v1.0.8

1. Fixed an issue in VCF output that caused occasional quality score small differences compared to GVCF output.
2. Updated LongPhase to version 1.7.

v1.0.7

1. Added memory guards and test functions to the full-alignment calling C implementation (#286 by @Chris Wright).
2. Increased the maximum mpileup read coverage to 2^20 to accomodate excessively high-coverage amplicon data (#292 by @Devon Ryan).
3. Updated LongPhase to version 1.6.

v1.0.6

1. Fixed stack overflow issue when the read coverage is excessively high (#282 by @Chris Wright, #265 by @ymcki).
2. Added reference caching for CRAM input (#278 by @Alex Leonard, #180 by @bartcharbon and @SamStudio8).
3. Fixed a bug that outputs RefCall calls when no variant is called by full-alignment model (#271).
4. Fixed a bug that variants below min coverage were still being called (#262).
5. Set --min_snp_af and --min_indel_af to 0.0 when --vcf_fn is provided (#261).

v1.0.5

1. Fixed the issue showing wrong multi-allelic AF when read coverage is excessively high (#241).
2. Added --base_err and --gq_bin_size options that can resolve the problem of having excessive GT ./. in GVCF output (#220).
3. Modified logs (#231, #225)

v1.0.4

1. Added showing command line and reference source in output VCF header.
2. Fixed a bug in showing the AF tag for 1/2 genotypes.
3. Added AD tag output.

v1.0.3

Fixed a bug when the contig name contains colons (#203)

v1.0.2

1. Added PacBio HiFi Revio model, check Pre-trained model for model usage.
2. Fixed a bug that halts the pipeline when there exists too few variant candidates (#198).

v1.0.1

1. Bumped up "WhatsHap" version to 1.7, the whatshap haplotag step is ~15% faster. (#193).
2. Fixed PL tag output error when ALT is N (#191, contributor @Dennis Hendriksen).

v1.0.0

1. Added Clair3 version number to the VCF header (#141).
2. Fixed the numpy.int issue when using newer numpy version (#165, PR contributor @Aaron Tyler).
3. The new version converts all IUPAC bases to 'N' in both VCF and GVCF output, use --keep_iupac_bases to keep the IUPAC bases (#153).
4. Added options --use_longphase_for_intermediate_phasing, --use_whatshap_for_final_output_phasing, --use_longphase_for_final_output_phasing, --use_whatshap_for_final_output_haplotagging to disambiguate intermediate phasing and final VCF phasing either using WhatsHap or LongPhase, old options are still usable (#164).
5. Fixed "shell script interpreter selection problem" when using Clair3 as a host user within a Docker container (#175).

v0.1-r12

1. CRAM input is supported (#117).
2. Bumped up dependencies' version to "Python 3.9" (#96), "TensorFlow 2.8", "Samtools 1.15.1", "WhatsHap 1.4".
3. VCF DP tag now shows raw coverage for both pileup and full-alignment calls (before r12, sub-sampled coverage was shown for pileup calls if average DP > 144, (#128).
4. Fixed Illumina representation unification out-of-range error in training (#110).