Paraphase

Summary of changes:

1. Updates to better handle targeted data
- Filter reads on rq (>=0.99), if rq is present in input bam
- Add a `--targeted` option for targeted data to drop the assumption of uniform coverage across the genome
- Add two optional parameters for targeted data
- `--min-read-variant`: Partially controls the number of supporting reads for a variant for identifying variants used for phasing. The cutoff for variant-supporting reads is determined by min(this number, max(5, depth\*0.11)). Default is 20. At standard WGS depth, the default value is overwritten by max(5, depth*0.11).
- Use cases: 1) Set this number low for low-coverage data or to increase sensitivity. 2) For targeted data with high coverage, set this number relatively high to avoid picking up sequencing errors and to reduce run time.
- `--min-read-haplotype`: Minimum number of unique supporting reads for a haplotype. Default is 4. For targeted data with high coverage, this cutoff can be increased to reduce errors and to reduce run time.

2. Updates to target regions:
- Update coordinates of some target regions to include full genes whenever possible: `pms2,ikbkg,hba,DDT,MBD3L2,DEFA1,PRY,CHRNA7,DHX40,GOLGA8A,IQCK,NXF2,OTOA,PDPK1,POTEI,RGPD1,RGPD3,RSPH10B,SIK1,TMLHE,CBS,KCNE1,CASTOR2,NBPF4,RGPD5,GOLGA8N,POTEB,ANKRD20A1,NSF`
- Add TNXB as a region on its own so that the full gene can be genotyped (the RCCX region only includes part of TNXB)

3. Algorithmic changes
- Improve fusion calling in cases of homozygous deletion
- Add some homozygous sites to cover target regions evenly during phasing to improve read assignment to haplotypes and variant calling
- Update a few gene-specific callers
- `hba`: Add calling of 4.2 deletion/duplication
- `smn1`: If homozygous throughout region, default to CN =2 instead of 1; Drop carrier call if only one SMN1 haplotype is found but the total CN of SERF1A/B (neighboring locus) is larger than the total CN of SMN1/2
- `ikbkg`: Improve calling of the 11.7kb deletion; Update the config to genotype the entire gene
- `ncf1`: Drop carrier call if only one NCF1 haplotype is found but the total CN of GTF2I (neighboring locus) is larger than the total CN of NCF1 family
- `rccx`: Better handle homozygous deletion cases
- `pms2`: Update the config to genotype the entire gene

4. Other changes:
- Support cram as input
- Standardize haplotype naming across regions: `{gene name}_{haplotype name}`

Summary of changes:
- Add `--write-nocalls-in-vcf` option to write no-call sites in the VCF

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