Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / NVIDIA-Genomics-Research/VariantWorks issues and pull requests

#171 - Bump nemo-toolkit from 0.10.1 to 1.6.0

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#170 - Bump numpy from 1.18.3 to 1.22.0

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#169 - simple_consensus_caller , how to automatically remove

Issue - State: open - Opened by jelber2 over 2 years ago

#168 - Relu

Pull Request - State: closed - Opened by avantikalal over 3 years ago

#167 - Apply softmax to the model only during inference

Pull Request - State: closed - Opened by ohadmo over 3 years ago
Labels: bug

#165 - Modified cnn

Pull Request - State: closed - Opened by avantikalal over 3 years ago

#164 - [encoder] fix bug in adding ref info to summary encoding

Pull Request - State: closed - Opened by tijyojwad over 3 years ago - 2 comments

#163 - [dataloader] improve hdf data loader

Pull Request - State: closed - Opened by tijyojwad over 3 years ago

#162 - Added Consensus CNN

Pull Request - State: open - Opened by rahulmohan almost 4 years ago

#161 - [consensus] add multi gpu training docs to consensus sample

Pull Request - State: closed - Opened by tijyojwad almost 4 years ago

#160 - [encoding] update encoding to add draft base and base quality

Pull Request - State: closed - Opened by tijyojwad almost 4 years ago
Labels: encodings, I/O

#159 - [sample] filtering to consensus sample

Issue - State: open - Opened by tijyojwad almost 4 years ago
Labels: samples

#158 - [loss] focal loss throwing an error when used in place of ce loss

Issue - State: open - Opened by tijyojwad almost 4 years ago
Labels: bug

#157 - Added attention consensus model

Pull Request - State: open - Opened by rahulmohan almost 4 years ago

#155 - Add tabix index file input option, catch invalid format error

Pull Request - State: closed - Opened by ntadimeti almost 4 years ago

#154 - Add input BAM files support to simple consensus caller sample

Pull Request - State: closed - Opened by ohadmo almost 4 years ago

#153 - Brass BEDPE

Pull Request - State: closed - Opened by mp15 about 4 years ago - 1 comment

#152 - BED/BEDPE Overwrite rather than create new typed columns + offbyone fix

Pull Request - State: closed - Opened by mp15 about 4 years ago - 2 comments

#151 - Adapt FastxWriter to support more arguments

Pull Request - State: closed - Opened by ohadmo about 4 years ago - 1 comment

#150 - [I/O] KeyErrors are thrown for info columns not present in a region

Issue - State: open - Opened by edawson about 4 years ago - 1 comment

#149 - [consensus_caller] fix categorical accuracy calculation

Pull Request - State: closed - Opened by tijyojwad about 4 years ago - 1 comment
Labels: bug, samples

#148 - [CI] Add nightly wheel package versioning

Pull Request - State: closed - Opened by ohadmo about 4 years ago

#147 - Support FASTA output format in FastxWriter class

Pull Request - State: closed - Opened by ohadmo about 4 years ago - 1 comment

#146 - [ci] fix CPU CI tests

Pull Request - State: closed - Opened by tijyojwad about 4 years ago

#145 - [io] add generic parser for BED files

Pull Request - State: closed - Opened by tijyojwad about 4 years ago - 2 comments
Labels: enhancement, I/O

#144 - Feature request: BEDPE format for ingesting SV data

Issue - State: closed - Opened by mp15 about 4 years ago - 8 comments
Labels: enhancement, I/O

#143 - [CI] Add full CI support- Auto-release & nightly builds

Pull Request - State: closed - Opened by ohadmo about 4 years ago

#142 - MultiZMW stitching, model structure inputs, log(0) fixes

Pull Request - State: closed - Opened by michaelbrownid about 4 years ago - 13 comments
Labels: enhancement, samples

#141 - VCFReader re-implemented with pysam

Pull Request - State: closed - Opened by ntadimeti about 4 years ago - 2 comments

#140 - New focal loss

Pull Request - State: closed - Opened by rahulmohan about 4 years ago

#139 - Add alternative setup instructions through Anaconda

Pull Request - State: closed - Opened by ohadmo about 4 years ago - 1 comment
Labels: documentation, sdk

#138 - [sample] add new sample with scalar vcf values

Pull Request - State: open - Opened by tijyojwad about 4 years ago
Labels: samples

#137 - [model] add optional softmax layer to consensus rnn

Pull Request - State: closed - Opened by tijyojwad about 4 years ago - 1 comment

#136 - simple_consensus_caller sample fails with negative probabilites.

Pull Request - State: closed - Opened by michaelbrownid about 4 years ago - 4 comments

#135 - [I/O] Update VCF -> cuDF parser with more optimized version

Issue - State: open - Opened by tijyojwad about 4 years ago
Labels: I/O

#134 - Removed softmax from RNN forward pass

Pull Request - State: closed - Opened by rahulmohan about 4 years ago

#133 - Add quality score output for the consensus pipeline

Pull Request - State: closed - Opened by ohadmo about 4 years ago
Labels: model

#132 - [encoder] support latest samtools mpileup for summary encoder

Issue - State: open - Opened by tijyojwad about 4 years ago
Labels: encodings

#131 - [model] add quality score output for consensus pipeline

Issue - State: closed - Opened by tijyojwad about 4 years ago
Labels: model

#130 - [loss] add focal loss support

Issue - State: closed - Opened by tijyojwad about 4 years ago
Labels: model

#129 - [I/O] VCFReader crashes when reading from regions that are empty

Issue - State: open - Opened by edawson about 4 years ago
Labels: bug, I/O

#128 - [samples] add inference sample for simple snp trainer

Pull Request - State: open - Opened by ohadmo about 4 years ago
Labels: samples

#127 - Added Focal Loss

Pull Request - State: closed - Opened by rahulmohan about 4 years ago - 1 comment

#126 - [IO] fix multi gpu data loading

Pull Request - State: closed - Opened by tijyojwad about 4 years ago
Labels: I/O

#125 - [docs] update docs to showcase new features

Pull Request - State: closed - Opened by tijyojwad about 4 years ago
Labels: documentation

#124 - [visualization] ReadPileup visualizer to take encoding as input

Issue - State: open - Opened by tijyojwad about 4 years ago
Labels: encodings

#123 - [I/O] HDF Data Loader not showing speedup for multi threaded

Issue - State: open - Opened by tijyojwad about 4 years ago - 1 comment
Labels: I/O

#122 - [consensus sample] add README and sample data

Pull Request - State: closed - Opened by tijyojwad about 4 years ago
Labels: samples

#121 - Added end-to-end DL4CCS training pipeline

Pull Request - State: closed - Opened by rahulmohan about 4 years ago

#120 - [network] add consensus rnn network

Pull Request - State: closed - Opened by tijyojwad about 4 years ago

#119 - Added Consensus RNN

Pull Request - State: closed - Opened by rahulmohan about 4 years ago

#118 - [summaryencoder] return positions as torch tensor from encoding call

Pull Request - State: closed - Opened by tijyojwad about 4 years ago - 1 comment
Labels: encodings

#116 - [I/O] Generalize HDF data loader

Issue - State: closed - Opened by tijyojwad about 4 years ago
Labels: I/O

#115 - Added Parallel Data Loader

Pull Request - State: closed - Opened by rahulmohan about 4 years ago - 1 comment

#114 - [vcfio] update VCF writing code

Pull Request - State: closed - Opened by tijyojwad about 4 years ago
Labels: I/O

#113 - [model] reference model for consensus calling

Issue - State: closed - Opened by tijyojwad over 4 years ago - 1 comment
Labels: model

#112 - [sdk] update VariantWorks installation to be based on conda

Issue - State: open - Opened by tijyojwad over 4 years ago
Labels: sdk

#111 - [docs] Extract code snippets from the `.rst` file into python scripts

Pull Request - State: closed - Opened by ohadmo over 4 years ago - 2 comments
Labels: documentation

#110 - [samples] add test data for snp trainer

Issue - State: open - Opened by tijyojwad over 4 years ago
Labels: samples

#109 - [samples] polishing sample code

Issue - State: closed - Opened by tijyojwad over 4 years ago
Labels: samples

#108 - [samples] add multi GPU support to snp caller sample

Issue - State: open - Opened by tijyojwad over 4 years ago
Labels: samples

#107 - [samples] add inference sample to variant caller trainer

Issue - State: open - Opened by tijyojwad over 4 years ago
Labels: samples

#106 - [Utils] Add Stitcher class for overlapping chunked encoded samples

Pull Request - State: closed - Opened by ohadmo over 4 years ago

#105 - Added Haploid Label Encoder

Pull Request - State: closed - Opened by rahulmohan over 4 years ago

#104 - [summary_encoder] insertions next to deletes

Issue - State: open - Opened by tijyojwad over 4 years ago
Labels: encodings

#103 - Review of SummaryEncoder

Pull Request - State: closed - Opened by ohadmo over 4 years ago

#102 - [vcfio] update VCF writer to corretly support all columns from DF

Issue - State: closed - Opened by tijyojwad over 4 years ago
Labels: bug, I/O

#101 - [encoders] add ability to expose scalar features

Issue - State: open - Opened by tijyojwad over 4 years ago
Labels: encodings

#100 - [vcfio] fix data type and improve perf

Pull Request - State: closed - Opened by tijyojwad over 4 years ago

#99 - Unite scripts under `samples` folder and the snippets in `docs/source/examples.rst`

Issue - State: closed - Opened by ohadmo over 4 years ago - 1 comment
Labels: documentation, enhancement

#98 - [Doc] Enforce Sphinx documentation generator

Pull Request - State: closed - Opened by ohadmo over 4 years ago - 3 comments
Labels: documentation

#96 - [vcfio] update data frame output and internal API

Pull Request - State: closed - Opened by tijyojwad over 4 years ago

#95 - stitcher for overlapping sequence predictions

Issue - State: closed - Opened by tijyojwad over 4 years ago
Labels: enhancement, encodings

#94 - [vcfio] INFO column data types are not preserved

Issue - State: closed - Opened by edawson over 4 years ago - 1 comment
Labels: enhancement, I/O

#93 - [vcfio] INFO/FORMAT field parser does not support number="G"

Issue - State: closed - Opened by edawson over 4 years ago
Labels: bug, I/O

#92 - Add haploid label encoder

Issue - State: closed - Opened by rahulmohan over 4 years ago - 2 comments
Labels: enhancement, encodings

#91 - Heuristic panel of normals, annotation and filtering API and CLI tools

Pull Request - State: closed - Opened by edawson over 4 years ago - 1 comment

#90 - [skip-ci][vcfio] update data frame output and internal API structure

Pull Request - State: closed - Opened by tijyojwad over 4 years ago

#89 - Added summary encoder

Pull Request - State: closed - Opened by rahulmohan over 4 years ago - 3 comments

#88 - [visualizer] Add visualization for variant encoded pileup

Pull Request - State: closed - Opened by ohadmo over 4 years ago - 2 comments

#87 - [docs] update example docs

Pull Request - State: closed - Opened by tijyojwad over 4 years ago

#86 - [summary_encoder] add summary encoder class to generate summary statistics encodings

Issue - State: closed - Opened by tijyojwad over 4 years ago
Labels: enhancement, encodings

#85 - [pileup_encoder] encoder layer configurability

Issue - State: open - Opened by tijyojwad over 4 years ago
Labels: enhancement, encodings

#84 - [io] add dataframe output for parsed I/O

Pull Request - State: closed - Opened by tijyojwad over 4 years ago

#83 - [sample_encoding] add multi sample support

Issue - State: open - Opened by tijyojwad over 4 years ago
Labels: enhancement, encodings

#82 - [pileup_encoder] indel encoding for pileups

Pull Request - State: closed - Opened by tijyojwad over 4 years ago

#81 - [pileup_encoder] fix pileup position indexing from bam file

Pull Request - State: closed - Opened by tijyojwad over 4 years ago
Labels: bug

#80 - [sdk] fix pip install

Pull Request - State: closed - Opened by tijyojwad over 4 years ago
Labels: bug

#79 - [io] load vcf entries into data frame

Issue - State: closed - Opened by tijyojwad over 4 years ago - 1 comment
Labels: enhancement, I/O

#78 - [Tests] Refactored mocked input handling

Pull Request - State: closed - Opened by ohadmo over 4 years ago
Labels: enhancement

#77 - [pileup_encoder] add encoding for indels

Issue - State: closed - Opened by tijyojwad over 4 years ago
Labels: enhancement

#73 - [data loader] add tests for data loader implementations

Issue - State: open - Opened by tijyojwad over 4 years ago
Labels: I/O

#57 - [tests] MockPyVCFReader test exposes underlying implementation details

Issue - State: closed - Opened by tijyojwad over 4 years ago
Labels: enhancement

#52 - [vcf_writer] add zygosity probability to INFO column

Issue - State: open - Opened by tijyojwad over 4 years ago
Labels: enhancement, I/O

#25 - [visualizer] add visualization module for encodings

Issue - State: closed - Opened by tijyojwad over 4 years ago - 2 comments
Labels: enhancement

#16 - [label_loader] improve filtering framework

Issue - State: open - Opened by tijyojwad over 4 years ago - 2 comments
Labels: enhancement, I/O