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Build # 2245

Build Type

push

travis-ci

Committed by droazen

Commit Message

Make sequence dictionary validation a bit less strict

-Require that the reference dictionary be a superset of the reads dictionary
 only when there is at least one CRAM input.

-When determining whether a superset relationship exists, do not take extended
 attributes (like the sequence MD5) into account; only consider the contig names
 and lengths.

-Do not require common contigs to occur at the same absolute indices across
 dictionaries (but do require that they occur in the same relative order).
 Contig indices were an issue for GATK3, but since hellbender relies on contig
 names for queries we can afford to disable this annoying check. If we later find
 that we need to turn it back on, we can easily do so.

-Updated tests appropriately:
    -Added test cases showing that extended attributes are ignored when checking
     for a superset.

    -Added test cases for various combinations of the new boolean options
     requireSuperset and checkContigIndices.

    -The existing integration test CRAMSupportIntegrationTest.testWrongRef()
     shows that we throw when a CRAM is provided as input with a reference
     that does not contain all of its contigs.

Run Details

19523 of 24661 relevant lines covered (79.17%)

1.73 hits per line