updated skalo with indel output

[rderelle]

• better sorting of indel groups
• output indel VCF file
• fixed detection of internal indel k-mers (but slow)
• changed default m value to 0.1 for consistency with ska align
• updated doc and a few log::info messages

[codecov]

Codecov Report

Attention: Patch coverage is 96.75926% with 7 lines in your changes missing coverage. Please review.

Project coverage is 94.41%. Comparing base (3ce160e) to head (e6fe692).
Report is 14 commits behind head on master.

Files with missing lines	Patch %	Lines
src/skalo/process_indels.rs	97.04%	6 Missing ⚠️
src/lib.rs	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #91      +/-   ##
==========================================
+ Coverage   93.43%   94.41%   +0.98%     
==========================================
  Files          24       25       +1     
  Lines        3943     4098     +155     
==========================================
+ Hits         3684     3869     +185     
+ Misses        259      229      -30     

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[johnlees]

This mostly looks good. Did you run cargo fmt?

Can you also add a test that the indels are output, as you did for the SNPs?

[rderelle]

@johnlees I added a test file for indel prediction/output. All done.

[johnlees]

Looks good thanks. I have run cargo fmt, and also updated the tests so that they actually compare against your correct results files.

I'll merge this when the tests pass again. When I do, would you be ready for me to release this as v0.4.0?