PE

.gitignore

@@ -11,3 +11,4 @@ gmon.out
 CMakeFiles
 CMakeCache.txt
 cmake_install.cmake
+assembler/src/tools/quality/results*

assembler/configs/.gitignore

@@ -3,8 +3,8 @@ debruijn/simplification.info
 debruijn/distance_estimation.info
 debruijn/detail_info_printer.info
 debruijn/log.properties
-debruijn/long_contigs/lc_config.info
-debruijn/long_contigs/lc_params.info
-debruijn/long_contigs/lc_libs.info
+debruijn/path_extend/pe_config.info
+debruijn/path_extend/pe_params.info
+debruijn/path_extend/pe_libs.info
 hammer/config.info
-_generic/
+_generic/

assembler/configs/debruijn/config.info.template

@@ -86,11 +86,13 @@ estimation_mode simple
 paired_metrics read_count
 ; read_count, product
 
-; repeat resolving mode (none split path_extend jump combined)
+; repeat resolving mode (none split path_extend combined)
 resolving_mode split
 
+use_scaffolder  true
+
 andrey_params {
-	#include "long_contigs/lc_params.info"
+	#include "path_extend/pe_params.info"
 }
 
 ; Produce info for all components of graph and run repeat resolver for each component.

assembler/configs/debruijn/distance_estimation.info.template

@@ -17,7 +17,29 @@ usual_de
 
 ; advanced distance estimator:
 
-ade
+sc_ade
+{
+    ;data dividing
+        threshold          80 ;maximal distance between two points in cluster
+
+    ;local maximum seeking
+        range_coeff          0.2 ;data_length*range_coeff := width of the averaging window
+        delta_coeff          0.4 ;data_length*delta_coeff := maximal difference between possible distance and real peak on the graph
+
+    ;fft smoothing
+        percentage          0.01 ;percent of data for baseline subraction
+        cutoff              3 ;the number of the lowest freqs in fourier decomp being taken
+
+    ;other
+        min_peak_points       3 ;the minimal number of points in cluster to be considered
+        inv_density         5.0 ;maximal inverse density of points in cluster to be considered
+
+    ;hard_mode arguments
+        derivative_threshold  0.2 ;threshold for derivative in hard mode
+
+}
+
+usual_ade
 {
     ;data dividing
         threshold          20 ;maximal distance between two points in cluster