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.

v0.1.101

Kvg call (#48)

• Call's output is now a phased gVCF

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 [email protected]
Co-authored-by: bshifaw [email protected]

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 current_interval directly into new_tree only if there are no overlaps. If there are overlaps, it calculates min_start and max_end to create a merged_interval. If two or more intervals overlap, the code will keep overwriting new_tree 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

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Co-authored-by: Kiran Garimella [email protected]
Co-authored-by: bshifaw [email protected]

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

v0.1.97

Kvg fix docker deps (#44)

• Fix Docker dependencies

• Perform phasing in parallel chunks

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

v0.1.95

Kvg clean read bubbles (#42)

• Correct reads by popping bubbles induced against the cleaned graph

• Only replace poor-scoring read paths

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

v0.1.93

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