Add Range codec (Update CRAM Codecs to CRAM 3.1)#1644
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yash-puligundla wants to merge 76 commits intosamtools:masterfrom
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Add Range codec (Update CRAM Codecs to CRAM 3.1)#1644yash-puligundla wants to merge 76 commits intosamtools:masterfrom
yash-puligundla wants to merge 76 commits intosamtools:masterfrom
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This was referenced Mar 21, 2023
…dded in the streams).
cmnbroad
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Nov 28, 2023
src/main/java/htsjdk/samtools/cram/compression/range/RangeDecode.java
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src/main/java/htsjdk/samtools/cram/compression/range/RangeDecode.java
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src/main/java/htsjdk/samtools/cram/compression/range/RangeDecode.java
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src/main/java/htsjdk/samtools/cram/compression/range/RangeDecode.java
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src/main/java/htsjdk/samtools/cram/compression/range/RangeCoder.java
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src/main/java/htsjdk/samtools/cram/compression/range/RangeDecode.java
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added 7 commits
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added 12 commits
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… stripe, nosize, cat flags
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Contributor
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@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. |
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Closing in favor of #1714. |
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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)