longcallD-v0.0.11

• Bugs fixes:
  • memory allocation(#21)
  • loop index not used in scanning qualities (#23)
• Speed improvement (#26)
• Add VAF (variant allele frequency) to output VCF (FORMAT field) (#22)

longcallD-v0.0.10

• Add --out-sv-rnames and --out-som-sv-rnames to output SV-supporing read names (tag: SVREADS) in FORMAT field of VCF
• Add CLEAN INFO tag for variants in clean regions, i.e., SNPs or simple small indels (≤5bp) in non-repetitive regions which are generally more reliable, to help with downstream filtering and benchmarking

longcallD-v0.0.9

• Fix variant calling close to start/end boundaries of chromosomes
• Add --out-sv-rnames and --out-som-sv-rnames to output SV-supporing read names (tag: SVREADS) in FORMAT field of VCF
• Add CLEAN INFO tag for variants in clean regions, i.e., SNPs or simple small indels (≤5bp) in non-repetitive regions which are generally more reliable, to help with downstream filtering and benchmarking

longcallD-v0.0.8

• Fix variant representation issues for overlapping variants
• Revoke ultraLowMem mode of WFA to avoid potential variant representation issues
• Fix output BAM errors
• Output BAM includes all reads (even those not used for variant calling)
• Fix a bug with --refine-aln

longcallD-v0.0.7

• sort reads internally before processing to fix potential inconsistency when multiple input BAM/CRAM files are provided

longcallD-v0.0.6

• Fix corrupted VCF output in v0.0.5
• Fix missing MEI header in VCF output
• Improved run time and memory usage (especially when mosaic variant calling enabled)
• Add --input-is-list and -X to support multiple input BAM/CRAM files of the same sample for variant calling

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