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Fix integer overflow bug in RMSMappingQuality #5435

Merged
merged 3 commits into from
Nov 28, 2018
Merged

Fix integer overflow bug in RMSMappingQuality #5435

merged 3 commits into from
Nov 28, 2018

Commits on Nov 19, 2018

  1. Fix integer overflow bug in RMSMappingQuality 

    Updated RMS Mapping quality annotations to be of type long/Long instead
of int/Integer. With int types, a large cohort could overflow
Integer.MAX_VALUE when handling sum of squared mapping qualities. With
long types this should not be a problem until we have off-world
colonies. This resolves issue 5433.
    @TedBrookings
    TedBrookings committed Nov 19, 2018
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Commits on Nov 27, 2018

  1. Moved getAttributeAsLongList to GATKProtectedVariantContextUtils

    @TedBrookings
    TedBrookings committed Nov 27, 2018
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  2. Changed to correct equality test for MISSING_VALUE_v4

    @TedBrookings
    TedBrookings committed Nov 27, 2018
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