longcallD-v0.0.5

• Add -s/--somatic/--mosaic to output low AF somatic/mosaic variant
• Add -T/--trans-elem; output TE (transposable/mobile element, Alu/L1/SVA) information for INS/DEL
• Add INFO:TSD;REPNAME in VCF for TE INS/DEL
• Add --refine-aln: refine read alignment based on MSA in output SAM/BAM/CRAM
• Fix a SegFault in ONT mode regarding BAM/SA tag
• Add -Oz for compressed VCF output
• Add --exclude-ctg & --all-ctg; --autosome-XY is default now
• Fix lower case ref base
• Fix compiling in macOS-x64

longcallD-v0.0.4

• Use static regions for multi-thread computing
• Extended phase set
• Fixed HP/PS tags in output phased bam
• Fixed a few edge cases
• Update(05/07/2025): re-compiled binary executables, -O3 added for WFA

longcallD-v0.0.3

• Fix a couple of corner cases

longcallD-v0.0.2

• Add -M/--min-mapq
• Fix check_eqx_cigar

longcallD-v0.0.1

First release of longcallD, a variant caller designed for detecting small variants and structural variants using long-read data.
It supports both PacBio HiFi and Oxford Nanopore reads.