Paraphase

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

This release includes some improvements to phasing and variant calling.
- Filter out spurious variants before phasing
- Filter out spurious haplotypes after phasing
- Better handle homozygous cases

This release extends Paraphase to resolve highly homologous genes listed below

- SMN1/SMN2 (spinal muscular atrophy)
- RCCX module
- CYP21A2 (21-Hydroxylase-Deficient Congenital Adrenal Hyperplasia)
- TNXB (Ehlers-Danlos syndrome)
- C4A/C4B (relevant in autoimmune diseases)
- PMS2 (Lynch Syndrome)
- STRC (hereditary hearing loss and deafness)
- IKBKG (Incontinentia Pigmenti)
- NCF1 (chronic granulomatous disease; Williams syndrome)
- NEB (Nemaline myopathy)
- F8 (intron 22 inversion, Hemophilia A)
- CFC1 (heterotaxy syndrome)