Whippet v0.10 isoform-level EM, Bias correction models

[timbitz]

This is a pretty massive PR that includes a complete re-implementation of quant.jl, the changes include (but are not limited to):

• Performance Increase: Huge run-time decrease for EM stage which now scales as a function of transcriptome complexity rather than read-depth! This is due to multi-mapping read storage into alignment path hashed equivalence classes!
• Far more accurate TpM quantification, producing TpM values for all annotated isoforms normalized by exact isoform length (vs. gene-level splice graph average before). Now, gene-level TpM becomes the sum of the isoform tpms in the gene. New output file formats iare .isoform.tpm.gz and .gene.tpm.gz.
• Multi-gene mapping reads whose edges don't fit any annotated isoform are assigned after EM based on gene-level proportions.
• Increased default iterations for EM which now completely converge in a few seconds, plus short-circuit of equivalence classes (isoform-level and multi-gene level) whose proportions have already converged.
• Bugfix in how multi-mapping paired reads were previously double counted during gene-expression EM.
• Substantially increased test coverage of quant.jl.

[codecov[bot]]

Codecov Report

Merging #58 into master will increase coverage by 3.56%. The diff coverage is 54.04%.

@@            Coverage Diff             @@
##           master      #58      +/-   ##
==========================================
+ Coverage   50.59%   54.15%   +3.56%     
==========================================
  Files          17       18       +1     
  Lines        1945     2323     +378     
==========================================
+ Hits          984     1258     +274     
- Misses        961     1065     +104

Impacted Files	Coverage Δ
src/paired.jl	0% <ø> (ø)	:arrow_up:
src/ebi.jl	80% <ø> (+80%)	:arrow_up:
src/reads.jl	30.18% <0%> (+16.85%)	:arrow_up:
src/io.jl	33.05% <10%> (-1.87%)	:arrow_down:
src/sgkmer.jl	80% <100%> (+1.42%)	:arrow_up:
src/graph.jl	93.51% <100%> (+1.76%)	:arrow_up:
src/align.jl	72.12% <100%> (+0.74%)	:arrow_up:
src/events.jl	56.94% <45.83%> (-0.26%)	:arrow_down:
src/bias.jl	49.09% <49.09%> (ø)
src/quant.jl	56.35% <56.61%> (+22.25%)	:arrow_up:
... and 8 more

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