- Increase system open file limit (github #9)
- May simplify joint-call for large pedigrees at high thread counts
- Improve error message when split reads map to an unknown chromosome (github #8)
- Fix "Illegal Instruction" error reported for some use cases (github #3)
- Removed gcc native cpu optimization in WFA2-lib believed to be causing this issue
- Added additional
--debugoutput to discover mode contig alignment logic
- Fix discover mode input path canonicalization (reversed flag logic)
- Add new joint-call
--report-supporting-readsoption to report read names supporting each variant
- CR-390 Canonicalize all discover mode input paths
- Also provide new
--disable-path-canonicalizationdiscover step option to store input paths as-is
- Also provide new
- CR-391 Don't create output directory until command line is validated
- CR-384 Add debug logging option
- High detail level intended to improve crash reports from external users
- Initially populated for breakpoint refinement only, debug log coverage will be expanded as required
- Expose clobber option to overwrite existing output directory
- CR-385 Improve error message for unexpected alignment patterns from VACmap
- This also adjusts some off-by-one errors in neighbor extension handling, which could cause infrequent changes to inversion output
- Note VACmap is still unsupported; working towards clear error messages for problematic alignments from any source
- CR-378 Improve error message for hard-clipped split read input
- CR-379 Improve error message when discover directory is missing
- CR-377 Remove
rqtag requirement in input alignment records
- CR-375 Fix infrequent discover mode failures due to invalid breakpoint ranges.
- Issue seems to have started with v0.12.0 via CR-340
- CR-327 Add local SV phasing
- Short-range phasing provided in VCF records wherever multiple hets are genotyped on one or more overlapping SV haplotypes
- CR-340 Improve handling of multi-breakpoint haplotypes
- Improves detection of complex SV breakpoints, especially for small inversions
- CR-333 Adjust alignment for long breakpoint homology
- Improves detection of high homology inversions
- CR-330 Expand trimmed read search region for small SV regions
- Improves detection of soft-clipped evidence for low homology insertions
Improve a number of discovery and scoring features related to inversions, inverted breakpoints and large deletions.
- CR-323 Improve scoring for a number of cases relevant to inversions and inverted breakpoints
- CR-321 Change contig flank size handling to improve large inversion calling
- CR-318 Expand trimmed read search region for large SV candidates
- Improves recall for inverted breakpoints and duplications
- CR-317 Standardize on csi indexing for bam output
- CR-324 Fix non-deterministic inversion output
Initial github release