diff --git a/referenceC/MANUAL_v1.4.pdf b/reference_C/MANUAL_v1.4.pdf
similarity index 100%
rename from referenceC/MANUAL_v1.4.pdf
rename to reference_C/MANUAL_v1.4.pdf
diff --git a/referenceC/MANUAL_v1.4.tex b/reference_C/MANUAL_v1.4.tex
similarity index 100%
rename from referenceC/MANUAL_v1.4.tex
rename to reference_C/MANUAL_v1.4.tex
diff --git a/referenceC/NGS2.sh b/reference_C/NGS2.sh
similarity index 100%
rename from referenceC/NGS2.sh
rename to reference_C/NGS2.sh
diff --git a/referenceC/PEAKY.R b/reference_C/PEAKY.R
similarity index 100%
rename from referenceC/PEAKY.R
rename to reference_C/PEAKY.R
diff --git a/referenceC/bedGraphToBigWig b/reference_C/bedGraphToBigWig
similarity index 100%
rename from referenceC/bedGraphToBigWig
rename to reference_C/bedGraphToBigWig
diff --git a/referenceC/combineReads.c b/reference_C/combineReads.c
similarity index 100%
rename from referenceC/combineReads.c
rename to reference_C/combineReads.c
diff --git a/referenceC/combineReads.h b/reference_C/combineReads.h
similarity index 100%
rename from referenceC/combineReads.h
rename to reference_C/combineReads.h
diff --git a/referenceC/complementReverse.c b/reference_C/complementReverse.c
similarity index 100%
rename from referenceC/complementReverse.c
rename to reference_C/complementReverse.c
diff --git a/referenceC/complementReverse.h b/reference_C/complementReverse.h
similarity index 100%
rename from referenceC/complementReverse.h
rename to reference_C/complementReverse.h
diff --git a/referenceC/extend.c b/reference_C/extend.c
similarity index 100%
rename from referenceC/extend.c
rename to reference_C/extend.c
diff --git a/referenceC/graphics.sh b/reference_C/graphics.sh
similarity index 100%
rename from referenceC/graphics.sh
rename to reference_C/graphics.sh
diff --git a/referenceC/make_hg19.sh b/reference_C/make_hg19.sh
similarity index 100%
rename from referenceC/make_hg19.sh
rename to reference_C/make_hg19.sh
diff --git a/referenceC/new.c b/reference_C/new.c
similarity index 98%
rename from referenceC/new.c
rename to reference_C/new.c
index 092faa7..c43de19 100644
--- a/referenceC/new.c
+++ b/reference_C/new.c
@@ -20,7 +20,7 @@
 
 #define PACKAGE "ICECap"
 #define VERSION "0.01"
-#define CHROMOSOMES 22
+#define CHROMOSOMES 25
 #define WIN_SHIFT1 1
 #define RESOLUTION 1000
 
@@ -245,7 +245,7 @@ number_for_key(char *key)
 	  }
 sprintf(zom,"%d",SCALE);
 sprintf(wind,"%d",window);
-sprintf(stamp,concat(concat(concat("/NewAnalysis_Z",zom),"_W"),wind)); 
+sprintf(stamp,concat(concat(concat("/Analysis_Z",zom),"_W"),wind)); 
     
 
  init(lane,folder,folderN,PATHBOWTIE,chrom_start,chrom_end,stamp,stamp2,stats);
@@ -335,7 +335,7 @@ printf("\n %d Chromosomes will be considered \n",chrom_end);
  
 if(strlen(folderN)==0){folderN=folder; }else{ sprintf(zom,"%d",SCALE);
 
-      sprintf(stamp,concat(concat(concat("/NewAnalysis_Z",zom),"_W"),wind));
+      sprintf(stamp,concat(concat(concat("/Analysis_Z",zom),"_W"),wind));
       mkdir(concat(concat(folder,lane),stamp),0777); mkdir(concat(concat(concat(concat(folder,lane),stamp),"/weights"),stamp2),0777);
       mkdir(concat(concat(concat(concat(concat(folder,lane),stamp),"/"),stats),stamp2),0777);
       mkdir(concat(concat(concat(concat(concat(concat(folder,lane),stamp),"/"),stats),stamp2),"/fdr"),0777);
@@ -691,8 +691,10 @@ fclose(fout6);
 FILE *tads= fopen(concat(concat(concat(concat(outdir,lane),"_Z"),zom),".tad"), "w+");
 FILE *peakY = fopen(concat(concat(concat(concat(outdir,lane),"_Z"),zom),".pkY"), "w+");
 FILE *peakY2 = fopen(concat(concat(concat(concat(outdir,lane),"_Z"),zom),".cool"), "w+");
+
 FILE *gff;
- FILE *peakC; 
+FILE *peakC; 
+
 FILE *wig= fopen(concat(concat(concat(concat(outdir,lane),"_Z"),zom),".wig"), "w+");
 
 pchic=0;
@@ -708,7 +710,8 @@ sprintf(sbait,"%d",i);
 if(strcasecmp(stringarray[i],"")!=0){sprintf(sbait,"%s",stringarray[i]);}
 
 FILE *peakC = fopen(concat(concat(concat(concat(concat(concat(outdir2,lane),"_BAIT_"),sbait),"_Z"),zom),".pkC"), "w+");
-FILE *gff = fopen(concat(concat(concat(concat(concat(concat(outdir2,lane),"_BAIT_"),sbait),"_Z"),zom),".gff"), "w+");
+FILE *gff = fopen(concat(concat(concat(concat(concat(outdir2,lane),"_BAIT_"),sbait),"_Z1"),".gff"), "w+");
+
 
 if(pchic==1){
 }else{
@@ -750,7 +753,7 @@ fprintf(tads,"%d\t",hic[i][j]);
 fdist=100000000;}
 if(hic[i][j]>0){
 if(j>=i){fprintf(peakY2,"%d\t%d\t%d\n",i,j,hic[i][j]);}
-printf("BOH: %d\t%d\t%d\t%d\n",i,j,chrombait[i],chrombait[j]);
+/* printf("BOH: %d\t%d\t%d\t%d\n",i,j,chrombait[i],chrombait[j]); */
 if(chrombait[i]!=chromgrid[j]){
 fprintf(peakY,"%d\t%d\t%d\t%f\t%f\t%f\n",totfragments[chrombait[i]-1]+cgrid(chrombait[i],baitpoints[chrombait[i]][i-totbaits[chrombait[i]-1]]+(1-pchic)*RESOLUTION,gp,gridpoints),j,hic[i][j],fdist,1,1);
 }else{
@@ -763,6 +766,9 @@ fprintf(peakY,"%d\t%d\t%d\t%f\t%f\t%f\n",totfragments[chrombait[i]-1]+cgrid(chro
 }
 }
 }
+if(pchic==1){
+if(hic[i][j]!=0){fprintf(gff,"%s\tICE\t%s\t%d\t%d\t%d\t+\t0\t.\n",record[chromgrid[j]].name_chromosome,sbait,gridpoints[chromgrid[j]][j-(totfragments[chromgrid[j]-1]+1)],gridpoints[chromgrid[j]][j-(totfragments[chromgrid[j]-1])],hic[i][j]);}
+}
 }
 
 fclose(peakC);
@@ -818,7 +824,7 @@ sprintf(command,"sed -i 's/chr//' %s",concat(concat(outdir,lane),".tsv"));
 system(command);
 printf("%s\n",command);
 
-sprintf(command,"R --vanilla < %sPEAKY.R --args %s %s %s %s %d ",folderrefC,outdir,concat(concat(concat(concat(outdir,lane),"_Z"),zom),".pkY"),concat(outdir,"/bins/"),concat(concat(outdir,lane),".tsv"),window);
+sprintf(command,"R --no-save < %sPEAKY.R --args %s %s %s %s %d ",folderrefC,outdir,concat(concat(concat(concat(outdir,lane),"_Z"),zom),".pkY"),concat(outdir,"/bins/"),concat(concat(outdir,lane),".tsv"),window);
 printf("%s\n",command);
 system(command);
 
diff --git a/referenceC/new2.c b/reference_C/new2.c
similarity index 100%
rename from referenceC/new2.c
rename to reference_C/new2.c
diff --git a/referenceC/new3.c b/reference_C/new3.c
similarity index 100%
rename from referenceC/new3.c
rename to reference_C/new3.c
diff --git a/referenceC/parallel b/reference_C/parallel
similarity index 100%
rename from referenceC/parallel
rename to reference_C/parallel
diff --git a/referenceC/plot.c b/reference_C/plot.c
similarity index 100%
rename from referenceC/plot.c
rename to reference_C/plot.c
diff --git a/referenceC/plot_mapping_portion.R b/reference_C/plot_mapping_portion.R
similarity index 100%
rename from referenceC/plot_mapping_portion.R
rename to reference_C/plot_mapping_portion.R
diff --git a/referenceC/plot_mapping_portion2.R b/reference_C/plot_mapping_portion2.R
similarity index 100%
rename from referenceC/plot_mapping_portion2.R
rename to reference_C/plot_mapping_portion2.R
diff --git a/referenceC/plot_pairing_portion.R b/reference_C/plot_pairing_portion.R
similarity index 100%
rename from referenceC/plot_pairing_portion.R
rename to reference_C/plot_pairing_portion.R
diff --git a/referenceC/plot_pairing_portion2.R b/reference_C/plot_pairing_portion2.R
similarity index 100%
rename from referenceC/plot_pairing_portion2.R
rename to reference_C/plot_pairing_portion2.R
diff --git a/referenceC/shiftrev.c b/reference_C/shiftrev.c
similarity index 97%
rename from referenceC/shiftrev.c
rename to reference_C/shiftrev.c
index b1183af..b3882e2 100644
--- a/referenceC/shiftrev.c
+++ b/reference_C/shiftrev.c
@@ -1,6 +1,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
+#include <ctype.h>
 
 #define LINE_MAX 0x4000
 
@@ -76,9 +77,9 @@ if(strncmp(vflag[i],"16",2)==0){
         while(*c!=0)
             {
             char* p2;
-                if(!isdigit(*c)) {       fprintf(stderr,"bad cigar string: %s\n",*cigar); return 0; }
+                if(!isdigit(*c)) {       fprintf(stderr,"bad cigar string: %s\n",cigar); return 0; }
             int n=strtol(c,&p2,10);
-                if(n<1){                 fprintf(stderr,"bad cigar string: %s\n",*cigar); return 0; }
+                if(n<1){                 fprintf(stderr,"bad cigar string: %s\n",cigar); return 0; }
                 switch(*p2)
                 {
                 case 'M':{ while(n>0) { icount++; --n; } break; }
@@ -97,9 +98,9 @@ if(strncmp(vflag[j],"16",2)==0){
         while(*c!=0)
             {
             char* p2;
-                if(!isdigit(*c)) {       fprintf(stderr,"bad cigar string: %s\n",*cigar); return 0; }
+                if(!isdigit(*c)) {       fprintf(stderr,"bad cigar string: %s\n",cigar); return 0; }
             int n=strtol(c,&p2,10);
-                if(n<1){                fprintf(stderr,"bad cigar string: %s\n",*cigar); return 0; }
+                if(n<1){                fprintf(stderr,"bad cigar string: %s\n",cigar); return 0; }
                 switch(*p2)
                 {
                 case 'M':{ while(n>0) { jcount++; --n; } break; }
diff --git a/referenceC/t.c b/reference_C/t.c
similarity index 100%
rename from referenceC/t.c
rename to reference_C/t.c
diff --git a/referenceC/test b/reference_C/test
similarity index 100%
rename from referenceC/test
rename to reference_C/test
diff --git a/referenceC/trim_galore b/reference_C/trim_galore
similarity index 98%
rename from referenceC/trim_galore
rename to reference_C/trim_galore
index 1dfbb28..9fb964c 100644
--- a/referenceC/trim_galore
+++ b/reference_C/trim_galore
@@ -44,7 +44,7 @@ file_sanity_check($filenames[0]);
 
 ########################################################################
 
-my $path_to_fastqc = '/usr/bin/fastqc';
+my $path_to_fastqc = '/well/jknight/software/rescomp/bin/fastqc';
 
 # Before we start let's have quick look if Cutadapt seems to be working with the path information provided
 # To change the path to Cutadapt use --path_to_cutadapt /full/path/to/the/Cutadapt/executable
@@ -54,7 +54,7 @@ if(defined $path_to_cutadapt){
   # we'll simply use this
 }
 else{
-  $path_to_cutadapt = '/usr/people/whgu0738/.local/bin/cutadapt'; # default, assuming it is in the PATH
+  $path_to_cutadapt = '/apps/well/python/2.7.11/bin/cutadapt'; # default, assuming it is in the PATH
   warn "Path to Cutadapt set as: '$path_to_cutadapt' (default)\n";
 }
 my $cutadapt_version;
@@ -338,7 +338,7 @@ sub trim{
 	  warn "  >>> Now performing adaptive quality trimming with a Phred-score cutoff of: $cutoff <<<\n\n";
 	  sleep (1);
 	  
-	  open (QUAL,"$path_to_cutadapt -e $error_rate -q $cutoff -a X $filename |") or die "Can't open pipe to Cutadapt: $!";
+	  open (QUAL,"$path_to_cutadapt -f fastq -e $error_rate -q $cutoff -a X $filename |") or die "Can't open pipe to Cutadapt: $!";
 
 	  my $qual_count = 0;
 	  
@@ -417,19 +417,19 @@ sub trim{
 	  if ( scalar(@filenames)%2 == 0){ # this is read 1 of a pair
 	      warn "\n  >>> Now performing adapter trimming for the adapter sequence: '$adapter' from file $temp <<< \n";
 	      sleep (1);
-	      $pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
+	      $pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -f fastq -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
 	  }
 	  else{                            # this is read 2 of a pair
 	      warn "\n  >>> Now performing adapter trimming for the adapter sequence: '$a2' from file $temp <<< \n";
 	      sleep (1);
-	      $pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -e $error_rate -O $stringency -a $a2 $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
+	      $pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -f fastq -e $error_rate -O $stringency -a $a2 $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
 	  }
       }
       ### Using the same adapter for both read 1 and read 2
       else{
 	  warn "\n  >>> Now performing adapter trimming for the adapter sequence: '$adapter' from file $temp <<< \n";
 	  sleep (3);
-	  $pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
+	  $pid = open3 (\*WRITER, \*TRIM, \*ERROR,"$path_to_cutadapt -f fastq -e $error_rate -O $stringency -a $adapter $output_dir$temp") or die "Failed to launch Cutadapt: $!\n";
       }
       
       close WRITER or die $!; # not needed
@@ -587,19 +587,19 @@ sub trim{
 	  if ( scalar(@filenames)%2 == 0){ # this is read 1 of a pair
 	      warn "\n  >>> Now performing quality (cutoff $cutoff) and adapter trimming in a single pass for the adapter sequence: '$adapter' from file $filename <<< \n";
 	      sleep (1);
-	      $pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt  -e $error_rate -q $cutoff -O $stringency $trim_n -a $adapter $filename") or die "Failed to launch Cutadapt: $!";
+	      $pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -f fastq -e $error_rate -q $cutoff -O $stringency $trim_n -a $adapter $filename") or die "Failed to launch Cutadapt: $!";
 	  }
 	  else{                            # this is read 2 of a pair
 	      warn "\n  >>> Now performing quality (cutoff $cutoff) and adapter trimming in a single pass for the adapter sequence: '$a2' from file $filename <<< \n";
 	      sleep (1);
-	      $pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt  -e $error_rate -q $cutoff -O $stringency $trim_n -a $a2 $filename") or die "Failed to launch Cutadapt: $!";
+	      $pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -f fastq -e $error_rate -q $cutoff -O $stringency $trim_n -a $a2 $filename") or die "Failed to launch Cutadapt: $!";
 	  }
       }
       ### Using the same adapter for both read 1 and read 2
       else{
 	  warn "\n  >>> Now performing quality (cutoff $cutoff) and adapter trimming in a single pass for the adapter sequence: '$adapter' from file $filename <<< \n";
 	  sleep (1);
-	  $pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt  -e $error_rate -q $cutoff -O $stringency $trim_n -a $adapter $filename") or die "Failed to launch Cutadapt: $!";
+	  $pid = open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -f fastq -e $error_rate -q $cutoff -O $stringency $trim_n -a $adapter $filename") or die "Failed to launch Cutadapt: $!";
       }
       
       close WRITER or die $!; # not needed
diff --git a/referenceC/util_sort b/reference_C/util_sort
similarity index 100%
rename from referenceC/util_sort
rename to reference_C/util_sort
diff --git a/referenceC/utilities.h b/reference_C/utilities.h
similarity index 100%
rename from referenceC/utilities.h
rename to reference_C/utilities.h
diff --git a/referenceC/utilities2.c b/reference_C/utilities2.c
similarity index 100%
rename from referenceC/utilities2.c
rename to reference_C/utilities2.c
diff --git a/referenceC/zlib.h b/reference_C/zlib.h
similarity index 100%
rename from referenceC/zlib.h
rename to reference_C/zlib.h