Add mirrored haplotype frequency inference

[mmyers1]

Infers mhBAF values which indicate the frequency of the minor haplotype for the corresponding bin. These values can be above 0.5 for samples in which where the minor haplotype is more abundant, which may indicate mirrored subclonal copy-number events.

PR includes required changes to plotting (to support values >0.5) as well as

• more flexible parsing of the clonal argument to compute_cn (it is now less dependent on the order that clusters are given)
• multiple initializations for clustering (default 10, user-modifiable)
• bugfix in cluster_bins to avoid "no solution" case where all silhouette scores are in [-1, 0)
• procedure to detect and correct haplotype switch errors (using piecewise constant fitting and thresholds)

[codecov-commenter]

Codecov Report

Merging #181 (5e29f6a) into master (e7b364d) will decrease coverage by 0.87%. The diff coverage is 24.73%.

@@            Coverage Diff             @@
##           master     #181      +/-   ##
==========================================
- Coverage   52.24%   51.36%   -0.88%     
==========================================
  Files          34       34              
  Lines        6774     6958     +184     
==========================================
+ Hits         3539     3574      +35     
- Misses       3235     3384     +149     

Impacted Files	Coverage Δ
src/hatchet/utils/count_alleles.py	34.23% <ø> (ø)
src/hatchet/utils/count_reads.py	40.13% <ø> (ø)
src/hatchet/utils/genotype_snps.py	61.94% <ø> (+0.54%)	:arrow_up:
src/hatchet/utils/plot_bins_1d2d.py	0.00% <ø> (ø)
src/hatchet/utils/plot_cn_1d2d.py	0.00% <0.00%> (ø)
src/hatchet/utils/combine_counts.py	16.40% <3.66%> (-2.36%)	:arrow_down:
src/hatchet/bin/HATCHet.py	56.43% <11.62%> (-2.34%)	:arrow_down:
src/hatchet/utils/ArgParsing.py	70.26% <54.54%> (-0.44%)	:arrow_down:
src/hatchet/utils/combine_counts_fw.py	61.18% <66.66%> (+0.07%)	:arrow_up:
src/hatchet/utils/cluster_bins.py	89.90% <91.22%> (-0.05%)	:arrow_down:
... and 6 more

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