samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Fix genotype validation error message #1499

Closed ldgauthier closed 4 years ago

ldgauthier commented 4 years ago

Actually report the VC alleles as the VC alleles, not the genotype alleles. Current error message is incorrect and not helpful.

codecov-commenter commented 4 years ago

Codecov Report

Merging #1499 into master will decrease coverage by 0.003%. The diff coverage is 0.000%.

@@               Coverage Diff               @@
##              master     #1499       +/-   ##
===============================================
- Coverage     69.243%   69.240%   -0.003%     
  Complexity      8792      8792               
===============================================
  Files            592       592               
  Lines          34860     34860               
  Branches        5815      5815               
===============================================
- Hits           24138     24137        -1     
- Misses          8420      8421        +1     
  Partials        2302      2302               
Impacted Files Coverage Δ Complexity Δ
.../htsjdk/variant/variantcontext/VariantContext.java 78.004% <0.000%> (ø) 237.000 <0.000> (ø)
...samtools/util/AsyncBlockCompressedInputStream.java 72.000% <0.000%> (-4.000%) 12.000% <0.000%> (-1.000%)
...htsjdk/samtools/util/nio/DeleteOnExitPathHook.java 90.476% <0.000%> (+9.524%) 4.000% <0.000%> (+1.000%)