v1.0.10

1. Fixed an out of range bug when outputing GVCF for non-human genome (#317.
2. Improve the calling speed when working with targeted amplicon data, Use —chunk_num=-1 to call variant without splitting genome into chunks (#306, contributor Elliot Hallmark).
3. Updated LongPhase to version 1.7.3 (#321.

v1.0.9

1. Fixed an issue in VCF header(#305 by @Monica Palafox Roberts).
2. Updated DP FORMAT description in the header.

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).