bacpop/ska.rust issues and pull requests

#83 - Possible run with k gretter than 63

Issue - State: open - Opened by kebern about 1 month ago - 5 comments
Labels: enhancement, not planned

#82 - Better default filtering options for ska distance

Pull Request - State: closed - Opened by johnlees about 2 months ago - 8 comments

#81 - incorrect calling # of SNPs

Issue - State: closed - Opened by PWSmit 2 months ago - 11 comments

#80 - ska delete upgrade

Pull Request - State: closed - Opened by johnlees 3 months ago - 1 comment

#79 - minor suggestions about "ska delete"

Issue - State: closed - Opened by rderelle 3 months ago - 2 comments

#78 - Possible faster bloom filter

Issue - State: open - Opened by johnlees 3 months ago - 1 comment

#77 - to merge ska cov with ska build for automatic min-count threshold [suggestion]

Issue - State: open - Opened by rderelle 4 months ago

#76 - Fix for ska cov with low counts

Pull Request - State: closed - Opened by johnlees 4 months ago

#75 - Simplified proportion reads computation

Pull Request - State: closed - Opened by apollis44 6 months ago - 1 comment

#74 - Adding max frequence reads parameter

Pull Request - State: closed - Opened by apollis44 7 months ago - 1 comment

#73 - Adding max reads parameter

Pull Request - State: closed - Opened by apollis44 7 months ago - 1 comment

#72 - Testing on a subsample of reads

Pull Request - State: closed - Opened by apollis44 7 months ago - 1 comment

#71 - Add files via upload

Pull Request - State: closed - Opened by apollis44 7 months ago

#70 - Consistent method for dealing with ref bias in ska map

Pull Request - State: closed - Opened by johnlees 8 months ago - 1 comment

#69 - different results from ska2 0.3.2 and 0.3.6

Issue - State: closed - Opened by danrlu 9 months ago - 3 comments

#68 - How do I cite this package?

Issue - State: closed - Opened by danrlu 9 months ago - 4 comments

#67 - nanopore data

Issue - State: closed - Opened by PWSmit 9 months ago - 3 comments

#66 - Fix double file prefix; update VCF parsing

Pull Request - State: closed - Opened by johnlees 9 months ago - 1 comment

#65 - Suggestion: ska map to only report positions of variable split-kmers

Issue - State: closed - Opened by rderelle 9 months ago - 7 comments
Labels: enhancement

#64 - Suggestion: consistent output suffixes in ska weed

Issue - State: closed - Opened by rderelle 11 months ago - 1 comment
Labels: enhancement

#63 - Filter tweaks

Pull Request - State: closed - Opened by johnlees 12 months ago - 1 comment

#63 - Filter tweaks

Pull Request - State: open - Opened by johnlees 12 months ago - 1 comment

#62 - Defaults and filtering tweaks

Issue - State: closed - Opened by johnlees about 1 year ago
Labels: enhancement

#61 - 0.3.4 candidate -- final feature requests

Pull Request - State: closed - Opened by johnlees about 1 year ago - 1 comment

#60 - Fix for multi-contig references in map

Pull Request - State: closed - Opened by johnlees about 1 year ago - 1 comment

#59 - `ska map` fails with some fragmented reference sequences

Issue - State: closed - Opened by tmaklin about 1 year ago - 3 comments

#58 - Fix for ska delete

Pull Request - State: closed - Opened by johnlees about 1 year ago - 1 comment

#57 - ska merge and delete not working

Issue - State: closed - Opened by rderelle about 1 year ago - 6 comments

#56 - strange behaviour for min-count (ska build)

Issue - State: closed - Opened by rderelle about 1 year ago - 9 comments

#55 - Add optional output filename option `-o` to `ska weed`.

Pull Request - State: closed - Opened by tmaklin about 1 year ago - 3 comments

#54 - request: Iterator trait for MergeSkaArray

Issue - State: closed - Opened by rderelle about 1 year ago - 1 comment
Labels: enhancement

#53 - Change middle base default filter to strict

Issue - State: closed - Opened by johnlees about 1 year ago

#52 - Possible changes to fastq input

Issue - State: open - Opened by johnlees over 1 year ago - 8 comments
Labels: enhancement

#51 - Feature request: filter out missing bases in ska align

Issue - State: closed - Opened by rderelle over 1 year ago - 3 comments
Labels: enhancement

#50 - Feature requests: different mixture model; combined ska build & cov

Issue - State: open - Opened by rderelle over 1 year ago - 2 comments
Labels: enhancement

#49 - Fix for multicopy palindromes

Pull Request - State: closed - Opened by johnlees over 1 year ago - 1 comment

#48 - 'Palindrome middle base not W/S: 78' in ska build

Issue - State: closed - Opened by jvfe over 1 year ago - 6 comments
Labels: bug

#47 - Alternatives for .skf format

Issue - State: open - Opened by johnlees over 1 year ago - 4 comments
Labels: enhancement

#46 - Restore filter accuracy for fastq input

Pull Request - State: closed - Opened by johnlees over 1 year ago

#45 - Degraded performance of k-mer filter from FASTQ files

Issue - State: closed - Opened by johnlees over 1 year ago - 14 comments
Labels: bug, enhancement

#44 - Enchanced filtering options

Pull Request - State: closed - Opened by johnlees over 1 year ago - 1 comment

#43 - Documentation improvements

Issue - State: closed - Opened by johnlees over 1 year ago
Labels: documentation

#42 - Add filter to ska map, and ambiguous filter to ska weed

Issue - State: closed - Opened by johnlees over 1 year ago - 1 comment
Labels: enhancement

#41 - Non-nucleotide bases produced within ska map alignment

Issue - State: closed - Opened by jdaeth274 over 1 year ago - 6 comments

#40 - Add k-mer counts per sample to ska nk; efficiency of dup counting

Pull Request - State: closed - Opened by johnlees over 1 year ago - 1 comment

#39 - Add kmer count per sample to ska nk output

Issue - State: closed - Opened by danrlu over 1 year ago - 7 comments
Labels: enhancement

#38 - The distance result is very different from the old version

Issue - State: closed - Opened by danrlu over 1 year ago - 7 comments

#37 - Mask repeats with Ns during ska map

Pull Request - State: closed - Opened by johnlees over 1 year ago - 1 comment

#36 - Add NJ trees to clustering script

Pull Request - State: closed - Opened by johnlees over 1 year ago - 1 comment

#35 - Add ska distance, and clustering script

Pull Request - State: closed - Opened by johnlees over 1 year ago - 1 comment

#34 - Add mode to automatically determine a count cutoff

Pull Request - State: closed - Opened by johnlees over 1 year ago - 1 comment

#33 - Fix filtering option name in documentation.

Pull Request - State: closed - Opened by tmaklin over 1 year ago - 1 comment

#32 - Add option for repeat mapping

Issue - State: closed - Opened by johnlees over 1 year ago
Labels: enhancement

#31 - Fix ambiguous bases in pseudoalignment

Pull Request - State: closed - Opened by johnlees over 1 year ago - 1 comment

#30 - Deal with palindromes

Pull Request - State: closed - Opened by johnlees over 1 year ago - 1 comment

#29 - Add automatic coverage determination

Issue - State: closed - Opened by johnlees over 1 year ago
Labels: enhancement

#28 - Reference bias in map with repeats

Issue - State: closed - Opened by johnlees over 1 year ago
Labels: bug

#27 - Consider palindromic self-rc k-mers

Issue - State: closed - Opened by johnlees over 1 year ago
Labels: bug

#26 - Add ska distance

Issue - State: closed - Opened by johnlees over 1 year ago - 2 comments
Labels: enhancement

#25 - add back ska distance and ska annotate?

Issue - State: closed - Opened by cammo0p over 1 year ago - 5 comments

#24 - Add 'reverse' weed to keep only selected split k-mers

Pull Request - State: closed - Opened by johnlees over 1 year ago - 1 comment

#23 - Do you have an estimated RAM usage per sample?

Issue - State: closed - Opened by danrlu over 1 year ago - 3 comments

#22 - Partial loading of skf

Issue - State: closed - Opened by johnlees over 1 year ago - 2 comments
Labels: enhancement, not planned

#21 - Move test dependencies to test only

Pull Request - State: closed - Opened by johnlees over 1 year ago - 1 comment

#20 - Faster filter for reads

Pull Request - State: closed - Opened by johnlees over 1 year ago - 1 comment

#19 - Memory optimisation: don't store whole build array

Pull Request - State: closed - Opened by johnlees over 1 year ago - 2 comments

#18 - Add tutorial with use cases

Issue - State: closed - Opened by johnlees almost 2 years ago - 1 comment
Labels: documentation

#17 - Alternatives for .skf format

Issue - State: closed - Opened by johnlees almost 2 years ago - 6 comments
Labels: enhancement

#16 - Add more types of quality score filtering

Pull Request - State: closed - Opened by johnlees almost 2 years ago - 1 comment

#15 - README update

Pull Request - State: closed - Opened by johnlees almost 2 years ago - 1 comment

#14 - Replace hashes with nthash

Pull Request - State: closed - Opened by johnlees almost 2 years ago

#13 - Add support for up to k=63 using u128

Pull Request - State: closed - Opened by johnlees almost 2 years ago - 2 comments

#12 - Actually need to remove second version check on tag push

Pull Request - State: closed - Opened by johnlees almost 2 years ago

#11 - Add a test of version number increase to gha

Pull Request - State: closed - Opened by johnlees almost 2 years ago

#10 - Add middle base to read count filtering

Pull Request - State: closed - Opened by johnlees almost 2 years ago - 1 comment

#9 - Add more alignment filtering options

Pull Request - State: closed - Opened by johnlees almost 2 years ago - 1 comment

#8 - Add logo to readme

Pull Request - State: closed - Opened by johnlees almost 2 years ago - 1 comment

#7 - Add logo

Pull Request - State: closed - Opened by johnlees almost 2 years ago

#6 - Try adding codecov

Pull Request - State: closed - Opened by johnlees almost 2 years ago - 1 comment

#5 - Add ambiguous genotypes in VCF output

Issue - State: open - Opened by johnlees almost 2 years ago - 1 comment
Labels: enhancement, not planned

#4 - Support k up to 63

Issue - State: closed - Opened by johnlees almost 2 years ago - 1 comment
Labels: enhancement

#3 - Add actions to automate release

Pull Request - State: closed - Opened by johnlees almost 2 years ago

#2 - Redo the alignment writer for ska map

Pull Request - State: closed - Opened by johnlees almost 2 years ago

#1 - Try clippy gha

Pull Request - State: closed - Opened by johnlees almost 2 years ago

GitHub / bacpop/ska.rust issues and pull requests