New stratp, better collapse, misc bugs

See updates wiki for details

Phab refactor

and other minor tweaks

Move to POA

And minor bug fixes

See wiki

https://github.com/ACEnglish/truvari/wiki/Updates#truvari-511

Fixing BNDs. Improving Refine

See https://github.com/ACEnglish/truvari/wiki/Updates#truvari-510

- Reference context sequence comparison is now deprecated and sequenc…

…e similarity calculation improved by also checking lexicographically minimum rotation's similarity. details

- Symbolic variants (<DEL>, <INV>, <DUP>) can now be resolved for sequence comparison when a --reference is provided. The function for resolving the sequences is largely similar to this discussion
- Symbolic variants can now match to resolved variants, even with --pctseq 0, with or without the new sequence resolving procedure.
- Symbolic variant sub-types are ignored e.g. <DUP:TANDEM> == <DUP>
- --sizemax now default to -1, meaning all variant ≥ --sizemin / --sizefilt are compared
- Redundant variants which are collapsed into kept (a.k.a. removed) variants now more clearly labeled (--removed-output instead of --collapsed-output)
- Fixed 'Unknown error' caused by unset TMPDIR (#229 and #245)
- Fixes to minor record keeping bugs in refine/ga4gh better ensure all variants are counted/preserved
- BND variants are now compared by bench (details)
- Cleaner outputs by not writing matching annotations (e.g. PctSeqSimilarity) that are None
- Major refactor of Truvari package API for easy reuse of SV comparison functions (details)

Small bug fixes

bench - Correctly filtering ALT=* alleles and monomorphic reference
stratify - Default behavior is to count variants within
collapse - Faster sub-chunking operations by dropping use of pyintervaltree
anno chunks - New command for identifying windows with a high number of SVs

Minor bug fixes

* `refine` & `stratify`
  * Fixed variant and bed boundary overlapping issue
* general
  * Definition of variants within a region now includes replacement style from TR callers having an anchor base 1bp upstream of catalog/includebed regions
  * Propagating MAFFT errors (#204)
  * FIPS compliance (#205)
  * Allow csi-indexed vcf files (#209)
  * bcftools sort tempfile (#213)

* collapse

  * Fewer comparisons needed per-chunk on average
  * Fixed --chain functionality (details)
  * Fixed --gt consolidation of format fields
* bench
  * Faster result at the cost of less complete annotations with --short flag
* refine
  * Assures variants are sequence resolved before incorporating into consensus
  * bench --passonly --sizemax parameters are used when building consensus for a region. Useful for refine --use-original-vcfs
  * When a refined region has more than 5k variants, it is skipped and a warning of the region is written to the log
  * Flag --use-region-coords now expands --region coordinates by 100bp (phab --buffer default) to allow variants to harmonize out of regions.
* general
  * Dynamic bed/vcf parsing tries to choose faster of streaming/fetching variants

Changes to regions and collapse

- Off by one error was mis-classifying some variants at the ends of regions as
within the region.
- Collapse's handling of genotypes (`--gt` and `--keep common` is faster)
- New ga4gh command for reformatting `bench` results