Fix PS tag

Dependency update

rand library had conflicting versions that prevented bioconda from
building. Also update pyo3 since it had a (likely irrelevant) security vunerability.

New Trio/Mosaic Modes.

See https://github.com/ACEnglish/kanpig/wiki/Updates/ for details.

pVCF improvements

- New --ab allele balance threshold lowers frequency of assigning erroneous compound heterozygous genotypes
- Experimental --squish changes gpenalty behavior to preferring simpler paths
- Fix score's gpenalty

Minor patch

- UI tweaks, including cleaner gt parameters
- Slight htslib bam record and other minor efficiency improvement
- Fix bug arising from ploidy==1 regions sometimes.
- Fix minor bugs around PS and HP tag counting/record keeping

phase tags and graph building

fixed bug which prevented phase tags from being pulled sometimes. graph
building is now sometimes optional, improving runtime & memory usage.

Faster, Smaller, More Accurate Genotyping

Kanpig now has sub-commands `gt` and `plup`. The new `plup` command will
extract reads and their SVs from a bam file into a small file that's
useful for long-term storage of reads. The `gt` command can now parse
these plup files much more quickly than parsing a bam.

The `gt` command will now (optionally) parse PS and HP tags in a bam to
increase genotyping accuracy as well as record long-range phasing
information in SV genotypes.

The `gt` command now uses kmedoid clustering instead of kmeans,
resulting in a modest improvement to genotyping accuracy.

Consistency Upgrades

* New filtering of haplotypes without paths increases accuracy
* New path scoring improves accuracy and consistency
* ZS and SS FORMAT fields replaced by KS reporting the score
* Requiring reads to span the full variant graph window including --chunksize buffer increases accuracy
* Exhaustive search of partial haplotypes
* Slight runtime reduction from avoidance of redundant path searches

Improvements

* ~8% speed increase from less work in the path-searching
* Partial haplotypes bug fix increases accuracy
* Fixed SQ and FT fields
* Dedicated writing thread helps reduce memory usage by preventing a backlog of completed variants while reading
* Default --out is stdout to allow easier compression/indexing (e.g. kanpig .. | bcftools sort -O z -o out.vcf.gz)
* IUPAC codes are fixed by kanpig according to vcf specifications (Issue #1)
* Fixed filtering of symbolic alts and BNDs
* Argument validation

v0.2.0

* Up to 40% reduction in runtime
* Hemizygous and sex chromosome aware genotyping with new `--ploidy-bed`
* Variants with alternate alleles of stars, monozygotic reference, and BNDs are filtered out
* PathScores now compared with average of size and sequence similarity for increased accuracy