From 881b445ed41f41588be932378795a87100c3d238 Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Thu, 10 Jan 2019 11:02:53 +0100
Subject: [PATCH 01/14] fixed max_pos calculation

---
 bin/1.2_filter_motifs/compareBed_runinfo.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bin/1.2_filter_motifs/compareBed_runinfo.R b/bin/1.2_filter_motifs/compareBed_runinfo.R
index 4888c02..ea6b1a6 100644
--- a/bin/1.2_filter_motifs/compareBed_runinfo.R
+++ b/bin/1.2_filter_motifs/compareBed_runinfo.R
@@ -52,9 +52,10 @@ data_filtered[[7]] <- data_filtered[[3]] - data_filtered[[2]]
 
 # adding column "contains_maxpos", containing flag (0 or 1)
 # max_pos is the position of maximum score of a footprint
+data_filtered[[8]] <- data_filtered[[8]] - data_filtered[[2]]
 data_filtered <- cbind(data_filtered, contains_maxpos = 0)
 data_filtered$contains_maxpos[intersect(which(data_filtered[[2]] <= data_filtered[[8]]), which(data_filtered[[3]] > data_filtered[[8]]))] = 1
-data_filtered[[8]] <- data_filtered[[8]] - data_filtered[[2]]
+data_filtered[[8]] <- data_filtered[[8]] + data_filtered[[2]]
 
 fwrite(data_filtered, output, col.names=FALSE, quote = FALSE, sep = '\t')
 

From b128196a2cf492a838af5940e926d4f6257f115f Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Thu, 10 Jan 2019 11:04:14 +0100
Subject: [PATCH 02/14] correct maxpos calculation

---
 bin/1.2_filter_motifs/compareBed_runinfo.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/1.2_filter_motifs/compareBed_runinfo.R b/bin/1.2_filter_motifs/compareBed_runinfo.R
index ea6b1a6..04b9f87 100644
--- a/bin/1.2_filter_motifs/compareBed_runinfo.R
+++ b/bin/1.2_filter_motifs/compareBed_runinfo.R
@@ -8,7 +8,7 @@
 #             adds a column with a flag "contains_maxpos"
 #             and creates a file with information of the bedtool comparison
 
-# parameters: Parameters are not named. Respect the parameter order.
+# parameters: Parameters are not named, respect the parameter order.
 #             min:            minimum footprint size threshold 
 #             max:            maximum footprint size threshold
 #             input_raw:      unfiltered BED-file

From 5343f6052f151429d2747727a7d2bdbd7ecbf8d0 Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Thu, 10 Jan 2019 12:18:54 +0100
Subject: [PATCH 03/14] fixed for correct contains_maxpos calculation

---
 bin/1.2_filter_motifs/compareBed_runinfo.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bin/1.2_filter_motifs/compareBed_runinfo.R b/bin/1.2_filter_motifs/compareBed_runinfo.R
index 04b9f87..2723fb5 100644
--- a/bin/1.2_filter_motifs/compareBed_runinfo.R
+++ b/bin/1.2_filter_motifs/compareBed_runinfo.R
@@ -52,10 +52,10 @@ data_filtered[[7]] <- data_filtered[[3]] - data_filtered[[2]]
 
 # adding column "contains_maxpos", containing flag (0 or 1)
 # max_pos is the position of maximum score of a footprint
-data_filtered[[8]] <- data_filtered[[8]] - data_filtered[[2]]
+data_filtered[[8]] <- data_filtered[[8]] + data_filtered[[2]]
 data_filtered <- cbind(data_filtered, contains_maxpos = 0)
 data_filtered$contains_maxpos[intersect(which(data_filtered[[2]] <= data_filtered[[8]]), which(data_filtered[[3]] > data_filtered[[8]]))] = 1
-data_filtered[[8]] <- data_filtered[[8]] + data_filtered[[2]]
+data_filtered[[8]] <- data_filtered[[8]] - data_filtered[[2]]
 
 fwrite(data_filtered, output, col.names=FALSE, quote = FALSE, sep = '\t')
 

From 4397f77c6357c4e6aed6b21b4a3c1d1665d1faf9 Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Thu, 10 Jan 2019 14:02:22 +0100
Subject: [PATCH 04/14] script for calculation of absolute max_pos values at
 start

---
 bin/1.2_filter_motifs/abs_max_score.R | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 bin/1.2_filter_motifs/abs_max_score.R

diff --git a/bin/1.2_filter_motifs/abs_max_score.R b/bin/1.2_filter_motifs/abs_max_score.R
new file mode 100644
index 0000000..b6e5de0
--- /dev/null
+++ b/bin/1.2_filter_motifs/abs_max_score.R
@@ -0,0 +1,24 @@
+#!/bin/Rscript
+
+# author: Jannik Hamp
+# email: jannik.hamp@googlemail.com
+
+# desciption: This script gets called by compareBed.sh
+
+# It calculates the absolute position of maximum score of the footprints.
+# This information is later used for an additional flag column in the bed file.
+
+library(data.table)
+args = commandArgs(TRUE)
+file = args[1]
+
+tab = fread(file, sep='\t')
+
+# check if data has less than 9 columns
+if (ncol(tab) < 9) {
+	stop("footprint file has less than 9 columns. exiting.")
+}
+
+tab[[8]] = tab[[2]] + tab[[8]]
+
+fwrite(tab, file, row.names=FALSE, col.names=FALSE, quote=FALSE, sep='\t')

From 9a4c9c1580090d5e8cd8793903bd71c886029caf Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Thu, 10 Jan 2019 14:03:18 +0100
Subject: [PATCH 05/14] added Rscript for maxpos calculation

---
 bin/1.2_filter_motifs/compareBed.sh | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/bin/1.2_filter_motifs/compareBed.sh b/bin/1.2_filter_motifs/compareBed.sh
index 38027f3..86adb6a 100644
--- a/bin/1.2_filter_motifs/compareBed.sh
+++ b/bin/1.2_filter_motifs/compareBed.sh
@@ -10,7 +10,7 @@
 #             For parameter description, run the script without parameters or -h.
 #             The output is a file with the filtered footprints and the log file FilterMotivs.stats
 
-# One R script is used, compareBed_runinfo.R, stored in the same directory.
+# Two R scripts are used, compareBed_runinfo.R and abs_max_score.R, stored in the same directory.
 
 # default parameters
 workdir=$PWD
@@ -181,7 +181,7 @@ cat $data | sed 's/[ \t]*$//' > "$workdir"/filtered.bed
 if [ -d "$motifs" ]
 then
 	# creates an array of all files with bed in its name in the directory $motifs  
-	declare -a motiffiles=(`ls $motifs | grep bed | sed "s|^|$motifs\/|g" | tr '\n' ' ' | sed "s|//|/|g"`)
+	declare -a motiffiles=(`ls $motifs | grep -i '.bed$' | sed "s|^|$motifs\/|g" | tr '\n' ' ' | sed "s|//|/|g"`)
 
 # the else case means, that the motiffiles were passed comma separated with no whitespace.
 else
@@ -219,6 +219,14 @@ if [ $all_empty == true ]
 		exit 1
 fi
 
+#calculate absolute max_score position
+Rscript abs_max_score.R "$workdir"/filtered.bed
+# check if Rscript executed without errors
+if [ $? -gt 0 ] 
+then
+	exit 1
+fi
+
 # comparing unknown footprints with regions of known motifs
 # comparison is done iteratively
 # remove overlapping regions in unknown footprints

From 327dd04e914a16812c4dc25426919f89d7536521 Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Thu, 10 Jan 2019 14:05:52 +0100
Subject: [PATCH 06/14] fixed for correct max_pos calculation after possible
 splitting

a new R script has been added, which calculates the absolut positions first. Here the relative positions are calculated again, after the column with contains_maxpos flags has been created.
---
 bin/1.2_filter_motifs/compareBed_runinfo.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/bin/1.2_filter_motifs/compareBed_runinfo.R b/bin/1.2_filter_motifs/compareBed_runinfo.R
index 2723fb5..075ed56 100644
--- a/bin/1.2_filter_motifs/compareBed_runinfo.R
+++ b/bin/1.2_filter_motifs/compareBed_runinfo.R
@@ -52,7 +52,6 @@ data_filtered[[7]] <- data_filtered[[3]] - data_filtered[[2]]
 
 # adding column "contains_maxpos", containing flag (0 or 1)
 # max_pos is the position of maximum score of a footprint
-data_filtered[[8]] <- data_filtered[[8]] + data_filtered[[2]]
 data_filtered <- cbind(data_filtered, contains_maxpos = 0)
 data_filtered$contains_maxpos[intersect(which(data_filtered[[2]] <= data_filtered[[8]]), which(data_filtered[[3]] > data_filtered[[8]]))] = 1
 data_filtered[[8]] <- data_filtered[[8]] - data_filtered[[2]]

From 20849d51f9fef4e882f43b667c8484a12b6c3abb Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Thu, 10 Jan 2019 14:37:37 +0100
Subject: [PATCH 07/14] forgot $path to start the new Rscript. now fixed

---
 bin/1.2_filter_motifs/compareBed.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/1.2_filter_motifs/compareBed.sh b/bin/1.2_filter_motifs/compareBed.sh
index 86adb6a..1cb3c1b 100644
--- a/bin/1.2_filter_motifs/compareBed.sh
+++ b/bin/1.2_filter_motifs/compareBed.sh
@@ -220,7 +220,7 @@ if [ $all_empty == true ]
 fi
 
 #calculate absolute max_score position
-Rscript abs_max_score.R "$workdir"/filtered.bed
+Rscript $path/abs_max_score.R "$workdir"/filtered.bed
 # check if Rscript executed without errors
 if [ $? -gt 0 ] 
 then

From 7514dfb2759e63ffe082452c7a7a2d002a81de40 Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Fri, 11 Jan 2019 10:36:27 +0100
Subject: [PATCH 08/14] Fixed 1 output value of FilterMotifs.stats output. Flag
 1 ratio was not correct, due to variable naming issue

---
 bin/1.2_filter_motifs/compareBed_runinfo.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/1.2_filter_motifs/compareBed_runinfo.R b/bin/1.2_filter_motifs/compareBed_runinfo.R
index 075ed56..b4f180f 100644
--- a/bin/1.2_filter_motifs/compareBed_runinfo.R
+++ b/bin/1.2_filter_motifs/compareBed_runinfo.R
@@ -74,6 +74,6 @@ loss_nt <- formatC(1 - sum_filtered/sum_data, digits = 2)
 length_data <- formatC(mean(data[[3]]-data[[2]]), digits = 4)
 # mean -ength of footprints after filter
 length_filtered <- formatC(mean(data_filtered[[7]]), digits = 4)
-stats <- data.frame(sum_nt_input = sum_data, sum_nt_filtered = sum_filtered, quotient_of_nt = difference_nt, loss_of_nt = loss_nt, mean_length_input = length_data, mean_length_filtered = length_filtered, flag_1_ratio = length(which(data_filtered$containsMaxpos == 1))/dim(data_filtered)[1])
+stats <- data.frame(sum_nt_input = sum_data, sum_nt_filtered = sum_filtered, quotient_of_nt = difference_nt, loss_of_nt = loss_nt, mean_length_input = length_data, mean_length_filtered = length_filtered, flag_1_ratio = length(which(data_filtered$contains_maxpos == 1))/dim(data_filtered)[1])
 stats <- t(stats)
 write.table(stats, output_stats, col.names = FALSE, quote = FALSE, sep = '\t')

From 6cd8c7fd9f665315bb7d552f706c19aaa9e20129 Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Fri, 11 Jan 2019 11:04:26 +0100
Subject: [PATCH 09/14] check if output ends with .bed

---
 bin/1.2_filter_motifs/compareBed.sh | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/bin/1.2_filter_motifs/compareBed.sh b/bin/1.2_filter_motifs/compareBed.sh
index 1cb3c1b..c50687a 100644
--- a/bin/1.2_filter_motifs/compareBed.sh
+++ b/bin/1.2_filter_motifs/compareBed.sh
@@ -10,7 +10,7 @@
 #             For parameter description, run the script without parameters or -h.
 #             The output is a file with the filtered footprints and the log file FilterMotivs.stats
 
-# Two R scripts are used, compareBed_runinfo.R and abs_max_score.R, stored in the same directory.
+# One R scripts is used, compareBed_runinfo.R, stored in the same directory.
 
 # default parameters
 workdir=$PWD
@@ -173,6 +173,10 @@ then
 	echo "directory $workdir does not exist. Please check parameter -w / --workdir"
 	exit 1
 fi
+if [[ ${output: -4: -1} != '.bed' ]]
+then
+	output=`echo $output | sed "s|$|.bed|g"`
+fi
 
 # remove trailing tabs in footprints
 cat $data | sed 's/[ \t]*$//' > "$workdir"/filtered.bed
@@ -219,14 +223,6 @@ if [ $all_empty == true ]
 		exit 1
 fi
 
-#calculate absolute max_score position
-Rscript $path/abs_max_score.R "$workdir"/filtered.bed
-# check if Rscript executed without errors
-if [ $? -gt 0 ] 
-then
-	exit 1
-fi
-
 # comparing unknown footprints with regions of known motifs
 # comparison is done iteratively
 # remove overlapping regions in unknown footprints
@@ -292,6 +288,7 @@ else
 fi
 
 # add fasta sequences to bed and create fasta file
+out_fasta=`echo $output | sed "s|.bed$|.fasta|g"`
 echo getting sequences from fasta-file
 bedtools getfasta -fi $fasta -bed "$workdir"/filtered_flagged.bed -bedOut >> $output
-bedtools getfasta -name -fi $fasta -bed "$output" -fo "$output".fasta
+bedtools getfasta -name -fi $fasta -bed "$output" -fo "$out_fasta"

From f1a0690387a34f9775567a3b8cf1d005f2d9faca Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Fri, 11 Jan 2019 11:04:39 +0100
Subject: [PATCH 10/14] Delete abs_max_score.R

---
 bin/1.2_filter_motifs/abs_max_score.R | 24 ------------------------
 1 file changed, 24 deletions(-)
 delete mode 100644 bin/1.2_filter_motifs/abs_max_score.R

diff --git a/bin/1.2_filter_motifs/abs_max_score.R b/bin/1.2_filter_motifs/abs_max_score.R
deleted file mode 100644
index b6e5de0..0000000
--- a/bin/1.2_filter_motifs/abs_max_score.R
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/bin/Rscript
-
-# author: Jannik Hamp
-# email: jannik.hamp@googlemail.com
-
-# desciption: This script gets called by compareBed.sh
-
-# It calculates the absolute position of maximum score of the footprints.
-# This information is later used for an additional flag column in the bed file.
-
-library(data.table)
-args = commandArgs(TRUE)
-file = args[1]
-
-tab = fread(file, sep='\t')
-
-# check if data has less than 9 columns
-if (ncol(tab) < 9) {
-	stop("footprint file has less than 9 columns. exiting.")
-}
-
-tab[[8]] = tab[[2]] + tab[[8]]
-
-fwrite(tab, file, row.names=FALSE, col.names=FALSE, quote=FALSE, sep='\t')

From 9144c1f9261a30f72b9a5af639fbff923697ed59 Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Fri, 11 Jan 2019 11:05:17 +0100
Subject: [PATCH 11/14] max_pos calculation is done in one Rscript

---
 bin/1.2_filter_motifs/compareBed_runinfo.R | 26 ++++++++++++++--------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/bin/1.2_filter_motifs/compareBed_runinfo.R b/bin/1.2_filter_motifs/compareBed_runinfo.R
index b4f180f..f45b4a0 100644
--- a/bin/1.2_filter_motifs/compareBed_runinfo.R
+++ b/bin/1.2_filter_motifs/compareBed_runinfo.R
@@ -27,12 +27,29 @@ output <- args[5]
 output_stats <- args[6]
 
 data_filtered <- fread(input_filtered, sep='\t')
+# data is the initial data before any comparisons have been done (-d parameter of compareBed.sh)
+data <- fread(input_raw, sep='\t')
 
 # check if data has less than 9 columns
 if (ncol(data_filtered) < 9) {
 	stop("footprint file has less than 9 columns. exiting.")
 }
 
+# define needed col names
+names(data)[2] <- "old_start"
+names(data_filtered)[c(2, 3, 8)] <- c("start", "end", "max_pos")
+# save corect column order
+correct_order <- c(names(data_filtered), names(data)[2])
+# compute new maxpos (relevant for splitted footprints)
+data_filtered <- merge(x=data_filtered, y=data[,c(2,4)], by.x=names(data_filtered)[4], by.y=names(data)[4], all.x=TRUE, all.y=FALSE, sort=FALSE)
+data_filtered <- data_filtered[, correct_order, with = FALSE]
+data_filtered[, max_pos := max_pos + old_start - start][, old_start := NULL]
+
+# adding column "contains_maxpos", containing flag (0 or 1)
+# max_pos is the position of maximum score of a footprint
+data_filtered <- cbind(data_filtered, contains_maxpos = 0)
+data_filtered[max_pos >= 0 & start + max_pos <= end, contains_maxpos := 1]
+
 # remove sequences that are smaller than minimum (parameter)
 # remove sequences that are longer than maximum (parameter)
 data_filtered <- data_filtered[which(data_filtered[[3]] - data_filtered[[2]] >= min),]
@@ -50,17 +67,8 @@ data_filtered[match(duplicants, names), name := paste0(name,".0")]
 # recalculate length of sequences
 data_filtered[[7]] <- data_filtered[[3]] - data_filtered[[2]]
 
-# adding column "contains_maxpos", containing flag (0 or 1)
-# max_pos is the position of maximum score of a footprint
-data_filtered <- cbind(data_filtered, contains_maxpos = 0)
-data_filtered$contains_maxpos[intersect(which(data_filtered[[2]] <= data_filtered[[8]]), which(data_filtered[[3]] > data_filtered[[8]]))] = 1
-data_filtered[[8]] <- data_filtered[[8]] - data_filtered[[2]]
-
 fwrite(data_filtered, output, col.names=FALSE, quote = FALSE, sep = '\t')
 
-# data is the initial data before any comparisons have been done (-d parameter of compareBed.sh)
-data <- fread(input_raw, sep='\t')
-
 # some statistics about the bedtool comparisons are stored in FilterMotifs.stats
 # number of nucleotides input
 sum_data <- sum(data[[3]]-data[[2]])

From 8ed11f2a2d8cec121a8ed87e69229024798b0c37 Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Fri, 11 Jan 2019 11:07:26 +0100
Subject: [PATCH 12/14] documentation

---
 bin/1.2_filter_motifs/compareBed.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/1.2_filter_motifs/compareBed.sh b/bin/1.2_filter_motifs/compareBed.sh
index c50687a..5aa5f45 100644
--- a/bin/1.2_filter_motifs/compareBed.sh
+++ b/bin/1.2_filter_motifs/compareBed.sh
@@ -120,7 +120,7 @@ then
 	echo "                                  default is the current directory"
 	echo "              -min --min          minimum size of footprints; default is 10"
 	echo "              -max --max          maximum size of footprints; default is 80"
-	echo "              -o   --output       output path/file ; default dir current directory and filename is newMotifs.bed and newMotifs.bed.fasta"
+	echo "              -o   --output       output path/file ; default dir current directory and filename is newMotifs.bed and newMotifs.fasta"
 	echo "              -h --help           shows this help message"
 	exit 0
 fi

From aa306f9c8b162ad1d9e8e532f0a8f5ffffedb015 Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Fri, 11 Jan 2019 11:23:23 +0100
Subject: [PATCH 13/14] changed stats file name to compareBed.stats

---
 bin/1.2_filter_motifs/compareBed.sh | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/bin/1.2_filter_motifs/compareBed.sh b/bin/1.2_filter_motifs/compareBed.sh
index 5aa5f45..d358865 100644
--- a/bin/1.2_filter_motifs/compareBed.sh
+++ b/bin/1.2_filter_motifs/compareBed.sh
@@ -8,7 +8,7 @@
 #             BED-format. 
 
 #             For parameter description, run the script without parameters or -h.
-#             The output is a file with the filtered footprints and the log file FilterMotivs.stats
+#             The output is a file with the filtered footprints and the log file compareBed.stats
 
 # One R scripts is used, compareBed_runinfo.R, stored in the same directory.
 
@@ -120,7 +120,7 @@ then
 	echo "                                  default is the current directory"
 	echo "              -min --min          minimum size of footprints; default is 10"
 	echo "              -max --max          maximum size of footprints; default is 80"
-	echo "              -o   --output       output path/file ; default dir current directory and filename is newMotifs.bed and newMotifs.fasta"
+	echo "              -o   --output       output path/file ; default dir current directory and filename is newMotifs.bed and newMotifs.bed.fasta"
 	echo "              -h --help           shows this help message"
 	exit 0
 fi
@@ -260,7 +260,7 @@ fi
 
 # remove short/long motivs, make unique ids (relevant for some splitted tfbs from subtract) and handle maxScorePosition
 # also creates a small output file with information about the comparison
-Rscript $path/compareBed_runinfo.R $min $max $data "$workdir"/filtered.bed "$workdir"/filtered_flagged.bed "$workdir"/FilterMotifs.stats
+Rscript $path/compareBed_runinfo.R $min $max $data "$workdir"/filtered.bed "$workdir"/filtered_flagged.bed "$workdir"/compareBed.stats
 # check if Rscript executed without errors
 if [ $? -gt 0 ] 
 then
@@ -277,14 +277,14 @@ then
 	fp_initial=`expr $fp_initial - 1`
 	fp_final=`cat "$workdir"/filtered.bed | wc -l`
 	fp_final=`expr $fp_final - 1`
-	echo $fp_initial | sed 's/^/initial number of footprints: /g' >> "$workdir"/FilterMotifs.stats
-	echo $fp_final | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/FilterMotifs.stats
+	echo $fp_initial | sed 's/^/initial number of footprints: /g' >> "$workdir"/compareBed.stats
+	echo $fp_final | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
 else
 	# output will be overwritten if it exists
 	rm -f $output
 	# add some final values to the log file
-	cat $data | wc -l | sed 's/^/initial number of footprints: /g' >> "$workdir"/FilterMotifs.stats
-	cat "$workdir"/filtered.bed | wc -l | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/FilterMotifs.stats
+	cat $data | wc -l | sed 's/^/initial number of footprints: /g' >> "$workdir"/compareBed.stats
+	cat "$workdir"/filtered.bed | wc -l | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
 fi
 
 # add fasta sequences to bed and create fasta file

From cb16c3cb842d87eca8bf055a4e6c7442b9077021 Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Fri, 11 Jan 2019 11:24:27 +0100
Subject: [PATCH 14/14] changed name of output compareBed.stats in description

---
 bin/1.2_filter_motifs/compareBed_runinfo.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/1.2_filter_motifs/compareBed_runinfo.R b/bin/1.2_filter_motifs/compareBed_runinfo.R
index f45b4a0..12a73a6 100644
--- a/bin/1.2_filter_motifs/compareBed_runinfo.R
+++ b/bin/1.2_filter_motifs/compareBed_runinfo.R
@@ -69,7 +69,7 @@ data_filtered[[7]] <- data_filtered[[3]] - data_filtered[[2]]
 
 fwrite(data_filtered, output, col.names=FALSE, quote = FALSE, sep = '\t')
 
-# some statistics about the bedtool comparisons are stored in FilterMotifs.stats
+# some statistics about the bedtool comparisons are stored in compareBed.stats
 # number of nucleotides input
 sum_data <- sum(data[[3]]-data[[2]])
 # number of nucleotides after filter