HiPhase v1.0.0

Changes

• Added support for tandem repeat calls from TRGT; minimum supported version - v0.5.0
• VCF index files (.tbi) are now automatically generated by HiPhase
• The reference FASTA file is now a required parameter for HiPhase; this change prevents sub-optimal performance caused by forgetting to specify the reference genome
• HiPhase source code is now released under new LICENSE file

Fixed

• Fixed an infinite looping error caused by variants with the same start POS but no overlapping mappings

HiPhase v0.10.2

Fixed

• Replaced a panic caused by large WFA edit distance with a human-readable error message (Resolves #15)

HiPhase v0.10.1

Fixed

• Corrected a panic caused by reference mismatches to produce a human-readable error message (Resolves #12)
• Fixed an issue parsing unexpected CIGAR strings for local re-alignment and SV deletions
• Added a check for gzip encoding and tabix index for input VCF file to prevent uninterpretable segfault in htslib (Resolves #13)

HiPhase v0.10.0

Changes

• Adds support for multi-threaded BAM I/O via shared thread pools. Internal testing with default parameters showed ~40% reduction in wall-clock time when haplotagging is enabled with 16 threads. User experience will vary based on file type, disk type, and I/O contention. Resolves #9.
• Adds --io-threads option for greater control over the number of threads used in the thread pool. Defaults to the same number provided to --threads.

HiPhase v0.9.0

Changes

• Adds support for CRAM input and output files. Resolves #6.
• The reference file (--reference) is now a required parameter for HiPhase. This prevents users from accidentally forgetting the reference file which leads to drastically different performance.

Fixed

• Corrected an error where bgzipped reference files were not correctly loading

HiPhase v0.8.1

Changes

• Adds --ignore-read-groups flag that will skip the read group checks for provided BAM files. This option can only be used to phase one dataset at a time. Resolves #3.
• Adds --haplotag-file <FILE> option that will create a TSV/CSV file containing read haplotag information. Resolves #4.

Fixed

• Corrected some typos in CLI help menu
• Changes HP tag in output BAM files from an i32 to a u8

HiPhase v0.8.0

Changes

Multi-sample VCF inputs are now supported:

• Users can provide VCFs with multiple samples; all samples being phased must appear in all provided VCF files
• Each sample will be phased independently of the other samples, and results placed in a phased, multi-sample VCF
• Only single sample BAM files are supported, and the sample name must be present in the read group (RG) sample (SM) tag and match the VCF sample identifier
• Haplotagging with multi-sample VCFs is also supported

HiPhase v0.7.3

v0.7.3 - 2023-03-20

Fixed

• Adjust linux release build process to improve portability. This release should be functionally identical to v0.7.2 so no update is needed for users without binary issues.

HiPhase - initial release

Initial release includes:

• Joint phasing of small variants and structural variants
• Support for multi-allelic variation
• Creates longer, correct phase blocks relative to the current best practice
• No downsampling of the data
• Novel algorithms: dual-mode allele assignment and core A* phasing algorithm
• Quality of life additions: innate multi-threading, simultaneous haplotagging and statistics generation