This release includes minor ease-of-use improvements, CNV output should be unchanged. The release version is updated to 1.0 to reflect that HiFiCNV is now operating as a stable part of our HiFi WGS pipeline.
- Add progress reporter to alignment scan
- Accelerate depth bin GC content computation
- Improve and parallelize algorithm to reduce fixed runtime overhead by ~5 min for human genome analysis with typical thread counts.
- Improve error message for failed depth estimation (#25)
- Improve error message for unmapped BAM input (#24)
- Improve error message for mismatched reference and BAM chromosomes (#23)
- Improve error message when BAM index is missing (#22)
- Add new data files to partially support hg19 and hs37d5
- Rename expected copy number example files from male/female to XY/XX
- New FAQ section to explain common errors
- Improved error message for cov-regex mismatch
- Improved error messaging for mismatches between aligned BAM contigs and provided reference file contigs
- Added support for minimap2-aligned BAM files
- Updated quickstart to specify supported upstream tools
- Improved error messaging for cov-regex mismatch
- Adjust linux release build process to improve portability
- Fixes a bug where optional files were being treated as required (HIFICNV-2)
- Segmentation and calling optimized for HiFi germline WGS
- Automatic GC-bias estimation and correction
- Generates bigwig tracks for depth and allele frequency to visualize CNV-scale events in IGV
- CNV output in bedgraph and VCF formats
- Efficient multi-threaded analysis