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Fixed a bug in IlluminaBasecallsToFastq where ADAPTERS_TO_CHECK could not be set as a CLP argument. (#1740)
Fixed a bug in GtcToVcf where where SOURCE fields populated from the Illumina manifest that contain a semicolon may be incorrectly populated in the INFO field of the VCF (#1738)
Updated CombineGenotypingArrayVcfs to handle differences in INFO:SOURCE field of a VCF generated by GtcToVcf (#1739)
Added more logging to IlluminaBaseCallsToSam/Fastq (#1735)