v0.3.1

Consistency improvements

• New filtering of haplotypes without paths increases accuracy
• New path scoring improves accuracy and consistency
• ZS and SS FORMAT fields replaced by KS reporting the score
• Requiring reads to span the full variant graph window including --chunksize buffer increases accuracy
• Exhaustive search of partial haplotypes
• Slight runtime reduction from avoidance of redundant path searches

Full Changelog: v0.3.0...v0.3.1

v0.3.0

General improvements

• ~8% speed increase from less work in the path-searching
• Partial haplotypes bug fix increases accuracy
• Fixed SQ and FT fields
• Dedicated writing thread helps reduce memory usage by preventing a backlog of completed variants while reading
• Default --out is stdout to allow easier compression/indexing (e.g. kanpig .. | bcftools sort -O z -o out.vcf.gz)
• IUPAC codes are fixed by kanpig according to vcf specifications (Issue #1)
• Fixed filtering of symbolic alts and BNDs
• Argument validation

Full Changelog: v0.2.0...v0.3.0

v0.2.0

• Up to 40% reduction in runtime
• Hemizygous and sex chromosome aware genotyping with new --ploidy-bed
• Variants with alternate alleles of stars, monozygotic reference, and BNDs are filtered out
• Comparing PathScores by their average size and sequence similarity increases accuracy

Full Changelog: v0.1.2...v0.2.0

v0.1.2

• New optional hompolymer filter doesn't kmerize long homopolymers
• Improved logging info
• Correcting GQ field
• Correcting kmer counting
• Small speed/memory/io improvements
  • Off-loaded annotation work from the single writer thread to the worker threads and using a large
    multiple of page size for the BufWriter capacity
  • Fewer bam file opens
  • Fewer clone operations

Full Changelog: v0.1.0...v0.1.2