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

Open

yash-puligundla wants to merge 66 commits intosamtools:masterfrom yash-puligundla:yp_cram_3_1_codecs

+6,102-1,081

Commits on Mar 5, 2024

adding comments to Frequencies.java

yash-puligundla
authored and
cmnbroad
committed
separate encode and decode classes

yash-puligundla
authored and
cmnbroad
committed
Add Frequency methods to encode and decode classes

yash-puligundla
authored and
cmnbroad
committed
clean up rans tests and add separate packages for rans 4x8 and nx16

yash-puligundla
authored and
cmnbroad
committed
filter out extra column from q40+dir file

yash-puligundla
authored and
cmnbroad
committed
rans nx16 order 1 freq tables + refactor

yash-puligundla
authored and
cmnbroad
committed
clean up

yash-puligundla
authored and
cmnbroad
committed
Update RAN test method names.
cmnbroad
committed
Remove unncessary params arg from uncompress methods (params are embedded in the streams).
cmnbroad
committed
Remove unnecessary RANSNx16Params state.
cmnbroad
committed
Fix bug in the case where the cat bit is set.
cmnbroad
committed
Reduce unncessary buffer allocation.
cmnbroad
committed
Thread RANSNx16 params through RANSNx16 implementation.
cmnbroad
committed
Dont initialize RANSNx16 decoding structures unless we're going to use them.
cmnbroad
committed
Move/inline RANS Nx16 D0N uncompress method into RANSNx16Decode.
cmnbroad
committed
Move/inline RANS Nx16 D1N uncompress method into RANSNx16Decode.
cmnbroad
committed
Move/inline RANS Nx16 E0N compress method into RANSNx16Encode.
cmnbroad
committed
Move/inline RANS Nx16 E1N compress method into RANSNx16Encode.
cmnbroad
committed
Suppress spotbugs warnings.
cmnbroad
committed
Don't initialize RANS4x8 decoding structure unless we're going to use them.

yash-puligundla
authored and
cmnbroad
committed
Move/inline RANS 4x8 E04 compress method into RANS4x8Encode.

yash-puligundla
authored and
cmnbroad
committed
Move/inline RANS 4x8 E14 compress method into RANS4x8Encode.

yash-puligundla
authored and
cmnbroad
committed
Move/inline RANS 4x8 D04 uncompress method into RANS4x8Decode.

yash-puligundla
authored and
cmnbroad
committed
Move/inline RANS 4x8 D14 uncompress method into RANS4x8Decode.

yash-puligundla
authored and
cmnbroad
committed
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

yash-puligundla
authored and
cmnbroad
committed
Add ransNx16 for format flags = 1,4,5 (N=32) and replace division with right shifts.

yash-puligundla
authored and
cmnbroad
committed
When CAT is true, add limit and rewind the outBuffer before returning it.

yash-puligundla
authored and
cmnbroad
committed
Add RANSTest with formatflags = 32, 33, 36, 37

yash-puligundla
authored and
cmnbroad
committed
Remove initialization of alphabet array.

yash-puligundla
authored and
cmnbroad
committed
Add RLE Encode and Decode. Works as expected for RANSNx16 Order 0

yash-puligundla
authored and
cmnbroad
committed
Move declaration of variables used within the for loop to inside the for loop

yash-puligundla
authored and
cmnbroad
committed
Convert symbols from int to byte

yash-puligundla
authored and
cmnbroad
committed
rename getInterleaveSize to getNumInterleavedRANSStates in RANSNx16Params

yash-puligundla
authored and
cmnbroad
committed
RLE encode and decode works as expected for RANSNx16 Order 1

yash-puligundla
authored and
cmnbroad
committed
add encode and decode Pack. Add test cases for pack

yash-puligundla
authored and
cmnbroad
committed
rename variable for better readability

yash-puligundla
authored and
cmnbroad
committed
add exception when num of distinct symbols = 0 or > 16

yash-puligundla
authored and
cmnbroad
committed
Add Decode Stripe to RANS Nx16. Add getFormatFlags() to RANSParams

yash-puligundla
authored and
cmnbroad
committed
Add test for Encoding when Stripe Flag is set

yash-puligundla
authored and
cmnbroad
committed
Fix Spot Bugs warn - Use && for logical and

yash-puligundla
authored and
cmnbroad
committed
Addressing the feedback from Aug 30, 2022

yash-puligundla
authored and
cmnbroad
committed
Use the Interop Test files from samtools-1.14/htslib-1.14/htscodecs/tests or ../htscodecs/tests depending on the env

yash-puligundla
authored and
cmnbroad
committed
Replace hex literals with bit flag masks in RANSInteropTest Data Provider

yash-puligundla
authored and
cmnbroad
committed
Addressing the feedback so far

yash-puligundla
authored and
cmnbroad
committed
rename methods that return boolean to start with 'is' instead of 'get'

yash-puligundla
authored and
cmnbroad
committed
debug

yash-puligundla
authored and
cmnbroad
committed
Addressing the feedback from 10/25/22

yash-puligundla
authored and
cmnbroad
committed
undo inadvertent deletion of RANSInterop roundtrip test logic

yash-puligundla
authored and
cmnbroad
committed
debug - add decodePack and decodeRLE on top of CAT flag

yash-puligundla
authored and
cmnbroad
committed
rewind outBuffer before it is returned

yash-puligundla
authored and
cmnbroad
committed
remove duplicate outBuffer creation

yash-puligundla
authored and
cmnbroad
committed
Addressing the feedback from oct 11, 2023 except implementing the Stripe Flag in RANS Nx16 encoder

yash-puligundla
authored and
cmnbroad
committed
Move common methods to CRAMInteropTestUtils class

yash-puligundla
authored and
cmnbroad
committed
Addressing the feedback from Nov 7 and Nov 20 - part 1

yash-puligundla
authored and
cmnbroad
committed
Addressing the feedback from Nov 7 and Nov 20 - part 2

yash-puligundla
authored and
cmnbroad
committed
Addressing the feedback from Nov 7 and Nov 20 - part 3

yash-puligundla
authored and
cmnbroad
committed
Addressing the feedback from Nov 7 and Nov 20 - part 4

yash-puligundla
authored and
cmnbroad
committed
Addressing the feedback from Nov 7 and Nov 20 - part 5

yash-puligundla
authored and
cmnbroad
committed
Addressing the feedback from Nov 7 and Nov 20 - part 6

yash-puligundla
authored and
cmnbroad
committed
Addressing the feedback from Nov 7 and Nov 20 - part 6

yash-puligundla
authored and
cmnbroad
committed
Move common code to CompressionUtils

yash-puligundla
authored and
cmnbroad
committed
Minor final review comments.
cmnbroad
committed
Use copies of the CRAM 3.1 interop test streams that originate inthe htscodecs repo.
cmnbroad
committed
Update to use the locally checked in CRAM 3.1 interop test data.
cmnbroad
committed
A little naming cleanup.
cmnbroad
committed
Fix issue introduced by conflict resolution of a rebase.
cmnbroad
committed