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BCF version detection is too permissive #1323

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cmnbroad opened this issue Mar 12, 2019 · 0 comments · Fixed by #1324
Closed

BCF version detection is too permissive #1323

cmnbroad opened this issue Mar 12, 2019 · 0 comments · Fixed by #1324
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cmnbroad commented Mar 12, 2019

The BCF codec attempts to validate the version of a BCF file on read, but is overly permissive and accepts any minor version newer than the the current one. As a result, BCF 2.2 files are not rejected, even though the BCF implementation is BCF 2.1.

Until very recently, newer BCF files would be rejected because they contained IDX fields in the VCF header, but those are likely valid now as a result of #1248.

The version test should be changed to reject newer BCF versions as well as older ones.

@cmnbroad cmnbroad added the bug label Mar 12, 2019
@cmnbroad cmnbroad self-assigned this Mar 12, 2019
lbergelson pushed a commit that referenced this issue Mar 13, 2019
…ntation. (#1324)

* Fix VCFFileReader test code to detect negative tests that should throw but don't.
* Reject BCF files when minor version doesn't match the current implementation.
* Fix unresolved javadoc reference.
* Fixes #1323
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