Version 3.2.1

Summary of changes:

• Fix problem working with CRAM
• Other minor changes:
  • Add RN tag to output bam. RN stands for region name, indicating reads used to analyze one region (paralog group)
  • Sort some output fields in the JSON, making it consistent from run to run
  • Clean up reported alleles, filtering out cases where all haplotypes are linked into one allele, or not all haplotypes are included when two alleles are reported
  • Fix getting sample ID from bam header when there are blank spaces
  • Fix logic for writing homozygous haplotypes in VCF (no haplotypes phased -> no haplotypes phased and no heterozygous variant sites)
  • Update two_cp_haplotypes when adjusting total_cn from 2 to 4 based on depth
  • Use all reads instead of unique reads for variant calling at edges of clipped haplotypes