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samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Add FQZComp Codec (Update CRAM Codecs to CRAM 3.1) #1704

Open yash-puligundla opened 5 months ago

yash-puligundla commented 5 months ago

NOTE: This PR is in draft as it is dependent on https://github.com/samtools/htsjdk/pull/1618 ,https://github.com/samtools/htsjdk/pull/1644 and https://github.com/samtools/htsjdk/pull/1663

Description: This PR is part of an effort to upgrade CRAM to v3.1. It adds the FQZcomp Decoder implementation.

List of Changes: Add FQZcomp Decoder Add FQZcompInteropTest to test the decoder using the test files from htscodecs. These interop tests use the files from samtools installation (samtools-1.14/htslib-1.14/htscodes/tests/fqzcomp)