Better genotype errors

[stschiff]

This pull request uses a newer version of sequence-formats, which improves the error message if a genotype file parsing error is encountered.

Example before:

Issues in genotype data parsing: SeqFormatException "Error while parsing: string. Error occurred when trying to parse this chunk: 
\"11X099\\n222299\\n222299\\n212299\\n221299\\n999910\\n999922\\n999911\\n999912\\n999910\\n999911\\n999910\\n\""

after:

Issues in genotype data parsing: SeqFormatException: Error while parsing: string. Offending line: 
11X099

Before:

Issues in genotype data parsing: SeqFormatException "Error while parsing: Failed reading: takeWhile1. Error occurred when trying to parse this chunk: 
\"2_1018704\\t2\\tnotanumber\\t1018704\\tA\\tG\\n2_1045331\\t2\\t2.6665e-2\\t1045331\\tG\\tA\\n2_1048955\\t2\\t2.6674e-2\\t1048955\\tA\\tG\\n2_1061166\\t2\\t2.6711e-2\\t1061166\\tT\\tC\\n2_1108637\\t2\\t2.8311e-2\\t1108637\\tG\\tA\\nrs0000\\t11\\t0.0\\t0\\tA\\tC\\nrs1111\\t11\\t1.0e-3\\t100000\\tA\\tG\\nrs2222\\t11\\t2.0e-3\\t200000\\tA\\tT\\nrs3333\\t11\\t3.0e-3\\t300000\\tC\\tA\\nrs4444\\t11\\t4.0e-3\\t400000\\tG\\tA\\nrs5555\\t11\\t5.0e-3\\t500000\\tT\\tA\\nrs6666\\t11\\t6.0e-3\\t600000\\tG\\tT\\n\""

after:

Issues in genotype data parsing: SeqFormatException: Error while parsing: Failed reading: takeWhile1.
Offending line: 2_1018704	2	notanumber	1018704	A	G

addresses #224 and partially #403

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 52.36%. Comparing base (44bf9c3) to head (731852a).
⚠️ Report is 4 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #404   +/-   ##
=======================================
  Coverage   52.36%   52.36%           
=======================================
  Files          37       37           
  Lines        6065     6065           
  Branches      648      648           
=======================================
  Hits         3176     3176           
  Misses       2241     2241           
  Partials      648      648           

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[nevrome]

Excellent! Can be merged right away 👍

One day maybe ParsingError {peContexts = ["108"], peMessage = "Failed reading: satisfy"} for broken .bed files could also be addressed, but this is already huge progress! Thank you!