Commit 7e7264a8 authored by J.K. Vis's avatar J.K. Vis
Browse files

Lowered extraction cut-off

parent 66abbabf
......@@ -8,8 +8,8 @@
// FILE INFORMATION:
// File: extractor.cc (depends on extractor.h)
// Author: Jonathan K. Vis
// Revision: 2.1.5
// Date: 2014/08/22
// Revision: 2.1.6
// Date: 2014/09/17
// *******************************************************************
// DESCRIPTION:
// This library can be used to generete HGVS variant descriptions as
......@@ -217,7 +217,7 @@ size_t extractor(std::vector<Variant> &variant,
// Calculate the LCS (possibly in reverse complement) of the two
// strings.
size_t const cut_off = reference_length < THRESHOLD_CUT_OFF ? 1 : EXTRACTION_CUT_OFF;
size_t const cut_off = reference_length < THRESHOLD_CUT_OFF ? 1 : weight_position;
std::vector<Substring> substring;
size_t const length = LCS(substring, reference, complement, reference_start, reference_end, 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: 2.1.5
// Date: 2014/09/12
// Revision: 2.1.6
// Date: 2014/09/17
// *******************************************************************
// 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 = "2.1.5";
static char const* const VERSION = "2.1.6";
// The character type used for all strings. For now it should just be
......@@ -91,11 +91,10 @@ static size_t const WEIGHT_SUBSTITUTION = 1; // i.e., >
// 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.
// reference length without any cut-off. Otherwise the weight_position
// is used as a cut-off. 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 = 250;
static double const TRANSPOSITION_CUT_OFF = 0.1;
......
......@@ -8,8 +8,8 @@
// FILE INFORMATION:
// File: extractor.i (SWIG interface file)
// Author: Jonathan K. Vis
// Revision: 2.1.5
// Date: 2014/08/22
// Revision: 2.1.6
// Date: 2014/09/17
// *******************************************************************
// 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 = "2.1.5";
static char const* const VERSION = "2.1.6";
// The character type used for all strings. For now it should just be
// a char.
......
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