bug fixes and additional QC

[balabanmetin]

• When phasing SNPs, shapeit -check does not create the {chromosome}_alignments.snp.strand.exclude if there is no SNPs to be excluded. Inputting shapeit a non-existent file raises an error. We now create an empty file instead when the exclude file is not created.
• Genotype SNPs now uses minimum coverage parameter self.mincov. Previously it has never been used.
• When input BAM and VCF files misses .bai and.tbi indices respectively, we detect and raise an exception. Otherwise the workflow crashes later and it is very difficult to find the reason why it happened.
• pandas depreciated feature is no longer used in cluster_bins

[codecov-commenter]

Codecov Report

Merging #194 (b2b1a49) into master (d3b38e4) will decrease coverage by 0.08%.
The diff coverage is 23.07%.

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@@            Coverage Diff             @@
##           master     #194      +/-   ##
==========================================
- Coverage   51.32%   51.25%   -0.08%     
==========================================
  Files          34       34              
  Lines        6963     6967       +4     
==========================================
- Hits         3574     3571       -3     
- Misses       3389     3396       +7     

Files Changed	Coverage Δ
src/hatchet/utils/genotype_snps.py	58.33% <0.00%> (-3.08%)	⬇️
src/hatchet/utils/phase_snps.py	56.55% <0.00%> (-0.40%)	⬇️
src/hatchet/utils/ArgParsing.py	70.29% <75.00%> (+0.03%)	⬆️

... and 2 files with indirect coverage changes

[mmyers1]

Looks reasonable.