commit ec2936eace3b16e2cc6a400c288525a4f8a4df21
Author: Florent Chuffart <florent.chuffart@ens-lyon.fr>
Date:   Thu Jul 3 11:22:20 2014 +0200

    Keep rejected common nuc in align_inter_strain_nucs

diff --git a/build/nucleominer_2.3.43.tar.gz b/build/nucleominer_2.3.43.tar.gz
new file mode 100644
index 0000000..2e162b7
Binary files /dev/null and b/build/nucleominer_2.3.43.tar.gz differ
diff --git a/doc/sphinx_doc/build/latex/NucleoMiner2.pdf b/doc/sphinx_doc/build/latex/NucleoMiner2.pdf
index a4beeee..53823c5 100644
Binary files a/doc/sphinx_doc/build/latex/NucleoMiner2.pdf and b/doc/sphinx_doc/build/latex/NucleoMiner2.pdf differ
diff --git a/doc/sphinx_doc/conf.py b/doc/sphinx_doc/conf.py
index b96ad50..ba03826 100644
--- a/doc/sphinx_doc/conf.py
+++ b/doc/sphinx_doc/conf.py
@@ -50,9 +50,9 @@ copyright = u'2012, Florent CHUFFART, Jean-Baptiste VEYRIERAS, Gael YVERT'
 # built documents.
 #
 # The short X.Y version.
-version = '2.3.42'
+version = '2.3.43'
 # The full version, including alpha/beta/rc tags.
-release = '2.3.42'
+release = '2.3.43'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/doc/sphinx_doc/rref.rst b/doc/sphinx_doc/rref.rst
index 45fe9f3..80a0008 100644
--- a/doc/sphinx_doc/rref.rst
+++ b/doc/sphinx_doc/rref.rst
@@ -745,7 +745,8 @@ Description
 ~~~~~~~~~~~
 
 This function filters TemplateFilter outputs according, not only genome
-area observerved properties, but also correlation and overlap threshold.
+area observerved properties, but also correlation and overlapping
+threshold.
 
 Usage
 ~~~~~
@@ -1247,7 +1248,7 @@ Details
 +---------------+---------------------------------------------------+
 | Author:       | Florent Chuffart                                  |
 +---------------+---------------------------------------------------+
-| Version:      | 2.3.42                                            |
+| Version:      | 2.3.43                                            |
 +---------------+---------------------------------------------------+
 | License:      | CeCILL                                            |
 +---------------+---------------------------------------------------+
diff --git a/src/DESCRIPTION b/src/DESCRIPTION
index 4710a2e..82da1ea 100644
--- a/src/DESCRIPTION
+++ b/src/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: nucleominer
 Maintainer: Florent Chuffart <florent.chuffart@ens-lyon.fr>
 Author: Florent Chuffart
-Version: 2.3.42
+Version: 2.3.43
 License: CeCILL 
 Title: nm
 Depends: seqinr, plotrix, DESeq, cachecache
diff --git a/src/R/nucleominer.R b/src/R/nucleominer.R
index c2305e0..12e8b27 100644
--- a/src/R/nucleominer.R
+++ b/src/R/nucleominer.R
@@ -199,7 +199,7 @@ nuc_width ##<< Width used to shift F and R reads.
 
 
 filter_tf_outputs = function(# Filter TemplateFilter outputs
-### This function filters TemplateFilter outputs according, not only genome area observerved properties, but also correlation and overlap threshold.
+### This function filters TemplateFilter outputs according, not only genome area observerved properties, but also correlation and overlapping threshold.
 tf_outputs, ##<< TemplateFilter outputs.
 chr, ##<< Chromosome observed, here chr is an integer.
 x_min, ##<< Coordinate of the first bp observed.
@@ -324,12 +324,6 @@ coord_max=20000000 ##<< A too big value to be a coord for a nucleosome lower bou
   tf_outs = list()
 	i = 1
   for (sample in samples) {
-		# print(sample$roi$chr)
-		# print(min_nuc_center)
-		# print(max_nuc_center)
-		# print(sample$outputs)
-		# tf_outs[[i]] = filter_tf_outputs(sample$outputs, sample$roi$chr, min_nuc_center, max_nuc_center)
-		# print(tf_outs[[i]])
 		tf_outs[[i]] = sample$outputs
 		tf_outs[[i]] = tf_outs[[i]][order(tf_outs[[i]]$center),]
     indexes[i] = 1
@@ -582,7 +576,8 @@ config=NULL, ##<< GLOBAL config variable
 								llr_score = llr_score_nvecs(list(reads_strain_ref1, reads_strain_ref2))
 								llr_scores = c(llr_scores, llr_score)
 								# Filtering on LOD Score
-								if (llr_score < llr_thres) {
+                # if (llr_score < llr_thres) {
+								if (TRUE) {
 									tmp_nuc = list()
 									# strain_ref1
 									tmp_nuc[[paste("chr_", strain_ref1, sep="")]] = chr
@@ -592,9 +587,6 @@ config=NULL, ##<< GLOBAL config variable
 									tmp_nuc[[paste("sd_", strain_ref1, sep="")]] = signif(sd(reads_strain_ref1),5)
 									tmp_nuc[[paste("nb_reads_", strain_ref1, sep="")]] = length(reads_strain_ref1)
 									tmp_nuc[[paste("index_nuc_", strain_ref1, sep="")]] = index_nuc_strain_ref1
-									# tmp_nuc[[paste("corr1_", strain_ref1, sep="")]] = signif(nuc_strain_ref1$nucs[[1]]$corr,5)
-									# tmp_nuc[[paste("corr2_", strain_ref1, sep="")]] = signif(nuc_strain_ref1$nucs[[2]]$corr,5)
-									# tmp_nuc[[paste("corr3_", strain_ref1, sep="")]] = signif(nuc_strain_ref1$nucs[[3]]$corr,5)
 									# strain_ref2
 									tmp_nuc[[paste("chr_", strain_ref2, sep="")]] = roi_strain_ref2$chr
 									tmp_nuc[[paste("lower_bound_", strain_ref2, sep="")]] = nuc_strain_ref2$lower_bound
@@ -603,14 +595,10 @@ config=NULL, ##<< GLOBAL config variable
 									tmp_nuc[[paste("sd_", strain_ref2, sep="")]] = signif(sd(reads_strain_ref2),5)
 									tmp_nuc[[paste("nb_reads_", strain_ref2, sep="")]] = length(reads_strain_ref2)
 									tmp_nuc[[paste("index_nuc_", strain_ref2, sep="")]] = index_nuc_strain_ref2
-									# tmp_nuc[[paste("corr1_", strain_ref2, sep="")]] = signif(nuc_strain_ref2$nucs[[1]]$corr,5)
-									# tmp_nuc[[paste("corr2_", strain_ref2, sep="")]] = signif(nuc_strain_ref2$nucs[[2]]$corr,5)
-									# tmp_nuc[[paste("corr3_", strain_ref2, sep="")]] = signif(nuc_strain_ref2$nucs[[3]]$corr,5)
 									# common
 									tmp_nuc[["llr_score"]] = signif(llr_score,5)
-									# print(tmp_nuc)
 									common_nuc = dfadd(common_nuc, tmp_nuc)
-								}
+                }
 							}
 						}
 					}
@@ -2045,9 +2033,9 @@ config=NULL ##<< GLOBAL config variable
         new_tmp_y[index_odd] = tmp_y
         new_tmp_x[index_even] = tmp_x_inter
         new_tmp_y[index_even] = tmp_y_inter
-        lines(new_tmp_x , new_tmp_y, lw=2)
+        lines(new_tmp_x , new_tmp_y, lwd=2)
         points(tmp_x, tmp_y, cex=4, pch=16, col="white")
-        points(tmp_x, tmp_y, cex=4, lw=2)
+        points(tmp_x, tmp_y, cex=4, lwd=2)
         text(tmp_x, tmp_y, 1:nrow(tf_nucs))
         if (is.null(config$LEGEND_LOD_POS)) {
           pos = 2
@@ -2148,7 +2136,7 @@ config=NULL ##<< GLOBAL config variable
       common_nuc_results = list()
       common_nuc_results[[paste(combi[1], combi[2], sep="_")]] = aligned_inter_strain_nucs
       unrs = get_unrs(combi, roi, cur_index, wp_maps, fuzzy_maps, common_nuc_results, config = config) 
-      rect(sign(x_min[[1]]) * unrs$lower_bound + shift[[1]], y_min[[1]], sign(x_min[[1]]) * unrs$upper_bound + shift[[1]], y_max[[2]], border=4, lw=10, col=adjustcolor(4, alpha.f = 0.05))        
+      rect(sign(x_min[[1]]) * unrs$lower_bound + shift[[1]], y_min[[1]], sign(x_min[[1]]) * unrs$upper_bound + shift[[1]], y_max[[2]], border=4, lwd=10, col=adjustcolor(4, alpha.f = 0.05))        
     }
 
 	}
