diff --git a/2-generate_gaps/extract_gaps.py b/2-generate_gaps/extract_gaps.py
index 416d547..06fff5a 100644
--- a/2-generate_gaps/extract_gaps.py
+++ b/2-generate_gaps/extract_gaps.py
@@ -271,7 +271,7 @@ def interval_merge(intervals):
 # splitting up the reference genome into the gaps 
 ########################################################
 
-fasta_fn = open(sys.argv[2]) 
+fasta_fn = open(sys.argv[2], "r") 
 output_fn = open(sys.argv[4], "w") 
 
 gap_offset = 0 
diff --git a/4-extract_reads/extract_reads.sh b/4-extract_reads/extract_reads.sh
index 97dab70..69f49e2 100644
--- a/4-extract_reads/extract_reads.sh
+++ b/4-extract_reads/extract_reads.sh
@@ -4,5 +4,15 @@ READ_BAM_FILE=$1
 BED_FILE=$2
 READSIZE=$3
 
-awk -v bam_file="$READ_BAM_FILE" -v read_size="${READSIZE}M" '{cmd="samtools view -h "bam_file" " $1":"$2"-"$3" | convert2bed --input=sam -"; while(( cmd | getline result ) > 0 ){split(result, array, "\t"); if(array[2] >= ($2-1) && array[3] <= ($3-1) && (array[5] <= 10 || array[8] != read_size) ){if(and(array[7], 64)){print array[4]".1" "\t" array[2] "\t" array[3] "\t" array[1] "\t" array[5] "\t" array[8];}else if(and(array[7], 128)){print array[4]".2" "\t" array[2] "\t" array[3] "\t" array[1] "\t" array[5] "\t" array[8];}else{print array[4] "\t" array[2] "\t" array[3] "\t" array[1] "\t" array[5] "\t" array[8];}}} close(cmd);}' ${BED_FILE} | sort -uk1,1
+awk -v bam_file="$READ_BAM_FILE" -v read_size="${READSIZE}M" \
+'{cmd="samtools view -h "bam_file" " $1":"$2"-"$3" | convert2bed --input=sam -"; \
+while(( cmd | getline result ) > 0 ){\
+    split(result, array, "\t"); \
+    if(array[2] >= ($2-1) && array[3] <= ($3-1) && (array[5] <= 10 || array[8] != read_size) ){\
+        if(and(array[7], 64)){print array[4]".1" "\t" array[2] "\t" array[3] "\t" array[1] "\t" array[5] "\t" array[8];}\
+        else if(and(array[7], 128)){print array[4]".2" "\t" array[2] "\t" array[3] "\t" array[1] "\t" array[5] "\t" array[8];}\
+        else{print array[4] "\t" array[2] "\t" array[3] "\t" array[1] "\t" array[5] "\t" array[8];}\
+    }\
+} \
+close(cmd);}' ${BED_FILE} | sort -uk1,1
 
diff --git a/4-extract_reads/parallel_extract_reads.sh b/4-extract_reads/parallel_extract_reads.sh
new file mode 100644
index 0000000..16f0759
--- /dev/null
+++ b/4-extract_reads/parallel_extract_reads.sh
@@ -0,0 +1,22 @@
+#!/bin/bash
+# Need GNU parallel
+
+module load parallel
+source $(which env_parallel.bash)
+
+#variables to change are:
+#{BED_FILES_FOLDER}
+#{READ_BAM_FILE}
+#{EXTRACT_READS_SCRIPT}
+#{NUM_FILES}
+#{THREAD}
+
+FILES=({BED_FILES_FOLDER}/*.bed)
+BED_FILE=${FILES[${SLURM_ARRAY_TASK_ID}]}
+OUT_READS=$(echo ${BED_FILE}.reads)
+
+# Check the parallel command first 
+env_parallel -j3 -k --dryrun /usr/bin/time -v -p -o "${OUT_READS}.time" bash {EXTRACT_READS_SCRIPT} {READ_BAM_FILE} {1} {READSIZE} '>' {2} ::: $(echo ${FILES[@]}) ::: $(echo ${FILES[@]} | awk '{for(i=1;i<=NF;i++) printf $i".reads ";}')
+env_parallel -j3 -k --progress /usr/bin/time -v -p -o "${OUT_READS}.time" bash {EXTRACT_READS_SCRIPT} {READ_BAM_FILE} {1} {READSIZE} '>' {2} ::: $(echo ${FILES[@]}) ::: $(echo ${FILES[@]} | awk '{for(i=1;i<=NF;i++) printf $i".reads ";}')
+
+module unload parallel
diff --git a/4-extract_reads/slurm_extract_reads.sh b/4-extract_reads/slurm_extract_reads.sh
index 62dc93e..bf5d4ff 100644
--- a/4-extract_reads/slurm_extract_reads.sh
+++ b/4-extract_reads/slurm_extract_reads.sh
@@ -18,6 +18,11 @@ FILES=({BED_FILES_FOLDER}/*.bed)
 BED_FILE=${FILES[${SLURM_ARRAY_TASK_ID}]}
 OUT_READS=$(echo ${BED_FILE}.reads)
 
-srun --output=${OUT_READS} /usr/bin/time -v -p -o "${OUT_READS}.time" sh {EXTRACT_READS_SCRIPT} {READ_BAM_FILE} ${BED_FILE} {READSIZE}
+srun --output=${OUT_READS} \
+/usr/bin/time -v -p -o "${OUT_READS}.time" \
+bash {EXTRACT_READS_SCRIPT} \
+{READ_BAM_FILE} \
+${BED_FILE} \
+{READSIZE}
 sleep 1
 
diff --git a/run_pipeline.sh b/run_pipeline.sh
index a93c6e7..8d9b650 100644
--- a/run_pipeline.sh
+++ b/run_pipeline.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 
 SRCFOLDER=$1
 #ref folders containing ref file:
@@ -11,29 +11,298 @@ READ_BAM=$6
 FIRST_PAIR=$7
 SECOND_PAIR=$8
 OUTPUT=$9
-THREAD=$10
-
-mkdir -p "${OUTPUT}/"
-#sh "${SRCFOLDER}/1-generate_chain/chain_install.sh" "${OUTPUT}/"
-#sh "${SRCFOLDER}/1-generate_chain/sample_run.sh" "${OLDREF}" "${NEWREF}" "${OUTPUT}/" "${SRCFOLDER}/1-generate_chain/chain_generate.sh" ${SEQ_FILE_EXT} "${OUTPUT}/"
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; /usr/bin/time -v -p -o "${OUTPUT}/${chr}_extracted_gaps.fa.time" python "${SRCFOLDER}/2-generate_gaps/extract_gaps.py" $i "${NEWREF}/$chr.${SEQ_FILE_EXT}" ${READSIZE} "${OUTPUT}/${chr}_extracted_gaps.fa"; done
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; /usr/bin/time -v -p -o "${OUTPUT}/${chr}_kmer_gaps.fasta.time" python "${SRCFOLDER}/2-generate_gaps/gaps_to_fasta.py" "${OUTPUT}/${chr}_extracted_gaps.fa" ${READSIZE} "${OUTPUT}/${chr}_kmer_gaps.fasta" 10; done
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; sh "${SRCFOLDER}/3-align_gaps/align_gaps.sh" "${OLDREF}/${chr}.${SEQ_FILE_EXT}" "${OUTPUT}/${chr}_kmer_gaps.fasta" ${THREAD} "${OUTPUT}/${chr}_aligned_gaps"; done
-mkdir "${OUTPUT}/bedfiles";
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; mkdir -p "${OUTPUT}/bedfiles/${chr}/"; /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/extract_regions.time" sh "${SRCFOLDER}/4-extract_reads/extract_regions.sh" "${OUTPUT}/${chr}_aligned_gaps.bam" "${OUTPUT}/bedfiles/${chr}/"; done
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; num_of_files=`ls -l ${OUTPUT}/bedfiles/${chr}/*.bed | wc -l`; sed_bed_files=$(echo ${OUTPUT}\/bedfiles\/${chr}/ | sed 's/\//\\\//g'); sed_read_scripts=$(echo ${SRCFOLDER}\/4-extract_reads\/extract_reads.sh | sed 's/\//\\\//g'); sed_read_bam=$(echo $READ_BAM | sed 's/\//\\\//g'); cat "${SRCFOLDER}/4-extract_reads/slurm_extract_reads.sh" | sed "s/{NUM_FILES}/$num_of_files/g" | sed "s/{THREAD}/$THREAD/g" | sed "s/{BED_FILES_FOLDER}/$sed_bed_files/g" | sed "s/{EXTRACT_READS_SCRIPT}/$sed_read_scripts/g" | sed "s/{READ_BAM_FILE}/$sed_read_bam/g" | sed "s/{READSIZE}/$READSIZE/g" > "${OUTPUT}/${chr}_samplejob.sh"; done
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; sbatch --wait "${OUTPUT}/${chr}_samplejob.sh"; done
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/merged_${chr}.bed.time" cat "${OUTPUT}/bedfiles/${chr}/"*.bed | sortBed -i - | mergeBed -i - > "${OUTPUT}/bedfiles/${chr}/merged_${chr}.bed"; done
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; mkdir -p "${OUTPUT}/bedfiles/${chr}/retired_bed/"; mkdir -p "${OUTPUT}/bedfiles/${chr}/constant_bed/"; done
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_regions.bed.time" python "${SRCFOLDER}/4-extract_reads/get_retired_regions.py" ${READSIZE} "${OUTPUT}/bedfiles/${chr}/merged_${chr}.bed" $i "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_regions.bed"; done
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_reads.bed.time" sh "${SRCFOLDER}/4-extract_reads/extract_reads_noprune.sh" ${READ_BAM} "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_regions.bed" > "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_reads.bed"; done
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; mkdir -p "${OUTPUT}/bedfiles/${chr}/reads/";  cat "${OUTPUT}/bedfiles/${chr}/"*.reads "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_reads.bed" > "${OUTPUT}/bedfiles/${chr}/updated_and_retired_reads.bed"; /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/extract_sequences_full.time" sh "${SRCFOLDER}/4-extract_reads/extract_sequence.sh" ${FIRST_PAIR} ${SECOND_PAIR} "${OUTPUT}/bedfiles/${chr}/updated_and_retired_reads.bed" "${OUTPUT}/bedfiles/${chr}/reads/"; done
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`;  /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/reads/paired_reads.time" bwa mem -M -t $THREAD "${NEWREF}/$chr.${SEQ_FILE_EXT}" "${OUTPUT}/bedfiles/${chr}/reads/reads_1.fastq" "${OUTPUT}/bedfiles/${chr}/reads/reads_2.fastq" | samtools view -h -F4 | samtools sort -m 16g -l0 > "${OUTPUT}/bedfiles/${chr}/reads/paired_reads.bam"; done
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`;  /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/reads/singletons_reads.time" bwa mem -M -t $THREAD "${NEWREF}/$chr.${SEQ_FILE_EXT}" "${OUTPUT}/bedfiles/${chr}/reads/singletons.fastq" | samtools view -h -F4 | samtools sort -m 16g -l0 > "${OUTPUT}/bedfiles/${chr}/reads/singletons_reads.bam"; done
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; sh "${SRCFOLDER}/0-align_reads.sh" "${NEWREF}/$chr.${SEQ_FILE_EXT}" "${OUTPUT}/bedfiles/${chr}/reads/reads" "${OUTPUT}/bedfiles/${chr}/reads/paired" $THREAD; done
-for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; sh "${SRCFOLDER}/0-align_singletons.sh" "${NEWREF}/$chr.${SEQ_FILE_EXT}" "${OUTPUT}/bedfiles/${chr}/reads/singletons.fastq" "${OUTPUT}/bedfiles/${chr}/reads/singletons" $THREAD; done
+THREAD=${10}
+
+
+function generate_chain(){
+    bash "${SRCFOLDER}/1-generate_chain/chain_install.sh" "${OUTPUT}"
+    bash "${SRCFOLDER}/1-generate_chain/sample_run.sh" \
+    "${OLDREF}" \
+    "${NEWREF}" \
+    "${OUTPUT}/" \
+    "${SRCFOLDER}/1-generate_chain/chain_generate.sh" \
+    ${SEQ_FILE_EXT} \
+    "${OUTPUT}/"
+}
+
+function generate_gaps(){
+    for i in `echo ${OUTPUT}/*.chain`; do 
+        local chr=`basename $i | sed s/.chain//`; \
+        /usr/bin/time -v -p -o "${OUTPUT}/${chr}_extracted_gaps.fa.time" \
+        python3 "${SRCFOLDER}/2-generate_gaps/extract_gaps.py" \
+        $i \
+        "${NEWREF}/$chr.${SEQ_FILE_EXT}" \
+        ${READSIZE} \
+        "${OUTPUT}/${chr}_extracted_gaps.fa"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`; \
+        /usr/bin/time -v -p -o "${OUTPUT}/${chr}_kmer_gaps.fasta.time" \
+        python3 "${SRCFOLDER}/2-generate_gaps/gaps_to_fasta.py" \
+        "${OUTPUT}/${chr}_extracted_gaps.fa" \
+        ${READSIZE} \
+        "${OUTPUT}/${chr}_kmer_gaps.fasta" \
+        10
+    done
+}
+
+function align_gaps(){
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`; \
+        bash "${SRCFOLDER}/3-align_gaps/align_gaps.sh" \
+        "${OLDREF}/${chr}.${SEQ_FILE_EXT}" \
+        "${OUTPUT}/${chr}_kmer_gaps.fasta" \
+        ${THREAD} \
+        "${OUTPUT}/${chr}_aligned_gaps"
+    done
+}
+
+function extract_reads(){
+    mkdir "${OUTPUT}/bedfiles"
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`; mkdir -p "${OUTPUT}/bedfiles/${chr}/"; \
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/extract_regions.time" \
+        bash "${SRCFOLDER}/4-extract_reads/extract_regions.sh" \
+        "${OUTPUT}/${chr}_aligned_gaps.bam" \
+        "${OUTPUT}/bedfiles/${chr}/"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        local num_of_files=`ls -l ${OUTPUT}/bedfiles/${chr}/*.bed | wc -l`
+        local sed_bed_files=$(echo ${OUTPUT}\/bedfiles\/${chr}/ | sed 's/\//\\\//g')
+        local sed_read_scripts=$(echo ${SRCFOLDER}\/4-extract_reads\/extract_reads.bash | sed 's/\//\\\//g')
+        local sed_read_bam=$(echo $READ_BAM | sed 's/\//\\\//g')
+        cat "${SRCFOLDER}/4-extract_reads/slurm_extract_reads.sh" | \
+        sed "s/{NUM_FILES}/$num_of_files/g" | \
+        sed "s/{THREAD}/$THREAD/g" | \
+        sed "s/{BED_FILES_FOLDER}/$sed_bed_files/g" | \
+        sed "s/{EXTRACT_READS_SCRIPT}/$sed_read_scripts/g" | \
+        sed "s/{READ_BAM_FILE}/$sed_read_bam/g" | \
+        sed "s/{READSIZE}/$READSIZE/g" > "${OUTPUT}/${chr}_samplejob.sh"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        sbatch --wait "${OUTPUT}/${chr}_samplejob.sh"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/merged_${chr}.bed.time" \
+        cat "${OUTPUT}/bedfiles/${chr}/"*.bed | sortBed -i - | mergeBed -i - > "${OUTPUT}/bedfiles/${chr}/merged_${chr}.bed"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        mkdir -p "${OUTPUT}/bedfiles/${chr}/retired_bed/"
+        mkdir -p "${OUTPUT}/bedfiles/${chr}/constant_bed/"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_regions.bed.time" \
+        python3 "${SRCFOLDER}/4-extract_reads/get_retired_regions.py" \
+        ${READSIZE} \
+        "${OUTPUT}/bedfiles/${chr}/merged_${chr}.bed" \
+        $i \
+        "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_regions.bed"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_reads.bed.time" \
+        bash "${SRCFOLDER}/4-extract_reads/extract_reads_noprune.sh" \
+        ${READ_BAM} \
+        "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_regions.bed" > "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_reads.bed"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        mkdir -p "${OUTPUT}/bedfiles/${chr}/reads/"
+        cat "${OUTPUT}/bedfiles/${chr}/"*.reads "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_reads.bed" > "${OUTPUT}/bedfiles/${chr}/updated_and_retired_reads.bed"
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/extract_sequences_full.time" \
+        bash "${SRCFOLDER}/4-extract_reads/extract_sequence.sh" \
+        ${FIRST_PAIR} \
+        ${SECOND_PAIR} \
+        "${OUTPUT}/bedfiles/${chr}/updated_and_retired_reads.bed" \
+        "${OUTPUT}/bedfiles/${chr}/reads/"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/reads/paired_reads.time" \
+        bwa mem -M -t $THREAD "${NEWREF}/$chr.${SEQ_FILE_EXT}" "${OUTPUT}/bedfiles/${chr}/reads/reads_1.fastq" "${OUTPUT}/bedfiles/${chr}/reads/reads_2.fastq" | \
+        samtools view -h -F4 | \
+        samtools sort -m 16g -l0 > "${OUTPUT}/bedfiles/${chr}/reads/paired_reads.bam"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/reads/singletons_reads.time" \
+        bwa mem -M -t $THREAD "${NEWREF}/$chr.${SEQ_FILE_EXT}" "${OUTPUT}/bedfiles/${chr}/reads/singletons.fastq" | \
+        samtools view -h -F4 | \
+        samtools sort -m 16g -l0 > "${OUTPUT}/bedfiles/${chr}/reads/singletons_reads.bam"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        bash "${SRCFOLDER}/0-align_reads.sh" \
+        "${NEWREF}/$chr.${SEQ_FILE_EXT}" \
+        "${OUTPUT}/bedfiles/${chr}/reads/reads" \
+        "${OUTPUT}/bedfiles/${chr}/reads/paired" \
+        $THREAD
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        bash "${SRCFOLDER}/0-align_singletons.sh" \
+        "${NEWREF}/$chr.${SEQ_FILE_EXT}" \
+        "${OUTPUT}/bedfiles/${chr}/reads/singletons.fastq" \
+        "${OUTPUT}/bedfiles/${chr}/reads/singletons" \
+        $THREAD
+    done
+}
+
+function extract_reads_with_parallel(){
+    mkdir "${OUTPUT}/bedfiles"
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`; mkdir -p "${OUTPUT}/bedfiles/${chr}/"; \
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/extract_regions.time" \
+        bash "${SRCFOLDER}/4-extract_reads/extract_regions.sh" \
+        "${OUTPUT}/${chr}_aligned_gaps.bam" \
+        "${OUTPUT}/bedfiles/${chr}/"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        local num_of_files=`ls -l ${OUTPUT}/bedfiles/${chr}/*.bed | wc -l`
+        local sed_bed_files=$(echo ${OUTPUT}\/bedfiles\/${chr}/ | sed 's/\//\\\//g')
+        local sed_read_scripts=$(echo ${SRCFOLDER}\/4-extract_reads\/extract_reads.bash | sed 's/\//\\\//g')
+        local sed_read_bam=$(echo $READ_BAM | sed 's/\//\\\//g')
+        cat "${SRCFOLDER}/4-extract_reads/parallel_extract_reads.sh" | \
+        sed "s/{NUM_FILES}/$num_of_files/g" | \
+        sed "s/{THREAD}/$THREAD/g" | \
+        sed "s/{BED_FILES_FOLDER}/$sed_bed_files/g" | \
+        sed "s/{EXTRACT_READS_SCRIPT}/$sed_read_scripts/g" | \
+        sed "s/{READ_BAM_FILE}/$sed_read_bam/g" | \
+        sed "s/{READSIZE}/$READSIZE/g" > "${OUTPUT}/${chr}_samplejob.sh"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        bash "${OUTPUT}/${chr}_samplejob.sh"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/merged_${chr}.bed.time" \
+        cat "${OUTPUT}/bedfiles/${chr}/"*.bed | sortBed -i - | mergeBed -i - > "${OUTPUT}/bedfiles/${chr}/merged_${chr}.bed"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        mkdir -p "${OUTPUT}/bedfiles/${chr}/retired_bed/"
+        mkdir -p "${OUTPUT}/bedfiles/${chr}/constant_bed/"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_regions.bed.time" \
+        python3 "${SRCFOLDER}/4-extract_reads/get_retired_regions.py" \
+        ${READSIZE} \
+        "${OUTPUT}/bedfiles/${chr}/merged_${chr}.bed" \
+        $i \
+        "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_regions.bed"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_reads.bed.time" \
+        bash "${SRCFOLDER}/4-extract_reads/extract_reads_noprune.sh" \
+        ${READ_BAM} \
+        "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_regions.bed" > "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_reads.bed"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        mkdir -p "${OUTPUT}/bedfiles/${chr}/reads/"
+        cat "${OUTPUT}/bedfiles/${chr}/"*.reads "${OUTPUT}/bedfiles/${chr}/retired_bed/retired_reads.bed" > "${OUTPUT}/bedfiles/${chr}/updated_and_retired_reads.bed"
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/extract_sequences_full.time" \
+        bash "${SRCFOLDER}/4-extract_reads/extract_sequence.sh" \
+        ${FIRST_PAIR} \
+        ${SECOND_PAIR} \
+        "${OUTPUT}/bedfiles/${chr}/updated_and_retired_reads.bed" \
+        "${OUTPUT}/bedfiles/${chr}/reads/"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/reads/paired_reads.time" \
+        bwa mem -M -t $THREAD "${NEWREF}/$chr.${SEQ_FILE_EXT}" "${OUTPUT}/bedfiles/${chr}/reads/reads_1.fastq" "${OUTPUT}/bedfiles/${chr}/reads/reads_2.fastq" | \
+        samtools view -h -F4 | \
+        samtools sort -m 16g -l0 > "${OUTPUT}/bedfiles/${chr}/reads/paired_reads.bam"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/reads/singletons_reads.time" \
+        bwa mem -M -t $THREAD "${NEWREF}/$chr.${SEQ_FILE_EXT}" "${OUTPUT}/bedfiles/${chr}/reads/singletons.fastq" | \
+        samtools view -h -F4 | \
+        samtools sort -m 16g -l0 > "${OUTPUT}/bedfiles/${chr}/reads/singletons_reads.bam"
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        bash "${SRCFOLDER}/0-align_reads.sh" \
+        "${NEWREF}/$chr.${SEQ_FILE_EXT}" \
+        "${OUTPUT}/bedfiles/${chr}/reads/reads" \
+        "${OUTPUT}/bedfiles/${chr}/reads/paired" \
+        $THREAD
+    done
+
+    for i in `echo ${OUTPUT}/*.chain`; do
+        local chr=`basename $i | sed s/.chain//`
+        bash "${SRCFOLDER}/0-align_singletons.sh" \
+        "${NEWREF}/$chr.${SEQ_FILE_EXT}" \
+        "${OUTPUT}/bedfiles/${chr}/reads/singletons.fastq" \
+        "${OUTPUT}/bedfiles/${chr}/reads/singletons" \
+        $THREAD
+    done
+}
+
+
+function main(){
+    mkdir -p "${OUTPUT}/"
+
+    local chain_existed=$(ls ${OUTPUT}/*.chain 2> /dev/null)
+    
+    if [[ ${#chain_existed} -gt 0 ]]; then
+        echo "Line "${LINENO}": In function "${FUNCNAME}": Use user offered chain "${chain_existed}
+    else
+        echo "Line "${LINENO}": In function "${FUNCNAME}": User does not offer chain file. Generating one."
+        generate_chain
+    fi
+
+    generate_gaps
+
+    align_gaps
+
+    if [[ -z ${11} ]]; then
+        extract_reads_with_parallel
+    else
+        extract_reads
+    fi
+}
+
+
+if [[ "${#BASH_SOURCE[@]}" -eq 1 ]]
+then
+    main "$@"
+fi
 
 #constant regions:
-#for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/constant_bed/constant_regions.bed.time" python "${SRCFOLDER}/4-extract_reads/get_constant_regions.py" ${READSIZE} $i "${OUTPUT}/bedfiles/${chr}/constant_bed/constant_regions.bed"; done
-#sbatch --wrap="for i in `echo ${OUTPUT}/*.chain`; do chr=`basename $i | sed s/.chain//`; /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/constant_bed/constant_reads.bed.time" sh "${SRCFOLDER}/4-extract_reads/extract_reads_noprune.sh" ${READ_BAM} "${OUTPUT}/bedfiles/${chr}/constant_bed/constant_regions.bed" > "${OUTPUT}/bedfiles/${chr}/constant_bed/constant_reads.bed"; done"
+#for i in `echo ${OUTPUT}/*.chain`; do local chr=`basename $i | sed s/.chain//`; /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/constant_bed/constant_regions.bed.time" python3 "${SRCFOLDER}/4-extract_reads/get_constant_regions.py" ${READSIZE} $i "${OUTPUT}/bedfiles/${chr}/constant_bed/constant_regions.bed"; done
+#sbatch --local wrap="for i in `echo ${OUTPUT}/*.chain`; do local chr=`basename $i | sed s/.chain//`; /usr/bin/time -v -p -o "${OUTPUT}/bedfiles/${chr}/constant_bed/constant_reads.bed.time" bash "${SRCFOLDER}/4-extract_reads/extract_reads_noprune.sh" ${READ_BAM} "${OUTPUT}/bedfiles/${chr}/constant_bed/constant_regions.bed" > "${OUTPUT}/bedfiles/${chr}/constant_bed/constant_reads.bed"; done"