Commit ae57cfdb authored by J.K. Vis's avatar J.K. Vis
Browse files

Version 2.1.5: updated cutoff scheme

parent 774a59db
......@@ -8,8 +8,8 @@
// FILE INFORMATION:
// File: extractor.cc (depends on extractor.h)
// Author: Jonathan K. Vis
// Revision: 2.1.4
// Date: 2014/08/21
// Revision: 2.1.5
// Date: 2014/08/22
// *******************************************************************
// DESCRIPTION:
// This library can be used to generete HGVS variant descriptions as
......@@ -457,7 +457,7 @@ size_t extractor_transposition(std::vector<Variant> &variant,
// Extract the LCS (from the whole reference string).
size_t const cut_off = static_cast<size_t>(TRANSPOSITION_CUT_OFF * static_cast<double>(sample_length));
size_t const cut_off = global_reference_length < THRESHOLD_CUT_OFF ? 1 : TRANSPOSITION_CUT_OFF * sample_length;
std::vector<Substring> substring;
size_t const length = LCS(substring, reference, complement, 0, global_reference_length, sample, sample_start, sample_end, cut_off);
......
......@@ -8,8 +8,8 @@
// FILE INFORMATION:
// File: extractor.h (implemented in extractor.cc)
// Author: Jonathan K. Vis
// Revision: 2.1.4
// Date: 2014/08/21
// Revision: 2.1.5
// Date: 2014/08/22
// *******************************************************************
// DESCRIPTION:
// This library can be used to generate HGVS variant descriptions as
......@@ -34,7 +34,7 @@ namespace mutalyzer
{
// Version string for run-time identification.
static char const* const VERSION = "2.1.4";
static char const* const VERSION = "2.1.5";
// The character type used for all strings. For now it should just be
......@@ -90,13 +90,13 @@ static size_t const WEIGHT_SEPARATOR = 1; // i.e., _, [, ], ;
static size_t const WEIGHT_SUBSTITUTION = 1; // i.e., >
// Cut-off constants. For normal extraction use the threshold to
// specify the maximum reference length without any cut-off. Otherwise
// the extraction cut-off is used.
// The for transpositions is set at a fraction of the sample length.
// Cut-off constants. The threshold is used to specify the maximum
// reference length without any cut-off. Otherwise the extraction
// cut-off is used. For transpositions the cut-off is specified as
// a fraction of the sample_length.
static size_t const THRESHOLD_CUT_OFF = 16000;
static size_t const EXTRACTION_CUT_OFF = 500;
static double const TRANSPOSITION_CUT_OFF = 0.3;
static size_t const EXTRACTION_CUT_OFF = 250;
static double const TRANSPOSITION_CUT_OFF = 0.1;
// This global variable is used to have access to the whole reference
......
......@@ -8,8 +8,8 @@
// FILE INFORMATION:
// File: extractor.i (SWIG interface file)
// Author: Jonathan K. Vis
// Revision: 2.1.4
// Date: 2014/08/21
// Revision: 2.1.5
// Date: 2014/08/22
// *******************************************************************
// DESCRIPTION:
// Defines the SWIG interface for the Extractor library for use in
......@@ -32,7 +32,7 @@ namespace mutalyzer
{
// Version string for run-time identification.
static char const* const VERSION = "2.1.4";
static char const* const VERSION = "2.1.5";
// The character type used for all strings. For now it should just be
// a char.
......
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