CHANGES IN VERSION 1.4.x
------------------------

BUG FIXES

    o Fixed uninitialised variable causing slightly stochastic behaviour.
    o Fixed bug blocking alternative PQS with zero-length loop to be found.
    o Fixed inefficient looping through long non-guanine sequence regions.
    o Updated default scoring parameters to slightly better-performing
      combination.
    o Removed bug-prone special support for edge mismatches.
    o Fixed integer division to floating point division in the
      computation of loop length mean.

CHANGES IN VERSION 1.3.x
------------------------

NEW FEATURES:

    o Added estimated time to complete (ETTC) to the progress line.
    o New default values for scoring parameters as a result from
      training on G4-seq experimental data and co-testing on a set
      of known quadruplexes from literature.
    o New PQS metadata reported: number of tetrads, bulges, mismatches
      and loop lengths. To get this data, use elementMetadata accessor
      function.
    o New algorithm option: reporting of all overlapping PQS.
    o Score distribution is reported. For each sequence position
      you get maximal score of PQS that was found overlapping
      the position. For details, see scoreDistribution function.
    o Novel scoring parameter: exponent of loop length mean
      in the scoring equation to express non-linear dependency
      of the PQS propensity to the loop lengths.

BUG FIXES

    o Minimal loop length is set back to 0 by default, but only
      one zero-length loop is allowed by the scoring system.
    o Fixed unintentional cast of loop length mean factor and loop
      standard deviation factors from float to integer.

CHANGES IN VERSION 1.2.x
------------------------

BUG FIXES

    o Minimal loop length is now set to 1 by default.
    o Removed linking dependency on the flowCore package.
    o Fixed bug responsible for a segmentation fault. Great credit
      belongs to Diego Andino for sending a bug report.

CHANGES IN VERSION 1.0.0
------------------------

    o Novel algorithm for identification of potential intramolecular
      G-quadruplex (G4) patterns in DNA sequence.
    o Supports multiple defects in G-runs like bulges or mismatches.
    o Provides the most accurate results currently available.
    o Highly customizable to detect even novel G4 types that might be
      discovered in the future.
