CHANGES IN VERSION 2.2.x
------------------------

SIGNIFICANT USER-VISIBLE CHANGES:

    o Default minimal PQS score was decreased from 52 to 47. The score 47
      shows the best balanced accuracy on new G4 sequencing data provided
      by Marsico et al. 2019.
      
BUG FIXES:

    o Fixed bug allowing unlimited length of third loop leading to 
      invalid memory access and random scores.

CHANGES IN VERSION 2.0.x
------------------------

NEW FEATURES:

    o The qsfinder algorithm is ~100 times faster on real-world sequences
      than before. The main idea of the optimization is to stop the
      exhaustive search when we are sure there can't be found better PQS.
      The optimization is applied only in non-overlapping mode.
    o New boolean argument called "deep". Once set to TRUE, pqsfinder will
      disable optimizations and run full exhaustive search.

SIGNIFICANT USER-VISIBLE CHANGES:

    o Default minimal PQS score was increased from 26 to 52. The score 52
      shows the best balanced accuracy on G4 sequencing data provided by
      Chambers et al. 2015.

BUG FIXES:

    o Fixed resolution of overlapping sequences. When multiple same-scoring
      PQS overlap, the shortest one is chosen.
    o Fixed incorrect PQS metadata. When PQS was found on antisense strand,
      corresponding run lengths and loop lengths were confused.

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.
