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Vcf int64 part2 #1004

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wants to merge 3 commits into from
Closed

Vcf int64 part2 #1004

wants to merge 3 commits into from

Commits on Dec 9, 2019

  1. Fixes BCF in-memory decoding with 64-bit integers. 

    Any 64-bit INFO field that wasn't the last in the list would cause
subsequent fields to be decoded incorrectly.

This commit fixes that, plus updates the tests accordingly so the bug
could be triggered.

Fixes the first part of samtools#999 (test1.vcf), but doesn't fix the second
part (BCF output silently being broken).

Fixes samtools/bcftools#1123
    @jkbonfield
    jkbonfield committed Dec 9, 2019
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Commits on Dec 11, 2019

  1. Additional checks to prevent writing invalid BCF containing 64-bit data

    @jkbonfield
    jkbonfield committed Dec 11, 2019
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Commits on Dec 12, 2019

  1. Limit 64-bit info to END tag (as suggested by Rob Davies). 

    Also adds check for rlen (END) field when trying to output to BCF.

Note: this will emit a warning per out-of-range value, but it is
expected that the frequency of these is very low.  If not, consider
this a good icentive to fix your pipelines!
    @jkbonfield
    jkbonfield committed Dec 12, 2019
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