[cudaextender] Add CUDA Extender module with Ungapped X-Drop extension #564

atadkase · 2020-09-17T23:31:20Z

Adds cudaextender module to GenomeWorks
Adds device and host pointer API sample
Adds end2end host pointer API test
Updates copyright regex

…me hsp_threshold to score_threshold

…ored_segment_pair

…implementation

…e/ungapped_extender_impl

cudaextender/include/claraparabricks/genomeworks/cudaextender/extender.hpp

cudaextender/samples/sample_cudaextender.cpp

cudaextender/include/claraparabricks/genomeworks/cudaextender/cudaextender.hpp

ahehn-nv

Looks good overall. Mostly requesting minor style improvements.

cudaextender/src/ungapped_xdrop.cu

cudaextender/tests/Test_CudaextenderEnd2End.cu

cudaextender/samples/sample_cudaextender.cpp

cudaextender/include/claraparabricks/genomeworks/cudaextender/utils.hpp

cudaextender/include/claraparabricks/genomeworks/cudaextender/extender.hpp

…e()->get_size<>();

This reverts commit b64c018.

This reverts commit cfb1daa.

…arget length swap

…sues

atadkase and others added 30 commits August 21, 2020 14:21

[cudaungappedextender] Add skeleton for API and sample usage in segalign

ba7a09c

[cudaungappedextender] fix copy-pasta

950e305

Add basic samples

a8fd9e4

[cudaungappedextender] Add sample data

75ae4ba

[cudaungappedextender] Correct obviously wrong data types

83748b4

[cudaue] Add return 0

ee2e3dd

[cudaue] namespace scope change

e28449b

[cudaue] Free CUDA memory in device sample

a7a3f07

[cudaue] Fix comment

03781e3

[cudaue] Primary formatting

a940113

[cudaungappedextender]Address comments

0a71edf

[cudaungappedextender] Change Anchors to Seeds and clang-format

1e5a4fe

[cudaungappedextender] update length

550d0a9

[cudaungappedextender] Change seedHits to seeds

d863ca1

[cudaungappedextender] const method

93c8e39

Merge branch 'dev-v0.6.0' into atadkase/ungapped_extender_sample

f86f618

[cudaungappedextender] Address review comments - default values; rena…

15a6728

…me hsp_threshold to score_threshold

[cudaungappedextender] Rename seed -> seed_pair; scored_segment -> sc…

6a1a185

…ored_segment_pair

[cudaungappedextender] propagate renaming changes

5a91b43

[cudaextender] Rename ungappedextender to extender; Add skeleton for …

0e57503

…implementation

[cudaextender] Make format

3a52056

[cudaextender] Add more files

58d15be

Merge remote-tracking branch 'clara-genomics/dev-v0.6.0' into atadkas…

e5e6a08

…e/ungapped_extender_impl

[cudaextender] refactor find_hsps

4bb2e2a

[cudaextender] rename function

2867834

[cudaextender] Working device_ptr sample

b77dc2e

[cudaextender] debug changes

8321c7b

[cudaextender] Remove redundant comma

623711c

[cudaextender] correct casts

bdf32de

[cudaextender] Fix parser copy-pasta; Remove debug prints

1376dd5

[cudaextender] Rename sub_mat as score_mat

c120c47

tijyojwad suggested changes Sep 24, 2020

View reviewed changes

atadkase and others added 2 commits September 25, 2020 10:44

[cudaextender] char to int8_t and reformat

6f08dd5

Merge branch 'dev-v0.6.0' into atadkase/ungapped_extender_impl

e558714

atadkase commented Sep 25, 2020

View reviewed changes

cudaextender/include/claraparabricks/genomeworks/cudaextender/cudaextender.hpp Show resolved Hide resolved

ahehn-nv requested changes Sep 28, 2020

View reviewed changes

atadkase and others added 12 commits September 28, 2020 10:28

[cudaextender] Const removal; signature updates with ref removal; siz…

4cca27b

…e()->get_size<>();

[cudaextender] enum class

cfb1daa

[cudaextender] Add NUC2 as enum

b64c018

[cudaextender] size_t->int64_t

1e258cf

[cudaextender] Make format

4d93eb0

[cudaextender] Make protected

bca8fe7

[cudaextender] Add attribution

c705cd5

Revert "[cudaextender] Add NUC2 as enum"

abedff8

This reverts commit b64c018.

Revert "[cudaextender] enum class"

4e54c99

This reverts commit cfb1daa.

[cudaextender] Revert enum to constexpr globals

c618f23

[cudaextender] Add consts and make get_size() uniform

6528beb

[cudaextender] Replace length() with get_size(); Fix bug with query/t…

e011a73

…arget length swap

ahehn-nv approved these changes Sep 29, 2020

View reviewed changes

atadkase added the cudaextender GPU-based seed extension algorithms label Oct 1, 2020

atadkase added 7 commits October 1, 2020 09:16

[cudaextender] Add issues for hardcoded vars

69604f1

[cudaextender] Add issues for kernel optimization and other kernel is…

3481796

…sues

[cudaextender] make format

8f41485

[cudaextender] Uniform comment names for host pointer API

961c2a5

[cudaextender] Remove TODO

86e71b1

[cudaextender] Remove todo

e6ffd17

[cudaextender] Make format

7993dd2

tijyojwad self-requested a review October 1, 2020 19:57

tijyojwad approved these changes Oct 1, 2020

View reviewed changes

atadkase merged commit e13a2da into NVIDIA-Genomics-Research:dev-v0.6.0 Oct 1, 2020

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[cudaextender] Add CUDA Extender module with Ungapped X-Drop extension #564

[cudaextender] Add CUDA Extender module with Ungapped X-Drop extension #564

atadkase commented Sep 17, 2020 •

edited

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[cudaextender] Add CUDA Extender module with Ungapped X-Drop extension #564

[cudaextender] Add CUDA Extender module with Ungapped X-Drop extension #564

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atadkase commented Sep 17, 2020 •

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