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Add RANS Nx16 codec (Update CRAM Codecs to CRAM 3.1) #1618

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Add RANS Nx16 codec (Update CRAM Codecs to CRAM 3.1) #1618

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Commits on Mar 5, 2024

  1. adding comments to Frequencies.java

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  2. separate encode and decode classes

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  3. Add Frequency methods to encode and decode classes

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  4. clean up rans tests and add separate packages for rans 4x8 and nx16

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  5. filter out extra column from q40+dir file

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  6. rans nx16 order 1 freq tables + refactor

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  7. clean up

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  8. Update RAN test method names.

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  9. Remove unncessary params arg from uncompress methods (params are embe… 

    …dded in the streams).
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  10. Remove unnecessary RANSNx16Params state.

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  11. Fix bug in the case where the cat bit is set.

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  12. Reduce unncessary buffer allocation.

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  13. Thread RANSNx16 params through RANSNx16 implementation.

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  14. Dont initialize RANSNx16 decoding structures unless we're going to us… 

    …e them.
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  15. Move/inline RANS Nx16 D0N uncompress method into RANSNx16Decode.

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  16. Move/inline RANS Nx16 D1N uncompress method into RANSNx16Decode.

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  17. Move/inline RANS Nx16 E0N compress method into RANSNx16Encode.

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  18. Move/inline RANS Nx16 E1N compress method into RANSNx16Encode.

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  19. Suppress spotbugs warnings.

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  20. Don't initialize RANS4x8 decoding structure unless we're going to use… 

    … them.
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  21. Move/inline RANS 4x8 E04 compress method into RANS4x8Encode.

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  22. Move/inline RANS 4x8 E14 compress method into RANS4x8Encode.

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  23. Move/inline RANS 4x8 D04 uncompress method into RANS4x8Decode.

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  24. Move/inline RANS 4x8 D14 uncompress method into RANS4x8Decode.

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  25. Fix normalized Frequency (4096), add normalize Frequency using bit sh… 

    …ift methods for RANS Nx16 Order 0 and Order 1, RANS Nx16 Order 0 and Order 1 with format flags = 1 works as expected when N=4
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  26. Add ransNx16 for format flags = 1,4,5 (N=32) and replace division wit… 

    …h right shifts.
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  27. When CAT is true, add limit and rewind the outBuffer before returning… 

    … it.
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  28. Add RANSTest with formatflags = 32, 33, 36, 37

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  29. Remove initialization of alphabet array.

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  30. Add RLE Encode and Decode. Works as expected for RANSNx16 Order 0

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  31. Move declaration of variables used within the for loop to inside the … 

    …for loop
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  32. Convert symbols from int to byte

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  33. rename getInterleaveSize to getNumInterleavedRANSStates in RANSNx16Pa… 

    …rams
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  34. RLE encode and decode works as expected for RANSNx16 Order 1

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  35. add encode and decode Pack. Add test cases for pack

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  36. rename variable for better readability

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  37. add exception when num of distinct symbols = 0 or > 16

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  38. Add Decode Stripe to RANS Nx16. Add getFormatFlags() to RANSParams

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  39. Add test for Encoding when Stripe Flag is set

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  40. Fix Spot Bugs warn - Use && for logical and

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  41. Addressing the feedback from Aug 30, 2022

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  42. Use the Interop Test files from samtools-1.14/htslib-1.14/htscodecs/t… 

    …ests or ../htscodecs/tests depending on the env
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  43. Replace hex literals with bit flag masks in RANSInteropTest Data Prov… 

    …ider
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  44. Addressing the feedback so far

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  45. rename methods that return boolean to start with 'is' instead of 'get'

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  46. debug

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  47. Addressing the feedback from 10/25/22

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  48. undo inadvertent deletion of RANSInterop roundtrip test logic

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  49. debug - add decodePack and decodeRLE on top of CAT flag

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  50. rewind outBuffer before it is returned

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  51. remove duplicate outBuffer creation

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  52. Addressing the feedback from oct 11, 2023 except implementing the Str… 

    …ipe Flag in RANS Nx16 encoder
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  53. Move common methods to CRAMInteropTestUtils class

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  54. Addressing the feedback from Nov 7 and Nov 20 - part 1

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  55. Addressing the feedback from Nov 7 and Nov 20 - part 2

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  56. Addressing the feedback from Nov 7 and Nov 20 - part 3

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  57. Addressing the feedback from Nov 7 and Nov 20 - part 4

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  58. Addressing the feedback from Nov 7 and Nov 20 - part 5

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  59. Addressing the feedback from Nov 7 and Nov 20 - part 6

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  60. Addressing the feedback from Nov 7 and Nov 20 - part 6

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  61. Move common code to CompressionUtils

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  62. Minor final review comments.

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  63. Use copies of the CRAM 3.1 interop test streams that originate inthe … 

    …htscodecs repo.
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  64. Update to use the locally checked in CRAM 3.1 interop test data.

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  65. A little naming cleanup.

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  66. Fix issue introduced by conflict resolution of a rebase.

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