Releases | Open Source Science

https://github.com/broadinstitute/hidive - v0.1.122

Kvg locityper tweaks (#70)

Tweak memory and disk space for tasks
Allow Rescue to retry
Disk space allocation proportional to number of loci to evaluate

- Rust
Published by github-actions[bot] about 1 year ago

https://github.com/broadinstitute/hidive - v0.1.121

Kvg locityper csv (#69)

Add locityper scripts to Docker image
Summarize results
Fix disk space error
Fixed typo
Fix typos
Shore up some final failing jobs

- Rust
Published by github-actions[bot] about 1 year ago

https://github.com/broadinstitute/hidive - v0.1.120

Kvg dedup (#68)

Remove duplicate reads before Locityper step
Try two test loci
Try with a different locus
Parallelize over genotyping step
Allow user to control how many sites to genotype at once
Allow for full and filtered bed files

- Rust
Published by github-actions[bot] about 1 year ago

https://github.com/broadinstitute/hidive - v0.1.119

Kvg genotype vcf (#67)

Start processing from VCF
Make sure we don't emit a read pair twice

- Rust
Published by github-actions[bot] about 1 year ago

https://github.com/broadinstitute/hidive - v0.1.118

Kvg interlaced (#66)

Paired-end reads are interleaved
Only emit paired-end reads
Update docker
Fixes to rescue
Fixes

- Rust
Published by github-actions[bot] about 1 year ago

https://github.com/broadinstitute/hidive - v0.1.117

Kvg interlaced (#65)

Paired-end reads are interleaved
Only emit paired-end reads
Update docker

- Rust
Published by github-actions[bot] about 1 year ago

https://github.com/broadinstitute/hidive - v0.1.116

Kvg more locityper (#64)

Fetch background region
Uncompress and index reference

- Rust
Published by github-actions[bot] about 1 year ago

https://github.com/broadinstitute/hidive - v0.1.115

Kvg locityper (#63)

Combine hidive rescue and locityper

- Rust
Published by github-actions[bot] about 1 year ago

https://github.com/broadinstitute/hidive - v0.1.114

Kvg update fastq wdl (#62)

Update workflow to output fq.gz files
Rev docker image references to 0.1.113

- Rust
Published by github-actions[bot] about 1 year ago

https://github.com/broadinstitute/hidive - v0.1.113

Kvg sccache (#61)

Fix build failure by upgrading to sccache-action to v0.0.9

- Rust
Published by github-actions[bot] about 1 year ago

https://github.com/broadinstitute/hidive - v0.1.109

Support multiple CYP2D6 copies, genotype each separately (#56)

Support multiple CYP2D6 copies, genotype each separately
Stricter validation of PharmVar dir
Decrease default min alignment score

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.108

Kvg call star alleles (#55)

Perform CYP2D6 typing on assemblies
Added workflow to train error correction models at varying kmer sizes
Summarize hidive results on repeat expansions

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.107

Kvg truth asms (#54)

Subset and align the truth data for easy comparison
Merge bams for easier visualization
Add read groups to alignments
Align phased reads to subsetted reference

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.106

Add star allele calculation scripts (#53)

Add star allele calculation scripts
Add reference star allele seqs from PharmVar 6.2
Fix for second-best match column
Full list of redundant star alleles

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.105

Kvg dep fix (#52)

Added missing pysam dependency to Docker image
Fixed github action runner for cd pipeline
Updated kmer clustering plot to filter out certain contigs
Fixed a bug with overlap window minimum lengths
Fixed Docker image tag for Cluster command
Fixed an edge case in plotting script. Added sample name to cluster contig names.
Retry read error correction a couple times in case of transient errors
Fixed issue where sometimes the proper position for a kmer in a read path is not found

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.104

Fix issue with font config for Rust binary build

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.102

Kvg sample and cohort wdls (#49)

Renamed WDLs
Fixed issue wherein back-to-back insertions and deletions in CIGAR strings were not handled properly.

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.101

Kvg call (#48)

Call's output is now a phased gVCF

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.100

Kvg update wdl 0.1.98 (#47)

Update WDL to latest Docker image
added fetches option to rescue.rs, option search all, contig, contig-and-interval, unmapped

Co-authored-by: Kiran Garimella kiran@broadinstitute.org Co-authored-by: bshifaw bshifaw@broadinstitute.com

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.99

Bs kvg improve model (#41)

Auto-detect where to search in a genome to rescue reads
Accumulate the merged intervals continuously rather than overwriting the tree each time. The final merging pass iterates over loci and tries to merge overlapping intervals within each contig. However, the code inserts currentinterval directly into newtree only if there are no overlaps. If there are overlaps, it calculates minstart and maxend to create a mergedinterval. If two or more intervals overlap, the code will keep overwriting newtree in each iteration, potentially losing previously calculated merged intervals from earlier iterations.
added fetches option to rescue.rs, option search all, contig, contig-and-interval, unmapped

Co-authored-by: Kiran Garimella kiran@broadinstitute.org Co-authored-by: bshifaw bshifaw@broadinstitute.com

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.98

Kvg improve wdl (#46)

Simplified WDL
Added reference sequence to disk space calculation
Change correct task's cpus from 4 to 8
Increase maxRetries for Rescue

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.97

Kvg fix docker deps (#44)

Fix Docker dependencies
Perform phasing in parallel chunks

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.96

Kvg phase (#43)

Remove dust and repetitive noise kmers from cleaning graph
Correct reads using a sliding window approach
New command (call) to emit two fully phased haplotypes

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.95

Kvg clean read bubbles (#42)

Correct reads by popping bubbles induced against the cleaned graph
Only replace poor-scoring read paths

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.94

Kvg improve coassemble (#40)

Fixed an issue where unmapped reads don't have a tid, thus can't be directly unwrapped
Discard reads that have any non-A/C/G/T bases.
Improve alignment trimming for proper variant characterization
Small improvements to superbubble cleaning
Improvements to training, simplification

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.93

Reverted rescue.rs to version that doesn't attempt to guess locations of relevant reads

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.92

Fix minor lint warnings and improve code quality (#25)

optimize imports and remove unused imports
unused variables commented out or underscore applied
comment unused functions
snake based name for anchorseq
clippy: add #[must_use] to functions
Fix: Disambiguate to_owned method call in graph.insert to resolve multiple applicable items error
Fix: Correct function signatures to resolve Clippy lints errors
Fix: Change argument to be passed by reference instead of by value
Fix: error: boolean to int conversion using if. for indegree and outdegreee functions
Fix: inefficienttostring. error: calling to_string on &&std::string::String
Fix: castpossibletruncation. error: casting usize to u8 may truncate the value
Fix: castpossibletruncation. Example error: casting usize to u8 may truncate the value
added function doc for function which may panic (cargo lint)
Fix items in documentation is missing backticks (cargo lint)
Fix "method/function could have a #[must_use] attribute" (cargo lint)
Fix "Variables can be used directly in the format" (cargo lint)
Fix "error: needless use of for_each" (cargo lint)
Fix "avoid wildcard imports" (cargo lint)
Fix "avoid implicitly cloning" (cargo lint)
Fix "docs for function returning Result missing # Errors section" (cargo lint)
Fix "test function passing of variable type" (cargo lint)
Fix:removed enumerate where needed, unused imports, unused variables (cargo lint)

Co-authored-by: bshifaw bshifaw@broadinstitute.com

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.91

Kvg dep cache (#39)

Cache Rust dependencies

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.90

Kvg dep cache (#38)

Cache Rust dependencies for faster builds

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.89

Align 150-bp windows from long read panel to reference to guess where to look for short reads (#37)

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.88

Add eval-model command and refactor train command (#36)

Added rock curves to train.rs, added eval_model.rs
fixing merger discrepancies, made function to create ml dataset, updated train.sh
have the eval_model.rs use the function to create datasets in the train.rs file

Co-authored-by: bshifaw bshifaw@broadinstitute.com

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.87

Save the GFA file too

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.86

Fixed typo

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/broadinstitute/hidive - v0.1.85

Restore ci_push workflow

- Rust
Published by github-actions[bot] over 1 year ago