v0.2.0

1. Added --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing/--use_heterozygous_snp_in_tumor_sample_for_intermediate_phasing option to support using either heterozygous SNPs in the normal sample or tumor sample for intermediate phasing. The previous versions used in_tumor_sample for phasing. In this new version, when testing with ONT 4kkz HCC1395/BL and using in_normal_sample for intermediate phasing, the SNV precision improved ~2%, while recall remained unchanged. in_normal_sample becomes the default from this version. However, if the coverage of normal sample is low, please consider switching back to using in_tumor_sample (#22, idea contributed by the longphase team @sloth-eat-pudding).
2. Added --use_heterozygous_indel_for_intermediate_phasing to include high quality heterozygous Indels for intermediate phasing. With this new option, the haplotagged tumor reads increased by ~3% in ONT 4khz HCC1395/BL, the option becomes default from this version.
3. Added a model that might provide a slightly better performance for liquid tumor. In this release, only ONT Dorado 5khz HAC for liquid tumor (-p ont_r10_dorado_hac_5khz_liquid) is provided. The model was trained with slightly higher normal contamination. We are testing out the new model with collaborator.
4. Added --use_longphase_for_intermediate_haplotagging option to replace WhatsHap haplotagging by LongPhase haplotagging to speed up read haplotagging process, the option becomes default from this version.
5. Bumped up Clair3 dependency to version 1.0.7, LongPhase to version 1.7.