v0.3.1

1. Added four options i. --use_heterozygous_snp_in_tumor_sample_and_normal_bam_for_intermediate_phasing, ii. --use_heterozygous_snp_in_normal_sample_and_normal_bam_for_intermediate_phasing, iii. --use_heterozygous_snp_in_tumor_sample_and_tumor_bam_for_intermediate_phasing, and iv. --use_heterozygous_snp_in_normal_sample_and_tumor_bam_for_intermediate_phasing. iii is equivalent to --use_heterozygous_snp_in_tumor_sample_for_intermediate_phasing added in v0.2.0. iv is equivalent to --use_heterozygous_snp_in_normal_sample_for_intermediate_phasing added in v0.2.0. Use normal bam for intermediate phasing was a request from @Sergey Aganezov. When the coverage of normal and tumor are similar, using normal bam for intermediate phasing has negligible difference from using tumor bam in our experiments using HCC1395/BL.
2. Added --haplotagged_tumor_bam_provided_so_skip_intermediate_phasing_and_haplotagging to use the haplotype information provided in the tumor bam directly and skip intermediate phasing and haplotagging. This option is useful when using ClairS in a pipeline in which the phasing of the tumor bam is done before running ClairS. BAM haplotagged by WhatsHap and LongPhase are accepted.
3. Bumped up Clair3 dependency to version 1.0.10, LongPhase to version 1.7.3.