protected boolean badSolidOffset( final GATKSAMRecord read, final int offset ) { return ReadUtils.isSOLiDRead(read) && RAC.SOLID_RECAL_MODE != RecalUtils.SOLID_RECAL_MODE.DO_NOTHING && !RecalUtils.isColorSpaceConsistent(read, offset); }
if (!ReadUtils.isSOLiDRead(read)) // If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base return true;