Paraphase

Summary of changes:
Minor update. Fix program error in low-depth or no-data regions. Completes analysis even when the input is a small bamlet (result is still a no-call).

Summary of changes:
- Improve PMS2/PMS2CL differentiation
- Output protein changes at five potentially pathogenic sites in OPN1LW/OPN1MW
- Update region definitions for some families
- Add a few regions for fusion calling
- CYP2D6, GBA, CYP11B1, the CFH gene cluster
- Improve VCFs. See documentation [here](https://github.com/PacificBiosciences/paraphase/blob/main/docs/vcf.md)
- For each region, all gene copies are now in a single VCF file per sample, reported as sample columns in the VCF.
- Report boundary coordinates and the truncated status of a haplotype in the VCF.
- Report groups of haplotypes on the same chromosome when this information is available.

Summary of changes:

- Added HBA1/HBA2 and OPN1LW/OPN1MW callers
- Added ~150 segmental duplication regions for GRCh38
- Improved gene callers
- F8: Improved calling of Intron22 inversion and Exon1-22 deletion
- NCF1: Improved assignment of genes to NCF1 vs. pseudogenes
- PMS2: Improved assignment of genes to PMS2 vs. pseudogene. Updated the coordinates of the region to phase
- IKBKG: Improved assignment of genes to IKBKG vs. pseudogene. Updated the coordinates of the region to phase
- RCCX: Better calling of a multi-allelic site IVS2-13A/C>G
- CFC1: Updated the coordinates of the region to phase
- For SMN1/STRC/PMS2/IKBKG/NCF1, variants are now called against the gene for gene haplotypes and against the paralog/pseudogene for paralog/pseudogene haplotypes
- Report F8 Intron 22 inversion and Exon1-22 deletion, and IKBKG 11.7kb deletion in VCFs
- Improved homopolymer/simple repeat masking before phasing
- Included filtered calls in VCFs
- Added GRCh37/hg19 support for 11 medically relevant gene families

- Speeds up single sample analysis through multiprocessing by genomic region (-t is enabled)
- Adds program version and command to BAM and VCF headers
- Fixed a bug that may lead to failed analysis in low coverage samples
- Fixed a bug in F8 analysis

- Fix low depth error so that even if one region fails depth check, the other regions will still produce results.
- Show version

This version includes some light updates to Paraphase
- Simplify config files
- Prevent non-zero exit code
- Minor algorithm improvements

Please note that a new input file is required - the reference genome fasta file (specify with `-r`)