NVIDIA-Genomics-Research GenomeWorks issues

NVIDIA-Genomics-Research / GenomeWorks

SDK for GPU accelerated genome assembly and analysis

https://clara-parabricks.github.io/GenomeWorks/

Apache License 2.0

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issues

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[cudamapper] Move print_paf() to public interface

#520 nvvishanthi closed 4 years ago
0
[cudapoa] modified adaptive banded alignment

#519 r-mafi closed 4 years ago
0
[cudaaligner] Extended test and fixed a bug in approximate banded Myers

#518 ahehn-nv closed 4 years ago
0
[cudamapper] Expose IndexDescriptor in public interface

#517 mimaric closed 4 years ago
0
[cudamapper] Expose print_paf() in public interface

#516 mimaric closed 4 years ago
0
[cudaaligner] alignment object extensions

#515 ahehn-nv closed 4 years ago
0
[cudamapper] Create public interface for IndexDescriptor

#514 nvvishanthi closed 4 years ago
1
[cudaaligner] banded myers with fixed bandwidth and low memory requirements

#513 ahehn-nv closed 4 years ago
1
[cudaaligner] Rearranging code in Test_AlignerGlobal.cpp

#512 ahehn-nv closed 4 years ago
1
[common] misc improvements

#511 ahehn-nv closed 4 years ago
1
[cudamapper] Add create_overlapper function to instantiate overlapper object

#510 nvvishanthi closed 4 years ago
3
[cudamapper] Create public interface for overlapper

#509 mimaric closed 4 years ago
0
[cudamapper] cudaMapper sample application

#508 nvvishanthi closed 4 years ago
8
[cudamapper] Do not apply minimizer frequency filtering by default when overlapping very few reads

#507 edawson closed 4 years ago
0
[cudamapper] Fasta index ids

#506 edawson closed 4 years ago
0
[cudaaligner] Tests should load data from file

#505 ahehn-nv opened 4 years ago
0
[cudamapper] Filtering parameters are too stringent for very small read sets

#504 edawson closed 4 years ago
0
[cudamapper] Overlaps at the same position in an index are dropped even when query and target files are not the same.

#503 edawson closed 4 years ago
0
[cudapoa] add tests for banded and adaptive alignment

#502 r-mafi closed 3 years ago
1
[ci] formatting: Do not sort using statements

#501 ahehn-nv closed 4 years ago
0
[ci] check-style: fixed 00db5134

#500 ahehn-nv closed 4 years ago
0
Revert "[ci] check-style: Changed diff format and show whitespace changes in …"

#499 ahehn-nv closed 4 years ago
2
[ci] check-style: Changed diff format and show whitespace changes in …

#498 ahehn-nv closed 4 years ago
0
[cudaaligner] fixes for banded Myers

#497 ahehn-nv closed 4 years ago
0
[cudapoa][cudaaligner] adding support for different types of gap penalty

#496 r-mafi opened 4 years ago
1
[cudapoa] Adaptive Banding - first draft

#495 r-mafi closed 4 years ago
1
[cudapoa] customizable number of cells per thread in NW kernels

#494 r-mafi closed 3 years ago
1
[cudamapper] Skip index pair which cause OOM errors

#493 mimaric closed 4 years ago
1
[SDK] Copy license to pygenomeworks folder before pip executes setup()

#492 ohadmo closed 4 years ago
0
[cudamapper] Split index pairs which cause OOM into multiple pairs of indices

#491 mimaric opened 4 years ago
0
[cudamapper] Process skipped pairs of indices separately

#490 mimaric opened 4 years ago
0
[cudamapper] Skip pairs of indices which cause out of memory errors

#489 mimaric closed 4 years ago
1
[sdk] update copyright headers

#488 tijyojwad closed 4 years ago
1
[CI] Add build Slack notifications

#487 ohadmo closed 4 years ago
1
[CI] Remove PyPI username from twine command

#486 ohadmo closed 4 years ago
0
[docs] Consolidate Build and Install sections in README

#485 nvvishanthi closed 4 years ago
0
[cudapoa] added missing band-width parameter to create Bat…

#484 r-mafi closed 4 years ago
0
[cudapoa] cudapoa binary input options

#483 r-mafi closed 3 years ago
1
[cudapoa] Fixes bug with multiple fasta logic

#482 atadkase closed 4 years ago
0
[cudamapper] Use pinned memory and single array in IndexHostCopy

#481 mimaric closed 4 years ago
1
[cudamapper] Passing correct parser to print_paf()

#480 mimaric closed 4 years ago
0
[CI] Upload to production PyPI server

#479 ohadmo closed 4 years ago
0
[cudamapper] Change default parameters for -w, -F, -r, -b, and -z.

#478 edawson closed 4 years ago
0
[pygw] better fix for intermittent test failure

#477 tijyojwad closed 4 years ago
2
[pygw] reference to stream getting lost in CudaAlignerBatch object

#476 tijyojwad opened 4 years ago
0
[common] Introduced CudaStream an RAII class to wrap cuda streams

#475 ahehn-nv closed 4 years ago
0
[pygw] temporary fix for intermittent test bug

#474 tijyojwad closed 4 years ago
4
[sdk] rename cga to gw across repo

#473 tijyojwad closed 4 years ago
0
[cudapoa] CUDAPOA Binary

#472 atadkase closed 4 years ago
0
[cudamapper] Default parameters should be hardened against many datasets / GPUs, match those of minimap2

#471 edawson closed 4 years ago
2

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