11. A method for identifying similarity between query samples and stored samples in an efficiently maintained reference library, the method comprising: receiving, by processing circuitry comprising at least one storage device and processor, a plurality of binary reference samples; processing, by the processing circuitry, each reference sample of the plurality of reference samples via operations including: assigning each reference sample a respective unique identifier; producing a reference sample fingerprint for each reference sample; and registering each respective unique identifier to reference sample fingerprint pair in a reference library via operations including: scoring the reference sample fingerprint with each previously stored fingerprint in the reference library to produce a first matching score; if the first matching score meets or exceeds a first threshold for a previously stored fingerprint, determining the reference sample fingerprint to be a duplicate of the previously stored fingerprint, and recording only a unique identifier associated with the reference sample fingerprint in the reference library, the unique identifier being marked as a duplicate of the previously stored fingerprint; and otherwise, if the first matching score is less than the first threshold for each previously stored fingerprint, storing a corresponding reference sample unique identifier to reference sample fingerprint pair in the reference library; receiving, by the processing circuitry, a binary query sample; processing, by the processing circuitry, the binary query sample via operations including: producing a query sample fingerprint from the binary query sample; scoring the query sample fingerprint with each previously stored fingerprint in the reference library to produce a second matching score; and for each previously stored fingerprint for which the second matching score meets or exceeds a second threshold, reporting a corresponding reference sample unique identifier associated with the previously stored fingerprint and the second matching score.
18. The method of claim 11 , wherein each of the reference samples is a code binary.