Feature/v3 pysam upgrade

[creisle]

Cherry-picks the commits in the other PR onto the develop_v3 branch (#264)

• new license
• libcurl add to actions file

BugFixes

• Use pandas instead of pysam to read vcf files

Breaking Changes

• drops support for python 3.6 (will add support for 3.9/3.10 in a subsequent pull)

Looks like a lot of the issues with the vcf reading part of pysam in later versions boils down to poor support for SVs in the underlying samtools/bcftools. There are some checks going on that make sense for indels/snps but break for SVs. Unfortunately this applies to all versions of pysam after 0.15.2. This short term solution is a drop-in replacement using pandas so we can bypass those checks.

Note: currently the pandas convert does so row-by-row, we can optimize this to perform these operations in the dataframe itself later if we find the performance lags, I wanted to keep the process as close to the current one as possible for this initial PR

[codecov[bot]]

Codecov Report

Merging #266 (9b3c72c) into develop_v3 (dd01854) will increase coverage by 0.03%. The diff coverage is 97.01%.

@@              Coverage Diff               @@
##           develop_v3     #266      +/-   ##
==============================================
+ Coverage       86.66%   86.70%   +0.03%     
==============================================
  Files              53       53              
  Lines            8843     8897      +54     
  Branches         2234     2310      +76     
==============================================
+ Hits             7664     7714      +50     
- Misses            719      722       +3     
- Partials          460      461       +1     

Flag	Coverage Δ
unittests	86.70% <97.01%> (+0.03%)	:arrow_up:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/mavis/tools/vcf.py	95.65% <97.01%> (+0.41%)	:arrow_up:
src/mavis/breakpoint.py	90.61% <0.00%> (-0.65%)	:arrow_down:

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