Add FQZComp Codec (Update CRAM Codecs to CRAM 3.1)#1704

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yash-puligundla wants to merge 84 commits intosamtools:masterfrom yash-puligundla:yp_cram_3_1_fqzcomp

+5,909-1,087

Commits on Oct 19, 2023

adding comments to Frequencies.java
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separate encode and decode classes
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Add Frequency methods to encode and decode classes
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clean up rans tests and add separate packages for rans 4x8 and nx16
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filter out extra column from q40+dir file
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rans nx16 order 1 freq tables + refactor
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clean up
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Update RAN test method names.

cmnbroad
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Remove unncessary params arg from uncompress methods (params are embedded in the streams).

cmnbroad
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Remove unnecessary RANSNx16Params state.

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

cmnbroad
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Reduce unncessary buffer allocation.

cmnbroad
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Thread RANSNx16 params through RANSNx16 implementation.

cmnbroad
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Dont initialize RANSNx16 decoding structures unless we're going to use them.

cmnbroad
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Move/inline RANS Nx16 D0N uncompress method into RANSNx16Decode.

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

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

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

cmnbroad
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Suppress spotbugs warnings.

cmnbroad
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Don't initialize RANS4x8 decoding structure unless we're going to use them.
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Move/inline RANS 4x8 E04 compress method into RANS4x8Encode.
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Move/inline RANS 4x8 E14 compress method into RANS4x8Encode.
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Move/inline RANS 4x8 D04 uncompress method into RANS4x8Decode.
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Move/inline RANS 4x8 D14 uncompress method into RANS4x8Decode.
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Fix normalized Frequency (4096), add normalize Frequency using bit shift 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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Add ransNx16 for format flags = 1,4,5 (N=32) and replace division with right shifts.
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When CAT is true, add limit and rewind the outBuffer before returning it.
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Add RANSTest with formatflags = 32, 33, 36, 37
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Remove initialization of alphabet array.
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Add RLE Encode and Decode. Works as expected for RANSNx16 Order 0
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Move declaration of variables used within the for loop to inside the for loop
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Convert symbols from int to byte
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rename getInterleaveSize to getNumInterleavedRANSStates in RANSNx16Params
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RLE encode and decode works as expected for RANSNx16 Order 1
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add encode and decode Pack. Add test cases for pack
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rename variable for better readability
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add exception when num of distinct symbols = 0 or > 16
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Add Decode Stripe to RANS Nx16. Add getFormatFlags() to RANSParams
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Add test for Encoding when Stripe Flag is set
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Fix Spot Bugs warn - Use && for logical and
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Addressing the feedback from Aug 30, 2022
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Use the Interop Test files from samtools-1.14/htslib-1.14/htscodecs/tests or ../htscodecs/tests depending on the env
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Replace hex literals with bit flag masks in RANSInteropTest Data Provider
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Addressing the feedback so far
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debug CI test failure
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Fix the htscodecs path
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rename methods that return boolean to start with 'is' instead of 'get'
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debug
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Addressing the feedback from 10/25/22
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undo inadvertent deletion of RANSInterop roundtrip test logic
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debug - add decodePack and decodeRLE on top of CAT flag
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rewind outBuffer before it is returned
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remove duplicate outBuffer creation
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Addressing the feedback from oct 11, 2023 except implementing the Stripe Flag in RANS Nx16 encoder
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Commits on Oct 26, 2023

Move common methods to CRAMInteropTestUtils class
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Commits on Dec 1, 2023

Addressing the feedback from Nov 7 and Nov 20 - part 1
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Commits on Dec 6, 2023

Addressing the feedback from Nov 7 and Nov 20 - part 2
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Addressing the feedback from Nov 7 and Nov 20 - part 3
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Commits on Dec 13, 2023

Addressing the feedback from Nov 7 and Nov 20 - part 4
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Commits on Dec 18, 2023

Addressing the feedback from Nov 7 and Nov 20 - part 5
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Commits on Dec 20, 2023

Addressing the feedback from Nov 7 and Nov 20 - part 6
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Commits on Dec 21, 2023

Addressing the feedback from Nov 7 and Nov 20 - part 6
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Commits on Jan 10, 2024

Move common code to CompressionUtils
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add Range Encode
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Fix RangeEncode for order 0 and formatflags=0x00
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rebase - Add Range Codec, RangeTest, RangeInteropTest for order, rle, stripe, nosize, cat flags
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Add uncompressEXT and decodePack to RangeDecode
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add Pack flag to tests
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Add Range encode and decode for EXT flag
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debug spotbugs error
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debug - add decodePack on top of CAT flag
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Addressing format related feedback from RANS PR that applies to Range Codec as well
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Rebase on RANS branch and use common methods from CRAMInteropTestUtils class
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Addressing feedback from nov 21 - part 1
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Commits on Jan 24, 2024

Addressing feedback from nov 21 - part 2
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Commits on Jan 29, 2024

Addressing feedback from nov 21, nov 28 - part 3
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Commits on Jan 30, 2024

Add NameTokenization Decoder
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Add NameTokenization Encoder
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add descriptive variable names
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Add unittests
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Use List<Token> instead of TokenStreams in NameTokenisationEncoder
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Addressing feedback from dec 5 - part 1
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Commits on Jan 31, 2024

Addressing feedback from dec 5 - part 2
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Commits on Feb 7, 2024

Add FQZComp Decoder
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