Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / eaasna/valik issues and pull requests
#137 - Gapped k-mers
Pull Request -
State: open - Opened by eaasna about 1 month ago
#136 - Decrease constants in thresholding and set threshold manually
Pull Request -
State: closed - Opened by eaasna about 1 month ago
- 1 comment
#135 - Always distribute metagenome search
Pull Request -
State: closed - Opened by eaasna 2 months ago
- 1 comment
#134 - Limit Stellar q-gram size to avoid memory error
Pull Request -
State: closed - Opened by eaasna 2 months ago
- 1 comment
#133 - Bump CI compiler versions
Pull Request -
State: open - Opened by eaasna 2 months ago
- 1 comment
#132 - Flag for Stellar only search
Pull Request -
State: closed - Opened by eaasna 3 months ago
- 1 comment
#131 - Redo "Increase max bound for search arguments (#126)"
Pull Request -
State: closed - Opened by eaasna 3 months ago
- 1 comment
#130 - Redo split parameter bounds
Pull Request -
State: closed - Opened by eaasna 3 months ago
- 1 comment
#129 - Revert "Increase max bound for search arguments (#126)"
Pull Request -
State: closed - Opened by eaasna 3 months ago
- 1 comment
#128 - Revert long
Pull Request -
State: closed - Opened by eaasna 3 months ago
- 1 comment
#127 - Refactor split parameter tuning
Pull Request -
State: closed - Opened by eaasna 3 months ago
- 1 comment
#126 - BoEIncrease max bound for search arguments
Pull Request -
State: closed - Opened by eaasna 3 months ago
- 1 comment
#125 - Consolidate unorderd containers
Pull Request -
State: closed - Opened by eaasna 4 months ago
- 1 comment
#124 - Generic alignment file I/O
Pull Request -
State: closed - Opened by eaasna 4 months ago
- 1 comment
#123 - [Fix] Inclusive comparison of k-mer occurrence counts
Pull Request -
State: closed - Opened by eaasna 4 months ago
- 1 comment
#122 - Dismiss low entropy patterns
Pull Request -
State: closed - Opened by eaasna 4 months ago
#121 - Repeat filtering: search in bins with highest entropy
Pull Request -
State: closed - Opened by eaasna 4 months ago
- 1 comment
#120 - Count segment minimisers in parallel
Pull Request -
State: closed - Opened by eaasna 4 months ago
- 1 comment
#119 - Fixup consolidate
Pull Request -
State: closed - Opened by eaasna 4 months ago
- 1 comment
#118 - Distributed search
Issue -
State: open - Opened by eaasna 4 months ago
Labels: enhancement
#117 - Cleanup output
Pull Request -
State: closed - Opened by eaasna 5 months ago
- 1 comment
#116 - Try to count segment minimisers in parallel
Pull Request -
State: closed - Opened by eaasna 5 months ago
- 1 comment
#115 - Update E-value calculations based on BLAST 2.16
Pull Request -
State: closed - Opened by eaasna 5 months ago
- 1 comment
#114 - Remove raptor data simulaiton submodule
Pull Request -
State: closed - Opened by eaasna 5 months ago
- 1 comment
#113 - Print warning for verbose output
Pull Request -
State: closed - Opened by eaasna 5 months ago
- 1 comment
#112 - Trim ID after first whitespace
Pull Request -
State: closed - Opened by eaasna 5 months ago
- 1 comment
#111 - Debug bucket borders
Pull Request -
State: closed - Opened by eaasna 5 months ago
#110 - Suggestions from code review
Pull Request -
State: closed - Opened by eaasna 5 months ago
- 1 comment
#109 - Remove duplicate alphabets and replace seqan2::String
Pull Request -
State: open - Opened by eaasna 8 months ago
- 1 comment
#108 - Runtime log
Pull Request -
State: closed - Opened by eaasna 8 months ago
#107 - Fix detailed runtime log
Pull Request -
State: closed - Opened by eaasna 9 months ago
- 1 comment
#106 - Precompute minimisers for k-mer count filtering
Pull Request -
State: closed - Opened by eaasna 9 months ago
- 1 comment
#105 - Always preprocess reference sequences for reference size dependant parameter deduction
Pull Request -
State: closed - Opened by eaasna about 1 year ago
- 1 comment
#104 - Find FNR for heuristic threshold
Pull Request -
State: closed - Opened by eaasna about 1 year ago
- 1 comment
#103 - Debug kmers
Pull Request -
State: closed - Opened by eaasna about 1 year ago
#102 - Do not write empty Stellar files
Issue -
State: open - Opened by eaasna about 1 year ago
Labels: enhancement
#101 - Refactor the argument parser
Pull Request -
State: closed - Opened by eaasna over 1 year ago
- 1 comment
#100 - [FIX] Remove whitespace from FASTA id
Pull Request -
State: closed - Opened by eaasna over 1 year ago
#99 - [INFRA] Update license
Pull Request -
State: closed - Opened by eaasna over 1 year ago
- 1 comment
#98 - Do not allow shared memory metagenome search
Pull Request -
State: closed - Opened by eaasna over 1 year ago
- 1 comment
#97 - Search vs consolidation time
Pull Request -
State: closed - Opened by eaasna over 1 year ago
- 1 comment
#96 - Join metadata tables into a single file
Pull Request -
State: closed - Opened by eaasna over 1 year ago
- 1 comment
#95 - Incorporate match consolidation into search
Pull Request -
State: closed - Opened by eaasna over 1 year ago
- 1 comment
#94 - Error rate instead of number of errors
Pull Request -
State: closed - Opened by eaasna over 1 year ago
#93 - Split query database
Pull Request -
State: closed - Opened by eaasna over 1 year ago
- 1 comment
#92 - Shared memory mode: pass queries in memory
Pull Request -
State: closed - Opened by eaasna over 1 year ago
- 1 comment
#91 - [FIX] Stellar DNA4 alphabet
Pull Request -
State: closed - Opened by eaasna over 1 year ago
- 1 comment
#90 - Call Stellar search functions
Pull Request -
State: closed - Opened by eaasna over 1 year ago
- 1 comment
#89 - fix: processing local data, locally inside of valik_search
Pull Request -
State: closed - Opened by SGSSGene almost 2 years ago
#88 - [FIX] clean up stellar3 arguments and valik argument parsing
Pull Request -
State: closed - Opened by eaasna almost 2 years ago
- 1 comment
#87 - [FIX] clean up stellar3 arguments and valik argument parsing
Pull Request -
State: closed - Opened by eaasna almost 2 years ago
- 1 comment
#86 - Merge or split long sequences into technical bins
Pull Request -
State: closed - Opened by eaasna almost 2 years ago
- 1 comment
#85 - Read reference metadata
Pull Request -
State: closed - Opened by eaasna almost 2 years ago
#84 - fix: return status in external_process is now parsed correctly
Pull Request -
State: closed - Opened by SGSSGene almost 2 years ago
#83 - fix: allow bin size 1
Pull Request -
State: closed - Opened by SGSSGene almost 2 years ago
#82 - [INFRA] measure external process time
Pull Request -
State: closed - Opened by eaasna almost 2 years ago
#81 - fix: updating badges url format and changing them to 'main'
Pull Request -
State: closed - Opened by SGSSGene almost 2 years ago
#80 - fix: ci workflows refere to main instead of master
Pull Request -
State: closed - Opened by SGSSGene almost 2 years ago
#79 - doc: adjusting the README to new parameters
Pull Request -
State: closed - Opened by SGSSGene almost 2 years ago
- 1 comment
#78 - fix: return error code on failed search
Pull Request -
State: closed - Opened by SGSSGene almost 2 years ago
- 2 comments
#77 - [INFRA] measure DREAM-Stellar search time
Pull Request -
State: closed - Opened by eaasna almost 2 years ago
#76 - [FEAT] Call parallel instances of Stellar search
Pull Request -
State: closed - Opened by eaasna almost 2 years ago
#75 - [FEAT] Create thread to call stellar as an external process
Pull Request -
State: closed - Opened by eaasna almost 2 years ago
- 1 comment
#74 - [FEAT] Write temporary bin-query FASTA files
Pull Request -
State: closed - Opened by eaasna about 2 years ago
- 1 comment
#73 - Feat/using shopping carts
Pull Request -
State: closed - Opened by SGSSGene about 2 years ago
- 1 comment
#72 - feat: adding cart_queue and external_process classes
Pull Request -
State: closed - Opened by SGSSGene about 2 years ago
#71 - Usecase c
Pull Request -
State: closed - Opened by eaasna about 2 years ago
#70 - Consolidate matches after distributed Stellar search
Pull Request -
State: closed - Opened by eaasna about 2 years ago
- 1 comment
#69 - Access sequence of interest and segment parameters for Stellar input
Pull Request -
State: closed - Opened by eaasna about 2 years ago
- 1 comment
#68 - Update lib/seqan3
Pull Request -
State: closed - Opened by eaasna about 2 years ago
#67 - Search output as unordered set of bin numbers
Pull Request -
State: closed - Opened by eaasna about 2 years ago
#66 - [FIX] divide *all* queries over threads
Pull Request -
State: closed - Opened by eaasna about 2 years ago
- 1 comment
#65 - [DOC]: Add doxygen documentation?
Issue -
State: closed - Opened by eaasna about 2 years ago
Labels: enhancement
#64 - CI tests using g++10-12
Pull Request -
State: closed - Opened by eaasna about 2 years ago
- 1 comment
#63 - Fix: write_output_file_parallel writes now to the file in parallel
Pull Request -
State: closed - Opened by SGSSGene about 2 years ago
- 1 comment
#62 - [FEAT] Write out segment sequences
Pull Request -
State: closed - Opened by eaasna about 2 years ago
- 1 comment
#61 - Insert instead of write out
Issue -
State: closed - Opened by eaasna about 2 years ago
#60 - Write out bin-query files for Stellar input
Pull Request -
State: closed - Opened by eaasna almost 3 years ago
#59 - Splitting into odd number of segments
Issue -
State: closed - Opened by eaasna almost 3 years ago
Labels: bug
#58 - Find binning vector for first minimiser
Pull Request -
State: closed - Opened by eaasna almost 3 years ago
- 1 comment
#57 - Generate ground truth to search a single split sequence
Pull Request -
State: closed - Opened by eaasna almost 3 years ago
- 2 comments
#56 - Remove default length from segment output
Pull Request -
State: closed - Opened by eaasna almost 3 years ago
- 1 comment
#55 - Parameter values make assertion fail
Pull Request -
State: closed - Opened by eaasna almost 3 years ago
#54 - Generate data for CLI tests
Pull Request -
State: closed - Opened by eaasna almost 3 years ago
- 1 comment
#53 - Reproducible test data
Pull Request -
State: closed - Opened by eaasna almost 3 years ago
- 1 comment
#52 - Pattern hits as bitvector
Pull Request -
State: closed - Opened by eaasna almost 3 years ago
#51 - Use threshold computation from Raptor library
Pull Request -
State: closed - Opened by eaasna almost 3 years ago
- 1 comment
#50 - Move relevant functions to `local_prefilter.hpp`
Pull Request -
State: closed - Opened by eaasna almost 3 years ago
- 1 comment
#49 - Valik index
Pull Request -
State: closed - Opened by eaasna almost 3 years ago
#48 - Use threshold computation from Raptor library
Issue -
State: closed - Opened by eaasna about 3 years ago
Labels: enhancement
#47 - Pattern hits as bitvector
Issue -
State: open - Opened by eaasna about 3 years ago
Labels: enhancement
#46 - Sliding pattern forward by one base
Issue -
State: open - Opened by eaasna about 3 years ago
Labels: enhancement
#45 - Create `valik_index` data structure
Issue -
State: closed - Opened by eaasna about 3 years ago
Labels: enhancement
#44 - Create segments from number of bins parameter
Pull Request -
State: closed - Opened by eaasna about 3 years ago
#43 - No binning bitvector for first minimiser of query `counting_table[0]`
Issue -
State: closed - Opened by eaasna about 3 years ago
Labels: bug
#42 - destroyed_indirectly_by_error crashes for me
Issue -
State: closed - Opened by marehr about 3 years ago
- 1 comment
Labels: bug
#41 - API tests for `make_pattern_bounds`
Pull Request -
State: closed - Opened by eaasna about 3 years ago
#40 - Better name for project
Pull Request -
State: closed - Opened by eaasna about 3 years ago
#39 - Better name for project
Pull Request -
State: closed - Opened by eaasna about 3 years ago
- 3 comments
#38 - local_prefilter::make_pattern_bounds produces invalid values for some special values.
Issue -
State: closed - Opened by marehr about 3 years ago
- 1 comment
Labels: bug