range Codec using the test files from htscodecs. These interop tests use the files from samtools installation (samtools-1.14/htslib-1.14/htscodes/tests/dat)

yash-puligundla commented 10 months ago

The Interop tests for Range Codec fail when the EXT flag is used. I will pick this up when I am back from my holiday.

yash-puligundla commented 7 months ago

@cmnbroad I have addressed all the comments from this round of feedback. This PR is ready for review. Let me know if you have any questions.