Fix for corrupted CO tag issue

[lbergelson]

• Someone on the forum reported an issue with a bam tag that was a long string instead of 2 characters. This is a fix, but not a test because i'm not sure how to build a bam that triggers isContaminant.

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[lbergelson]

@pshapiro4broad I updated it to master and now it's failing with:

Gradle suite > Gradle test > picard.vcf.UpdateVcfSequenceDictionaryTest > testUpdateVcfSequenceDictionary[2](/dev/stdout) FAILED
    java.lang.IllegalArgumentException: Output format type is not set, or could not be inferred from the output path. If a path was used, does it have a valid VCF extension (.vcf, .vcf.gz, .bcf)?
        at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.build(VariantContextWriterBuilder.java:462)
        at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.build(VariantContextWriterBuilder.java:415)
        at picard.vcf.UpdateVcfSequenceDictionary.doWork(UpdateVcfSequenceDictionary.java:89)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
        at picard.vcf.UpdateVcfSequenceDictionaryTest.testUpdateVcfSequenceDictionary(UpdateVcfSequenceDictionaryTest.java:105)
Finished 4700 tests

Not sure what that's about. Rebased it again to be sure and pushing, maybe it's just something transient.

[lbergelson]

Seems to be fixed. Will merged once this all passes.