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mumandco_v3.7.sh
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mumandco_v3.7.sh
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#!/bin/bash
version="3.7"
##################################################################################
############################## EDIT PATHS AND NAMES ##############################
##################################################################################
### Paths to Additional tools/scripts ###
NUCMER=$(which nucmer)
DELTAFILTER=$(which delta-filter)
SHOWCOORDS=$(which show-coords)
SAMTOOLS=$(which samtools)
#change to yes if paths to samtools and blast have been added
#blast_step="no"
#SAMTOOLS="/usr/bin/samtools"
#BLASTN="/usr/bin/blastn"
#BLASTDB="/usr/bin/makeblastdb"
##Genomes for alignments##
#reference_assembly="./yeast.tidy.fa"
#genome_size=12500000
#query_assembly="./yeast_tidy_DEL100.fa"
##output file names for alignment and filtering##
#ref="yeast_tidy"
#query="DEL100"
#alignments_folder="DEL100_alignments"
##output file name for SV detection##
#prefix="DEL100_test_v2.1"
##if you want to remove intemediate files at the end put "yes"##
cleanup="yes"
##subtelomeric regions file
#filter_subtelomeric_region="no"
#subtelo_coords="subtelomeric_regions_file.csv"
#DNA_filter="no"
while [[ $# -gt 0 ]]
do
key="$1"
case "$key" in
-r|--reference_genome)
reference_assembly="$2"
shift
shift
;;
-q|--query_genome)
query_assembly="$2"
shift
shift
;;
-g|--genome_size)
genome_size="$2"
shift
shift
;;
-o|--output)
prefix="$2"
shift
shift
;;
-t|--threads)
threads="$2"
shift
shift
;;
esac
done
###################################################################################
###################################################################################
###################################################################################
####align genomes to one another###
echo ""
echo "Nucmer alignment of genomes, filtering and converting to coordinates"
echo ""
if [ $genome_size -le 100000000 ]
then
$NUCMER --threads ${threads} --maxmatch --nosimplify -p ""$prefix"_ref" $reference_assembly $query_assembly
$DELTAFILTER -m ""$prefix"_ref".delta > ""$prefix"_ref".delta_filter
$SHOWCOORDS -T -r -c -l -d -g ""$prefix"_ref".delta_filter > ""$prefix"_ref".delta_filter.coordsg
$SHOWCOORDS -T -r -c -l -d ""$prefix"_ref".delta_filter > ""$prefix"_ref".delta_filter.coords
$NUCMER --threads ${threads} --maxmatch --nosimplify -p ""$prefix"_query" $query_assembly $reference_assembly
$DELTAFILTER -m ""$prefix"_query".delta > ""$prefix"_query".delta_filter
$SHOWCOORDS -T -r -c -l -d -g ""$prefix"_query".delta_filter > ""$prefix"_query".delta_filter.coordsg
$SHOWCOORDS -T -r -c -l -d ""$prefix"_query".delta_filter > ""$prefix"_query".delta_filter.coords
else
if [ $genome_size -le 500000000 ]
then
$NUCMER --threads ${threads} --maxmatch -l 100 -c 500 -p ""$prefix"_ref" $reference_assembly $query_assembly
$DELTAFILTER -m ""$prefix"_ref".delta > ""$prefix"_ref".delta_filter
$SHOWCOORDS -T -r -c -l -d -g ""$prefix"_ref".delta_filter > ""$prefix"_ref".delta_filter.coordsg
$SHOWCOORDS -T -r -c -l -d ""$prefix"_ref".delta_filter > ""$prefix"_ref".delta_filter.coords
$NUCMER --threads ${threads} --maxmatch -l 100 -c 500 -p ""$prefix"_query" $query_assembly $reference_assembly
$DELTAFILTER -m ""$prefix"_query".delta > ""$prefix"_query".delta_filter
$SHOWCOORDS -T -r -c -l -d -g ""$prefix"_query".delta_filter > ""$prefix"_query".delta_filter.coordsg
$SHOWCOORDS -T -r -c -l -d ""$prefix"_query".delta_filter > ""$prefix"_query".delta_filter.coords
else
echo "My what a large genome you have, this may take some time"
$NUCMER --threads ${threads} --maxmatch -l 500 -c 500 -p ""$prefix"_ref" $reference_assembly $query_assembly
$DELTAFILTER -m ""$prefix"_ref".delta > ""$prefix"_ref".delta_filter
$SHOWCOORDS -T -r -c -l -d -g ""$prefix"_ref".delta_filter > ""$prefix"_ref".delta_filter.coordsg
$SHOWCOORDS -T -r -c -l -d ""$prefix"_ref".delta_filter > ""$prefix"_ref".delta_filter.coords
$NUCMER --threads ${threads} --maxmatch -l 500 -c 500 -p ""$prefix"_query" $query_assembly $reference_assembly
$DELTAFILTER -m ""$prefix"_query".delta > ""$prefix"_query".delta_filter
$SHOWCOORDS -T -r -c -l -d -g ""$prefix"_query".delta_filter > ""$prefix"_query".delta_filter.coordsg
$SHOWCOORDS -T -r -c -l -d ""$prefix"_query".delta_filter > ""$prefix"_query".delta_filter.coords
fi
fi
#!/bin/bash
mkdir "$prefix"_alignments
alignments_folder=""$prefix"_alignments"
mv ""$prefix"_ref".delta* $alignments_folder/
mv ""$prefix"_query".delta* $alignments_folder/
echo " #"
echo " # #"
echo " # #"
echo " ###############################"
echo " # #"
echo " # MUM&Co is open for business #"
echo " # version ${version} #"
echo " ###############################"
############################################################################################################
################################DELETIONS, INSERTIONS AND TRANSLOCATIONS####################################
############################################################################################################
##USES SHOW-COORDS WITH G OPTION FOR GLOBAL ALIGNMENTS##
echo ""
echo ""
echo "######################################################################################################"
echo " USING GLOBAL ALIGNMENT COORDINATES FOR DELETIONS, INSERTIONS AND TRANSLOCATIONS"
echo "######################################################################################################"
echo ""
###Begin Filtering###
##filter out chrMT and aligned contigs that don't match the primary matched contigs.
echo ""
echo "Matching chromosomes based on names, using '_' seperator and filtering chrMT"
echo ""
####How to say, from row 1 to row 14 ?? and not having to write it all out seperately####
#tail -n +5 "$alignments_folder/""$prefix"_ref".delta_filter.coordsg" | sed 's/_/\t/g' |\
# awk '!/chrMT/{for(i=15;i<=NF;++i) if($14==$i) {print $0}}' |\
# sed 's/\t/_/15g' \
# >""$prefix"_ref".coordsg_matched
#tail -n +5 "$alignments_folder/""$prefix"_query".delta_filter.coordsg" | \
# awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12"\t"$13"\t"$15"\t"$14}' |\
# sed 's/_/\t/g' |\
# awk '!/chrMT/{for(i=15; i<=NF; ++i) if($i==$14) {print $0}}' |\
# sed 's/\t/_/15g' |\
# awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12"\t"$13"\t"$15"\t"$14}' \
# > ""$prefix"_query".coordsg_matched
##get average quality
average_quality=$(tail -n +5 "$alignments_folder/""$prefix"_ref".delta_filter.coordsg" | awk '{sum+=$7} END{print sum/NR}')
### filter for alignment less than 10kb (limit on translocation size)
### filter for any alignment overlapping another with more than 50bp and with lower quality
tail -n +5 "$alignments_folder/""$prefix"_ref".delta_filter.coordsg" |\
sort -k15,15d -k3,3n |\
awk '{if($5>10000) print $0}' |\
awk 'BEGIN{qual=0};\
{if(qual==0 && $13=="1") {print $0; qual=$7; start=$3; end=$4; contig=$15}\
else if(qual==0 && $13=="-1") {print $0; qual =$7; start=$4; end=$3; contig=$15}\
else if(contig!=$15 && $13=="1") {print $0; qual=$7; start=$3; end=$4; contig=$15}\
else if(contig!=$15 && $13=="-1") {print $0; qual=$7; start=$4; end=$3; contig=$15}\
else if(contig==$15 && $13=="1" && $3 >=start+50 && $3 <=end-50 && $7 <=qual || contig==$15 && $13=="1" && $4 >=start+50 && $4 <=end-50 && $7 <=qual) {}\
else if(contig==$15 && $13=="-1" && $3 >=start+50 && $3 <=end-50 && $7 <=qual || contig==$15 && $13=="-1" && $4 >=start+50 && $4 <=end-50 && $7 <=qual) {}\
else if($13=="1") {print $0; qual=$7; start=$3; end=$4; contig=$15}\
else if($13=="-1") {print $0; qual=$7; start=$4; end=$3; contig=$15}}'|\
sort -k15,15d -k3,3nr |\
awk 'BEGIN{qual=0};\
{if(qual==0 && $13=="1") {print $0; qual=$7; start=$3; end=$4; contig=$15}\
else if(qual==0 && $13=="-1") {print $0; qual =$7; start=$4; end=$3; contig=$15}\
else if(contig!=$15 && $13=="1") {print $0; qual=$7; start=$3; end=$4; contig=$15}\
else if(contig!=$15 && $13=="-1") {print $0; qual=$7; start=$4; end=$3; contig=$15}\
else if(contig==$15 && $13=="1" && $3 >=start+50 && $3 <=end-50 && $7 <=qual || contig==$15 && $13=="1" && $4 >=start+50 && $4 <=end-50 && $7 <=qual) {}\
else if(contig==$15 && $13=="-1" && $3 >=start+50 && $3 <=end-50 && $7 <=qual || contig==$15 && $13=="-1" && $4 >=start+50 && $4 <=end-50 && $7 <=qual) {}\
else if($13=="1") {print $0; qual=$7; start=$3; end=$4; contig=$15}\
else if($13=="-1") {print $0; qual=$7; start=$4; end=$3; contig=$15}}'|\
sort -k14,14d -k1,1n |\
awk 'BEGIN{qual=0};\
{if(qual==0 && $12=="1") {print $0; qual=$7; start=$1; end=$2; contig=$14}\
else if(qual==0 && $12=="-1") {print $0; qual =$7; start=$2; end=$1; contig=$14}\
else if(contig!=$14 && $12=="1") {print $0; qual=$7; start=$1; end=$2; contig=$14}\
else if(contig!=$14 && $12=="-1") {print $0; qual=$7; start=$2; end=$1; contig=$14}\
else if(contig==$14 && $12=="1" && $1 >=start+50 && $1 <=end-50 && $7 <=qual || contig==$14 && $12=="1" && $2 >=start+50 && $2 <=end-50 && $7 <=qual) {}\
else if(contig==$14 && $12=="-1" && $1 >=start+50 && $1 <=end-50 && $7 <=qual || contig==$14 && $12=="-1" && $2 >=start+50 && $2 <=end-50 && $7 <=qual) {}\
else if($12=="1") {print $0; qual=$7; start=$1; end=$2; contig=$14}\
else if($12=="-1") {print $0; qual=$7; start=$2; end=$1; contig=$14}}' |\
sort -k14,14d -k1,1nr |\
awk 'BEGIN{qual=0};\
{if(qual==0 && $12=="1") {print $0; qual=$7; start=$1; end=$2; contig=$14}\
else if(qual==0 && $12=="-1") {print $0; qual =$7; start=$2; end=$1; contig=$14}\
else if(contig!=$14 && $12=="1") {print $0; qual=$7; start=$1; end=$2; contig=$14}\
else if(contig!=$14 && $12=="-1") {print $0; qual=$7; start=$2; end=$1; contig=$14}\
else if(contig==$14 && $12=="1" && $1 >=start+50 && $1 <=end-50 && $7 <=qual || contig==$14 && $12=="1" && $2 >=start+50 && $2 <=end-50 && $7 <=qual) {}\
else if(contig==$14 && $12=="-1" && $1 >=start+50 && $1 <=end-50 && $7 <=qual || contig==$14 && $12=="-1" && $2 >=start+50 && $2 <=end-50 && $7 <=qual) {}\
else if($12=="1") {print $0; qual=$7; start=$1; end=$2; contig=$14}\
else if($12=="-1") {print $0; qual=$7; start=$2; end=$1; contig=$14}}' > ""$prefix"_pre_list.txt"
#tail -n +5 "$alignments_folder/""$prefix"_ref".delta_filter.coordsg" |\
# sort -k15,15d -k3,3n |\
# awk '{if($5>10000) print $0}' |\
# awk 'BEGIN{qual=0};\
# {if(qual==0) {print $0; qual=$7; mid=($3+$4)/2; contig=$15}\
# else if(contig!=$15) {print $0; qual=$7; mid=($3+$4)/2; contig=$15}\
# else if(contig==$15 && $3>$4 && $3 >=mid && $4 <=mid && $7 <qual) {}\
# else if(contig==$15 && $4>$3 && $4 >=mid && $3 <=mid && $7 <qual) {}\
# else {print $0; qual=$7; mid=($3+$4)/2; contig=$15}}'|\
# sort -k15,15d -k3,3nr |\
# awk 'BEGIN{qual=0};\
# {if(qual==0) {print $0; qual=$7; mid=($1+$2)/2; contig=$15}\
# else if(contig!=$15) {print $0; qual=$7; mid=($1+$2)/2; contig=$15}\
# else if(contig==$15 && $1>$2 && $1 >=mid && $2 <=mid && $7 <qual) {}\
# else if(contig==$15 && $2>$1 && $2 >=mid && $1 <=mid && $7 <qual) {}\
# else {print $0; qual=$7; mid=($1+$2)/2; contig=$15}}'|\
# sort -k14,14d -k1,1n |\
# awk 'BEGIN{qual=0};\
# {if(qual==0) {print $0; qual=$7; mid=($1+$2)/2; contig=$14}\
# else if(contig!=$14) {print $0; qual=$7; mid=($1+$2)/2; contig=$14}\
# else if(contig==$14 && $1>$2 && $1 >=mid && $2 <=mid && $7 <qual) {}\
# else if(contig==$14 && $2>$1 && $2 >=mid && $1 <=mid && $7 <qual) {}\
# else {print $0; qual=$7; mid=($1+$2)/2; contig=$14}}'|\
# sort -k14,14d -k1,1nr |\
# awk 'BEGIN{qual=0};\
# {if(qual==0) {print $0; qual=$7; mid=($1+$2)/2; contig=$14}\
# else if(contig!=$14) {print $0; qual=$7; mid=($1+$2)/2; contig=$14}\
# else if(contig==$14 && $1>$2 && $1 >=mid && $2 <=mid && $7 <qual) {}\
# else if(contig==$14 && $2>$1 && $2 >=mid && $1 <=mid && $7 <qual) {}\
# else {print $0; qual=$7; mid=($1+$2)/2; contig=$14}}' > ""$prefix"_pre_list.txt"
#
#
#
##filter any remaining alignments with less than (1.25 x standard deviation) less than the average of the remaining alignments
average_quality=$(cat ""$prefix"_pre_list.txt" | awk '{sum+=$7} END{print sum/NR}')
if [[ "$average_quality" == "100" ]]
then
cat ""$prefix"_pre_list.txt" | awk '{print $14"\t"$15}' | sort | uniq > ""$prefix"_chromosome_pairs.txt"
awk 'NR==FNR{a[$1,$2]++;next};a[$14,$15] {print $0}' ""$prefix"_chromosome_pairs.txt" "$alignments_folder/""$prefix"_ref".delta_filter.coordsg" > ""$prefix"_ref".coordsg_matched
awk 'NR==FNR{a[$1,$2]++;next};a[$15,$14] {print $0}' ""$prefix"_chromosome_pairs.txt" "$alignments_folder/""$prefix"_query".delta_filter.coordsg" > ""$prefix"_query".coordsg_matched
else
stdev125=$(cat ""$prefix"_pre_list.txt" | awk '{sum=sum+$7 ; sumX2+=(($7)^2)} END{print 1.25*(sqrt(sumX2/(NR) - ((sum/NR)^2)))}')
quality_filt=$(echo $average_quality - $stdev125 | bc)
cat ""$prefix"_pre_list.txt" | awk -v quality_filt="$quality_filt" '{if($7 > quality_filt) print $14"\t"$15}' | sort | uniq > ""$prefix"_chromosome_pairs.txt"
awk 'NR==FNR{a[$1,$2]++;next};a[$14,$15] {print $0}' ""$prefix"_chromosome_pairs.txt" "$alignments_folder/""$prefix"_ref".delta_filter.coordsg" > ""$prefix"_ref".coordsg_matched
awk 'NR==FNR{a[$1,$2]++;next};a[$15,$14] {print $0}' ""$prefix"_chromosome_pairs.txt" "$alignments_folder/""$prefix"_query".delta_filter.coordsg" > ""$prefix"_query".coordsg_matched
fi
if [[ $filter_subtelomeric_region == "yes" ]]
then
##All those calls that start before the end of the subtelomeric region or finish after are filtered
echo ""
echo "Removing calls in subtelomeric regions"
echo ""
awk 'FNR==NR{a[$1]=$2"\t"$3;next} ($14 in a) {print $0"\t"a[$14]}' $subtelo_coords ""$prefix"_ref".coordsg_matched |\
awk '{if($2 > $16 && $1 < $17) {print $0}}' |\
awk -F'\t' 'BEGIN { OFS = FS }; NF{NF-=2};1' > ""$prefix"_ref".coordsg_matched_subtelofilt
awk 'FNR==NR{a[$1]=$2"\t"$3;next} ($15 in a) {print $0"\t"a[$15]}' $subtelo_coords ""$prefix"_query".coordsg_matched |\
awk '{if($4 > $16 && $3 < $17) {print $0}}' |\
awk -F'\t' 'BEGIN { OFS = FS }; NF{NF-=2};1' > ""$prefix"_query".coordsg_matched_subtelofilt
#################################################################################
##########getting gaps from subtelomeres to beginning of alignments##############
#################################################################################
awk 'FNR==NR{a[$1]=$2"\t"$3;next} ($14 in a) {print $0"\t"a[$14]}' $subtelo_coords ""$prefix"_ref".coordsg_matched_subtelofilt |\
awk 'BEGIN{chrr=0} \
{if(chrr==0 && $1>$16){print $0; chrr=$14} \
{if(chrr==0 && $1<$16){chrr=$14} \
{if(chrr!=$14 && $1>$16) {print $0; chrr=$14}\
{if(chrr!=$14 && $1<$16) {chrr=$14}}}}}' |\
awk '{if($13==1){print $14"\t"$15"\t1\t"$1"\t"$1-1"\tdeletion\t1\t"$3} \
{if($13!=1){print $14"\t"$15"\t1\t"$1"\t"$1-1"\tdeletion\t"$3"\t"$9}}}' \
> ""$prefix"_ref".coordsg_matched_startgap
awk 'FNR==NR{a[$1]=$2"\t"$3;next} ($14 in a) {print $0"\t"a[$14]}' $subtelo_coords ""$prefix"_ref".coordsg_matched_subtelofilt \
> ""$prefix"_ref".coordsg_matched_endgap_temp
tac ""$prefix"_ref".coordsg_matched_endgap_temp |\
awk 'BEGIN{chrr=0} \
{if(chrr==0 && $2<$17){print $0; chrr=$14} \
{if(chrr==0 && $2>$17){chrr=$14} \
{if(chrr!=$14 && $2<$17) {print $0; chrr=$14}\
{if(chrr!=$14 && $2>$17) {chrr=$14}}}}}' |\
awk '{if($13==1){print $14"\t"$15"\t"$2"\t"$8"\t"$8-$2"\tdeletion\t"$4"\t"$9} \
{if($13!=1){print $14"\t"$15"\t"$2"\t"$8"\t"$8-$2"\tdeletion\t1\t"$4}}}' \
> ""$prefix"_ref".coordsg_matched_endgap
cat ""$prefix"_ref".coordsg_matched_startgap ""$prefix"_ref".coordsg_matched_endgap > ""$prefix"_ref".coordsg_matched_subtelogap
awk 'FNR==NR{a[$1]=$2"\t"$3;next} ($14 in a) {print $0"\t"a[$14]}' $subtelo_coords ""$prefix"_query".coordsg_matched_subtelofilt |\
awk 'BEGIN{chrr=0} \
{if(chrr==0 && $1>$16){print $0; chrr=$14} \
{if(chrr==0 && $1<$16){chrr=$14} \
{if(chrr!=$14 && $1>$16) {print $0; chrr=$14}\
{if(chrr!=$14 && $1<$16) {chrr=$14}}}}}' |\
awk '{if($13==1){print $15"\t"$14"\t1\t"$3"\t"$3-1"\tinsertion\t1\t"$1} \
{if($13!=1){print $15"\t"$14"\t1\t"$4"\t"$4-1"\tinsertion\t"$2"\t"$9}}}' \
> ""$prefix"_query".coordsg_matched_startgap
awk 'FNR==NR{a[$1]=$2"\t"$3;next} ($14 in a) {print $0"\t"a[$14]}' $subtelo_coords ""$prefix"_query".coordsg_matched_subtelofilt \
> ""$prefix"_query".coordsg_matched_endgap_temp
tac ""$prefix"_query".coordsg_matched_endgap_temp |\
awk 'BEGIN{chrr=0} \
{if(chrr==0 && $2<$17){print $0; chrr=$14} \
{if(chrr==0 && $2>$17){chrr=$14} \
{if(chrr!=$14 && $2<$17) {print $0; chrr=$14}\
{if(chrr!=$14 && $2>$17) {chrr=$14}}}}}' |\
awk '{if($13==1){print $15"\t"$14"\t"$4"\t"$8"\t"$8-$4"\tinsertion\t"$2"\t"$9} \
{if($13!=1){print $15"\t"$14"\t"$3"\t"$8"\t"$8-$3"\tinsertion\t1\t"$4}}}' \
> ""$prefix"_query".coordsg_matched_endgap
cat ""$prefix"_query".coordsg_matched_startgap ""$prefix"_query".coordsg_matched_endgap > ""$prefix"_query".coordsg_matched_subtelogap
cat ""$prefix"_ref".coordsg_matched_subtelogap ""$prefix"_query".coordsg_matched_subtelogap |\
awk '{if($5>50) print $0}' > $prefix.coordsg_subtelogaps_50
cat $prefix.coordsg_subtelogaps_50 |\
awk '{if($5>1000) print $0}' > $prefix.coordsg_subtelogaps_1000
rm ""$prefix"_ref".coordsg_matched_endgap_temp
rm ""$prefix"_ref".coordsg_matched_startgap
rm ""$prefix"_ref".coordsg_matched_endgap
rm ""$prefix"_query".coordsg_matched_endgap_temp
rm ""$prefix"_query".coordsg_matched_startgap
rm ""$prefix"_query".coordsg_matched_endgap
else
cp ""$prefix"_ref".coordsg_matched ""$prefix"_ref".coordsg_matched_subtelofilt
cp ""$prefix"_query".coordsg_matched ""$prefix"_query".coordsg_matched_subtelofilt
fi
#############################################
###################INDELS####################
#############################################
echo ""
echo "Finding alignment gaps"
echo ""
cat ""$prefix"_ref".coordsg_matched_subtelofilt |\
awk 'BEGIN{startref=0; chr=""; gap=0; startq=0} \
{if(chr==$15) {gap=$1-startref; print $0"\t"startref"\t"$1"\t"gap"\t"startq"\t"$3; startref=$2; startq=$4} \
if(chr!=$15) {print $0; chr=$15; startref=$2; startq=$4}}' \
> ""$prefix"_ref".coordsg_matched_subtelofilt_gaps
cat ""$prefix"_query".coordsg_matched_subtelofilt |\
awk 'BEGIN{startq=0; chr=""; gap=0; startref=0} \
{if(chr==$14) {gap=$1-startq; print $0"\t"startref"\t"$3"\t"gap"\t"startq"\t"$1; startq=$2; startref=$4; startq=$2} \
if(chr!=$14) {print $0; chr=$14; startq=$2; startref=$4}}' \
> ""$prefix"_query".coordsg_matched_subtelofilt_gaps
###remove SVS smaller than 50 for 1000bp and remove unecessary columns###
echo ""
echo "Filtering for size labelling SV"
echo ""
cat ""$prefix"_ref".coordsg_matched_subtelofilt_gaps |\
awk '{if($18>50){print $14"\t"$15"\t"$16"\t"$17"\t"$18"\tdeletion\t"$19"\t"$20}}' |\
sort -k1,1 -k3V > ""$prefix"_ref".gaps_50
cat ""$prefix"_ref".gaps_50 | awk '{if($5>1000){print $0}}' > ""$prefix"_ref".gaps_1000
##again for reciprical and also swap chromosome names between ref and query, ref in far left column as in deletions##
cat ""$prefix"_query".coordsg_matched_subtelofilt_gaps |\
awk '{if($18>50){print $15"\t"$14"\t"$16"\t"$17"\t"$18"\tinsertion\t"$19"\t"$20}}' |\
sort -k1,1 -k3V > ""$prefix"_query".gaps_50
cat ""$prefix"_query".gaps_50 | awk '{if($5>1000){print $0}}' > ""$prefix"_query".gaps_1000
#############################################
###############TRANSLOCATIONS################
#############################################
echo ""
echo "Finding translocation fragments"
echo ""
###keep only query contigs that are associated with two or more reference chromosomes
cat ""$prefix"_ref".coordsg_matched_subtelofilt | awk '{print $15}' | sort -u > transloc_list.txt
cat transloc_list.txt | while read chromosome
do
associated_chromosomes=$(cat ""$prefix"_ref".coordsg_matched_subtelofilt | awk -v chromosome="$chromosome" '{if($15==chromosome) print $14}' | sort -u | wc -l)
if [ $associated_chromosomes -gt 1 ]
then
cat ""$prefix"_ref".coordsg_matched_subtelofilt | awk -v chromosome="$chromosome" '{if($15==chromosome) print $0}' >$prefix.$chromosome.transloc_pairing
fi
done
transloc_true=$( find . -maxdepth 1 -type f -name '*.transloc_pairing' | wc -l )
if [ $transloc_true -gt 0 ]
then
cat *.transloc_pairing | sort -k14,14 -k1V > $prefix.transloc_candidate_alignments
rm *.transloc_pairing
rm transloc_list.txt
###remove smaller false translocations that lie inside the larger true fragment then concatenate again
cat $prefix.transloc_candidate_alignments | awk 'BEGIN{chr=""; start=""; stop=""}; \
{if($14==chr && $1>start && $2<stop) {} \
else if($14==chr) {print $0; chr=$14; start=$1; stop=$2} \
else {print $0; chr=$14; start=$1; stop=$2}} \
{if(chr=="") {print $0; chr=$14; start=$1; stop=$2}}' \
> $prefix.transloc_candidate_alignments2
###need to fix for INVERTED SEGMENTS!!!!!!!!!!!!
cat $prefix.transloc_candidate_alignments2 | awk 'BEGIN{chrr=""; chrq=""; startr=0; endr=0; startq=0; endq=0; link=0}\
{if(chrq=="") {chrr=$14; chrq=$15; startr=$1; endr=$2; startq=$3; endq=$4; orientation=$13}\
else if(chrr==$14 && chrq==$15) {endr=$2; endq=$4; orientation=$13}\
else if(chrr==$14 && chrq!=$15) {print $0"\t"chrr"\t"chrq"\t"startr"\t"endr"\t"endr-startr"\ttransloc\t"startq"\t"endq"\t"orientation; startr=$1; endr=$2; startq=$3; endq=$4; chrq=$15; orientation=$13}\
else if(chrr!=$14){print $0"\t"chrr"\t"chrq"\t"startr"\t"endr"\t"endr-startr"\ttransloc\t"startq"\t"endq"\t"orientation; startr=$1; endr=$2; startq=$3; endq=$4; chrr=$14; chrq=$15; orientation=$13}}\
END{print $0"\t"chrr"\t"chrq"\t"startr"\t"endr"\t"endr-startr"\ttransloc\t"startq"\t"endq"\t"orientation}'|\
awk '{print $16"\t"$17"\t"$18"\t"$19"\t"$20"\t"$21"\t"$22"\t"$23"\t"$24}' \
> $prefix.transloc_candidate_alignments3_fragments
##remove many small fragments and join the large fragments which they broke"
cat $prefix.transloc_candidate_alignments3_fragments | awk '{if($5< 10000) print $1"\t"$2"\t"$3"\t"$4"\t"$5"\ttransloc_10000"$6"\t"$7"\t"$8}' > ""$prefix"_ref".fragments_less10000
cat $prefix.transloc_candidate_alignments3_fragments | awk '{if($5>=10000) print $0}'> $prefix.transloc_candidate_alignments4_fragments10000
##AGAIN remove smaller false translocations that lie inside the larger true fragment then concatenate again
cat $prefix.transloc_candidate_alignments4_fragments10000 | awk 'BEGIN{chr=""; start=""; stop=""}; \
{if($1==chr && $3>start && $4<stop) {} \
else if($1==chr) {print $0; chr=$1; start=$3; stop=$4} \
else {print $0; chr=$1; start=$3; stop=$4}} \
{if(chr=="") {print $0; chr=$1; start=$3; stop=$4}}' \
> $prefix.transloc_candidate_alignments5_fragments10000
cat $prefix.transloc_candidate_alignments5_fragments10000 | awk 'BEGIN{chrr=""; chrq=""; startr=0; endr=0; startq=0; endq=0; link=0}\
{if(chrq=="") {chrr=$1; chrq=$2; startr=$3; endr=$4; startq=$7; endq=$8; orientation=$9}\
else if(chrr==$1 && chrq==$2) {endr=$4; endq=$8}\
else if(chrr==$1 && chrq!=$2) {print $0"\t"chrr"\t"chrq"\t"startr"\t"endr"\t"endr-startr"\ttransloc\t"startq"\t"endq"\t"orientation; startr=$3; endr=$4; startq=$7; endq=$8; chrq=$2; orientation=$9}\
else if(chrr!=$1){print $0"\t"chrr"\t"chrq"\t"startr"\t"endr"\t"endr-startr"\ttransloc\t"startq"\t"endq"\t"orientation; startr=$3; endr=$4; startq=$7; endq=$8; chrr=$1; chrq=$2; orientation=$9}}\
END{print $0"\t"chrr"\t"chrq"\t"startr"\t"endr"\t"endr-startr"\ttransloc\t"startq"\t"endq"\t"orientation}'|\
awk '{print $10"\t"$11"\t"$12"\t"$13"\t"$14"\t"$15"\t"$16"\t"$17"\t"$18}' \
> $prefix.transloc_candidate_alignments6_fragments10000
##this makes sure that at the end the orientation of the fragment will reverse the start and stop positions
##this will be returned to the orignal orientation but only after the correct borders are identified downstream
cat $prefix.transloc_candidate_alignments6_fragments10000 |\
awk '{if($9 == "-1") {print $1"\t"$2"\t"$4"\t"$3"\t"$5"\t"$6"\t"$7"\t"$8} else {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8}}' \
> $prefix.transloc_candidate_alignments7_fragments10000
rm $prefix.transloc_candidate_alignments
rm $prefix.transloc_candidate_alignments2
rm $prefix.transloc_candidate_alignments3_fragments
rm $prefix.transloc_candidate_alignments4_fragments10000
rm $prefix.transloc_candidate_alignments5_fragments10000
rm $prefix.transloc_candidate_alignments6_fragments10000
else
touch $prefix.transloc_candidate_alignments7_fragments10000
touch ${prefix}_ref.fragments_less10000
rm transloc_list.txt
fi
#
#rows=$(wc -l ""$prefix"_ref".fragments_big | awk '{print $1}')
#cat ""$prefix"_ref".fragments_big | awk -v rowss="$rows" 'BEGIN{all=""; chrr=""; chrq=""; start=0; link=0; startq=0; endq=0} \
# {if(chrr==$1 && chrq==$2 && rowss!=NR) {end=$4; endq=$8; link=1} \
# {if(chrr==$1 && chrq!=$2 && link==0 && rowss!=NR) {print all; chrq=$2; start=$3; startq=$7; endq=$8; all=$0} \
# {if(chrr!="" && chrr!=$1 && link==0 && rowss!=NR) {print all; chrr=$1; chrq=$2; start=$3; startq=$7; all=$0} \
# {if(chrr==$1 && chrq!=$2 && link==1 && rowss!=NR) {print chrr"\t"chrq"\t"start"\t"end"\t"end-start"\ttransloc\t"startq"\t"endq; link=0; chrq=$2; start=$3; startq=$7; all=$0} \
# {if(chrr!="" && chrr!=$1 && link==1 && rowss!=NR) {print chrr"\t"chrq"\t"start"\t"end"\t"end-start"\ttransloc\t"startq"\t"endq; link=0; chrr=$1; chrq=$2; start=$3; startq=$7; all=$0} \
# {if(chrr=="") {chrr=$1; chrq=$2; start=$3; startq=$7; all=$0} \
# {if(chrr==$1 && chrq!=$2 && link==1 && rowss==NR) {print chrr"\t"chrq"\t"start"\t"end"\t"end-start"\ttransloc\t"startq"\t"endq"\n"$0} \
# {if(chrr==$1 && chrq==$2 && rowss==NR) {print chrr"\t"chrq"\t"start"\t"$4"\t"$4-start"\ttransloc\t"startq"\t"$8} \
# {if(chrr==$1 && chrq!=$2 && link==0 && rowss==NR) {print all"\n"$0} \
# {if(chrr!=$1 && link==0 && rowss==NR) {print all"\n"$0} \
# {if(chrr!=$1 && link==1 && rowss==NR) {print chrr"\t"chrq"\t"start"\t"end"\t"end-start"\ttransloc\t"startq"\t"endq"\n"$0}}}}}}}}}}}}' \
# >""$prefix"_ref".fragments_more500concat
#
#cat ${prefix}_ref.fragments_more500concat | awk '{if($2 ~ /_/) print $0}' > ${prefix}_ref.fragments_more500concat2
#cp ${prefix}_ref.fragments_more500concat ${prefix}_ref.fragments_more500concat2
#cat ${prefix}_ref.fragments_more500concat2 | awk '{print $2}' | sed 's/_/\t/g' > ${prefix}_ref.fragments_more500concat2_list
#rm ${prefix}_ref.fragments_more500concat
#cat "$alignments_folder/""$prefix"_ref".delta_filter.coordsg" | awk '{print $14}' | sort | uniq > chromosome_list.txt
#paste ${prefix}_ref.fragments_more500concat2 ${prefix}_ref.fragments_more500concat2_list > ${prefix}_ref.fragments_more500concat3
#awk 'NR==FNR{a[$1]++;next}; a[$10] {print $0}' chromosome_list.txt ${prefix}_ref.fragments_more500concat3 > ${prefix}_ref.fragments_more500concat4
#cat ${prefix}_ref.fragments_more500concat4 | awk '{if($1==$10 || $1==$9) print $0}' | cut -d $'\t' -f1-8 > ${prefix}_ref.fragments_more500concat
#rm ""$prefix"_ref".coordsg_matched_subtelofilt2
#rm ""$prefix"_ref".fragments
#rm ""$prefix"_ref".fragments_less500
#rm ""$prefix"_ref".fragments_more500
#rm ""$prefix"_ref".fragments_big
#rm ""$prefix"_ref".fragments_more500concat2
#rm ""$prefix"_ref".fragments_more500concat2_list
#rm chromosome_list.txt
#rm ""$prefix"_ref".fragments_more500concat3
#rm ""$prefix"_ref".fragments_more500concat4
#############################################
##############LARGE INVERSIONS###############
#############################################
echo ""
echo "Checking alignment sense for inversions involving majority of single chromosome bases"
echo ""
##alignments with a change in the sense compared to the reference##
##if query contigs are not orientated to the reference prior to alignment, this will look like enitre contigs are inverted##
#cat ""$prefix"_ref".coordsg_matched | awk '{if($14==$15 && $12!=$13) print $14"\t"$15"\t"$1"\t"$2"\t"$5"\tinversion\t"$3"\t"$4}' > ""$prefix"_ref".coordsg_matched_largeinv_temp
##merge inverted fragments only split by 500bp##
#cat ""$prefix"_ref".coordsg_matched_largeinv_temp | \
# awk 'BEGIN{chrr=""; startr=0; endr=0; startq=0; endq=0}; \
# {if(chrr==$1 && $3-endr<500) {print $0"\tneighbour"; chrr=$1; startr=$3; endr=$4; startq=$7; endq=$8} \
# else {print $0; chrr=$1; startr=$3; endr=$4; startq=$7; endq=$8}
# {if(chrr!=$1) {print $0; chrr=$1; startr=$3; endr=$4; startq=$7; endq=$8}}}' \
# > ""$prefix"_ref".coordsg_matched_largeinv_temp2
#rows1=$(wc -l ""$prefix"_ref".coordsg_matched_largeinv_temp2 | awk '{print $1}')
#cat ""$prefix"_ref".coordsg_matched_largeinv_temp2 | \
# awk -v rowss="$rows1" 'BEGIN{agg="first"; chrr=""; chrq=""; startr=0; endr=0; startq=0; endq=0} \
# {if(agg=="" && $9=="" && rowss!=NR) {print all; all=$0; startr=$3; endr=$4; startq=$7; endq=$8; agg=$9} \
# {if($9=="neighbour" && $4<=endr && rowss!=NR){chrr=$1; chrq=$2; endq=$8; agg=$9} \
# {if($9=="neighbour" && $4>=endr && rowss!=NR){chrr=$1; chrq=$2; endr=$4; endq=$8; agg=$9} \
# {if(agg=="neighbour" && $9=="" && rowss!=NR) {print chrr"\t"chrq"\t"startr"\t"endr"\t"endr-startr"\tinversion\t"startq"\t"endq"\taggregated"; all=$0; startr=$3; endr=$4; startq=$7; endq=$8; agg=$9} \
# {if(agg=="first"){all=$0; startr=$3; endr=$4; startq=$7; endq=$8; agg=$9} \
# {if(rowss==NR && $9=="neighbour" && $4<=endr) {print $1"\t"$2"\t"startr"\t"endr"\t"endr-startr"\tinversion\t"startq"\t"endq"\taggregated"} \
# {if(rowss==NR && $9=="neighbour" && $4>endr) {print $1"\t"$2"\t"startr"\t"$4"\t"$4-startr"\tinversion\t"startq"\t"endq"\taggregated"} \
# {if(rowss==NR && $9=="" && agg=="neighbour") {print chrr"\t"chrq"\t"startr"\t"endr"\t"endr-startr"\tinversion\t"startq"\t"endq"\taggregated\n"$0} \
# {if(rowss==NR && $9=="" && agg==""){print all"\n"$0}}}}}}}}}}' > ""$prefix"_ref".coordsg_matched_largeinv_temp3
#cat ""$prefix"_ref".coordsg_matched_largeinv_temp3 | awk '{if($9=="aggregated") {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8} else {print $0}}' > ""$prefix"_ref".coordsg_matched_largeinv
#rm ""$prefix"_ref".coordsg_matched_largeinv_temp
#rm ""$prefix"_ref".coordsg_matched_largeinv_temp2
#rm ""$prefix"_ref".coordsg_matched_largeinv_temp3
echo ""
echo ""
echo "######################################################################################################"
echo " USING NON-GLOBAL ALIGNMENT FOR INVERSIONS, DUPLICATIONS AND CONTRACTIONS"
echo "######################################################################################################"
echo ""
echo ""
echo "Matching chromosomes based on names, using '_' seperator and filtering chrMT"
echo ""
#tail -n +5 "$alignments_folder/""$prefix"_ref".delta_filter.coords" | sed 's/_/\t/' | awk '!/chrMT/{if($14==$15) {print $0}; if($14==$16) {print $0}}' |\
# awk '{if($16 == "") {print $0}} \
# {if($16!="") {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12"\t"$13"\t"$14"\t"$15"_"$16}}' \
# > ""$prefix"_ref".coords_matched
awk 'NR==FNR{a[$1,$2]++;next};a[$14,$15] {print $0}' ""$prefix"_chromosome_pairs.txt" "$alignments_folder/""$prefix"_ref".delta_filter.coords" > ""$prefix"_ref".coords_matched
##All those calls that start before the end of the subtelomeric region or finish after are filtered
if [[ $filter_subtelomeric_region == "yes" ]]
then
awk 'FNR==NR{a[$1]=$2"\t"$3;next} ($14 in a) {print $0"\t"a[$14]}' $subtelo_coords ""$prefix"_ref".coords_matched |\
awk '{if($2 > $16 && $1 < $17) {print $0}}' |\
awk -F'\t' 'BEGIN { OFS = FS }; NF{NF-=2};1' > ""$prefix"_ref".coords_matched_subtelofilt
else
cp ""$prefix"_ref".coords_matched ""$prefix"_ref".coords_matched_subtelofilt
fi
awk 'NR==FNR{a[$1,$2]++;next};a[$15,$14] {print $0}' ""$prefix"_chromosome_pairs.txt" "$alignments_folder/""$prefix"_query".delta_filter.coords" > ""$prefix"_query".coords_matched
##All those calls that start before the end of the subtelomeric region or finish after are filtered
if [[ $filter_subtelomeric_region == "yes" ]]
then
awk 'FNR==NR{a[$1]=$2"\t"$3;next} ($14 in a) {print $0"\t"a[$14]}' $subtelo_coords ""$prefix"_query".coords_matched |\
awk '{if($2 > $16 && $1 < $17) {print $0}}' |\
awk -F'\t' 'BEGIN { OFS = FS }; NF{NF-=2};1' > ""$prefix"_query".coords_matched_subtelofilt
else
cp ""$prefix"_query".coords_matched ""$prefix"_query".coords_matched_subtelofilt
fi
#############################################
#################INVERSIONS##################
#############################################
echo ""
echo "Looking for interchromosomal changes in alignment sense, filtering for 1kb fragments and merging closely neighbouring calls"
echo ""
##Now looking for region within the same chromosome which swap sense and then take the size of the swapped sense
##Get the sense of the majority of the alignments between any two chromosomes and record as the same (1) or opposite (-1) as done with the alignment##
cat ""$prefix"_ref".coordsg_matched_subtelofilt | \
awk '{print $0"\t"$13*$6}' |\
awk '{a[$15]+=$16} END{for(i in a) {print i,a[i]}}' |\
sed 's/ /\t/g' | while read chr
do
chr2=$( echo $chr | awk '{print $1}' )
sense=$( echo $chr | awk '{print $2}' )
cat ${prefix}_ref.coordsg_matched | awk '{print $14"\t"$15}' | sort -u | awk -v chr2="$chr2" -v sense="$sense" '{if($2==chr2) print $1"\t"$2"\t"sense}'
done |\
awk '{if($3>0) {print $1"\t"$2"\t1"} else {print $1"\t"$2"\t-1"}}' > ""$prefix"_ref".coords_matched.sense
awk 'FNR==NR{c[$1, $2, $3]++;next} (($14, $15, 1) in c) {print $0"\t1"}' ""$prefix"_ref".coords_matched.sense ""$prefix"_ref".coords_matched_subtelofilt > ""$prefix"_ref".coords_matched_subtelofilt_sensetemp1
awk 'FNR==NR{c[$1, $2, $3]++;next} (($14, $15, -1) in c) {print $0"\t-1"}' ""$prefix"_ref".coords_matched.sense ""$prefix"_ref".coords_matched_subtelofilt > ""$prefix"_ref".coords_matched_subtelofilt_sensetemp2
cat ""$prefix"_ref".coords_matched_subtelofilt_sensetemp1 ""$prefix"_ref".coords_matched_subtelofilt_sensetemp2 | \
sort -k14,14 -k1V > ""$prefix"_ref".coords_matched_subtelofilt_sense
##look for change in global alignment sense and local##
cat ""$prefix"_ref".coords_matched_subtelofilt_sense | \
awk '{if($13!=$16) {print $0"\tinversion"}}' > ""$prefix"_ref".coords_matched_subtelofilt_sense_inv
##trimmed and inverted coordinates in query##
cat ""$prefix"_ref".coords_matched_subtelofilt_sense_inv | \
awk '{print $14"\t"$15"\t"$1"\t"$2"\t"$5"\tinversion\t"$4"\t"$3}' > ""$prefix"_ref".coords_matched_subtelofilt_sense_inv_trimmed
cat ""$prefix"_ref".coords_matched_subtelofilt_sense_inv_trimmed| \
awk '$5>=50{print $0}' > ""$prefix"_ref".inv_50
cat ""$prefix"_ref".inv_50 | \
awk '$5>=1000{print $0}' > ""$prefix"_ref".inv_1000
###label any overlapping inversion calls or within 500bp (can be changed but seems fair for 1kb calls) as neighbours###
cat ""$prefix"_ref".inv_1000 | \
awk 'BEGIN{chrr=""; startr=0; endr=0; startq=0; endq=0}; \
{if(chrr==$1 && $3-endr<500) {print $0"\tneighbour"; chrr=$1; startr=$3; endr=$4; startq=$7; endq=$8} \
else {print $0; chrr=$1; startr=$3; endr=$4; startq=$7; endq=$8}
{if(chrr!=$1) {print $0; chrr=$1; startr=$3; endr=$4; startq=$7; endq=$8}}}' \
> ""$prefix"_ref".inv_1000_neighbours
##this is just used to help print the last line during aggregation
rows2=$(wc -l ""$prefix"_ref".inv_1000_neighbours | awk '{print $1}')
###aggregate all neighbours and take the proper start and end in reference, needs to have same name in both ref and query chromosome###
cat ""$prefix"_ref".inv_1000_neighbours | \
awk -v rowss="$rows2" 'BEGIN{agg="first"; chrr=""; chrq=""; startr=0; endr=0; startq=0; endq=0} \
{if(agg=="" && $9=="" && rowss!=NR) {print all; all=$0; startr=$3; endr=$4; startq=$7; endq=$8; agg=$9} \
{if($9=="neighbour" && $4<=endr && rowss!=NR){chrr=$1; chrq=$2; endq=$8; agg=$9} \
{if($9=="neighbour" && $4>=endr && rowss!=NR){chrr=$1; chrq=$2; endr=$4; endq=$8; agg=$9} \
{if(agg=="neighbour" && $9=="" && rowss!=NR) {print chrr"\t"chrq"\t"startr"\t"endr"\t"endr-startr"\tinversion\t"startq"\t"endq"\taggregated"; all=$0; startr=$3; endr=$4; startq=$7; endq=$8; agg=$9} \
{if(agg=="first"){all=$0; startr=$3; endr=$4; startq=$7; endq=$8; agg=$9} \
{if(rowss==NR && $9=="neighbour" && $4<=endr) {print $1"\t"$2"\t"startr"\t"endr"\t"endr-startr"\tinversion\t"startq"\t"endq"\taggregated"} \
{if(rowss==NR && $9=="neighbour" && $4>endr) {print $1"\t"$2"\t"startr"\t"$4"\t"$4-startr"\tinversion\t"startq"\t"endq"\taggregated"} \
{if(rowss==NR && $9=="" && agg=="neighbour") {print chrr"\t"chrq"\t"startr"\t"endr"\t"endr-startr"\tinversion\t"startq"\t"endq"\taggregated\n"$0} \
{if(rowss==NR && $9=="" && agg==""){print all"\n"$0}}}}}}}}}}' \
> ""$prefix"_ref".inv_1000_neighbours_agg
rm ""$prefix"_ref".coords_matched.sense
rm ""$prefix"_ref".coords_matched_subtelofilt_sensetemp1
rm ""$prefix"_ref".coords_matched_subtelofilt_sensetemp2
rm ""$prefix"_ref".coords_matched_subtelofilt_sense_inv
rm ""$prefix"_ref".coords_matched_subtelofilt_sense_inv_trimmed
rm ""$prefix"_ref".inv_1000_neighbours
#############################################
################DUPLICATIONS#################
#############################################
echo ""
echo "Locating alignment overlaps for duplication assignment"
echo ""
##Get all alignments that overlap greater than 50bp with the previous alignment, tag those were sense gets inverted##
##change value of query overlap if both strands in opposite sense to ref##
cat ""$prefix"_ref".coords_matched_subtelofilt |\
awk 'BEGIN{chrr=""; chrq=""; endr=0; endq=0} \
{if(chrr==$14 && chrq==$15 && $13==sense && endr>=$1+50) {print $0"\t"startr"\t"endr"\t"startq"\t"endq"\t"$1-endr"\t"sense"\t"$3-endq"\ttandem_dup"; startr=$1; endr=$2; startq=$3; endq=$4; sense=$13} \
{if(chrr==$14 && chrq==$15 && $13!=sense && endr>=$1+50) {print $0"\t"startr"\t"endr"\t"startq"\t"endq"\t"$1-endr"\t"sense"\tINVERTED\ttandem_dup_rev"; startr=$1; endr=$2; startq=$3; endq=$4; sense=$13} \
{if(chrr==$14 && chrq==$15 && endr<$1+50) {startr=$1; endr=$2; startq=$3; endq=$4; sense=$13} \
{if(chrr==$14 && chrq!=$15) {chrq=$15; startr=$1; endr=$2; startq=$3; endq=$4; sense=$13} \
{if(chrr!=$14) {chrr=$14; chrq=$15; startr=$1; endr=$2; startq=$3; endq=$4; sense=$13}}}}}}' |\
awk '{if($22!="INVERTED" && $13==-1 && $21==-1) \
{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12"\t"$13"\t"$14"\t"$15"\t"$16"\t"$17"\t"$18"\t"$19"\t"$20"\t"$21"\t"$22*-1"\t"$23}\
else {print $0}}' > ""$prefix"_ref".coords_matched_subtelofilt2
##remove rDNA##
if [[ $rDNA_filter == "yes" ]]
then
cat ""$prefix"_ref".coords_matched_subtelofilt2 |\
awk '{if($14=="chrXII" && $1<=445500) {print$0} \
{if($14=="chrXII" && $2>=485500) {print $0}\
{if($14!="chrXII") {print $0}}}}' > ""$prefix"_ref".coords_overlaps
else
cp ""$prefix"_ref".coords_matched_subtelofilt2 ""$prefix"_ref".coords_overlaps
fi
##list of pure clean, less than 50bp overlaps or gaps in the query and with an overlap in the reference##
cat ""$prefix"_ref".coords_overlaps | awk '{if($22!="INVERTED" && $22<=50 && $22>=-50) {print $0"\tclean"}}' > ""$prefix"_ref".coords_overlaps_clean
##list of positive gaps with and without corresponding deletion##
cat ""$prefix"_ref".coords_overlaps | awk '{if($22!="INVERTED" && $22>50) {print $0}}' > ""$prefix"_ref".coords_overlaps_pos
##Only print those overlaps, with a gap following the overlap, with those that match locations of insertions in the 50bp calls in both senses##
awk 'FNR==NR{c[$2, $3, $4]++;next} (($15, $17, $1) in c) > 0' ""$prefix"_query".gaps_50 ""$prefix"_ref".coords_overlaps_pos > ""$prefix"_ref".coords_overlaps_pos_tempforward
awk 'FNR==NR{c[$2, $3, $4]++;next} (($15, $1, $17) in c) > 0' ""$prefix"_query".gaps_50 ""$prefix"_ref".coords_overlaps_pos > ""$prefix"_ref".coords_overlaps_pos_tempreverse
cat ""$prefix"_ref".coords_overlaps_pos_tempforward ""$prefix"_ref".coords_overlaps_pos_tempreverse > ""$prefix"_ref".coords_overlaps_pos_match
cat ""$prefix"_ref".coords_overlaps_pos_match ""$prefix"_ref".coords_overlaps_clean |\
sort -k1,1 -k3V |\
awk '{print $14"\t"$15"\t"$1"\t"$17"\t"$20*-1"\tduplication\t"$19"\t"$3}' > ""$prefix"_ref".coords_dups_50
cat ""$prefix"_ref".coords_dups_50 | awk '$5>=1000{print $0}' > ""$prefix"_ref".coords_dups_1000
rm ""$prefix"_ref".coords_matched_subtelofilt2
rm ""$prefix"_ref".coords_overlaps
rm ""$prefix"_ref".coords_overlaps_clean
rm ""$prefix"_ref".coords_overlaps_pos
rm ""$prefix"_ref".coords_overlaps_pos_tempforward
rm ""$prefix"_ref".coords_overlaps_pos_tempreverse
rm ""$prefix"_ref".coords_overlaps_pos_match
#############################################
################CONTRACTIONS#################
#############################################
echo ""
echo "Locating alignment overlaps for contraction assignment"
echo ""
##Get all alignments that overlap greater than 50bp with the previous alignment, tag those were sense gets inverted##
##change value of query overlap if both strands in opposite sense to ref##
cat ""$prefix"_query".coords_matched_subtelofilt |\
awk 'BEGIN{chrr=""; chrq=""; endr=0; endq=0} \
{if(chrr==$14 && chrq==$15 && $13==sense && endr>=$1+50) {print $0"\t"startr"\t"endr"\t"startq"\t"endq"\t"$1-endr"\t"sense"\t"$3-endq"\ttandem_dup"; startr=$1; endr=$2; startq=$3; endq=$4; sense=$13} \
{if(chrr==$14 && chrq==$15 && $13!=sense && endr>=$1+50) {print $0"\t"startr"\t"endr"\t"startq"\t"endq"\t"$1-endr"\t"sense"\tINVERTED\ttandem_dup_rev"; startr=$1; endr=$2; startq=$3; endq=$4; sense=$13} \
{if(chrr==$14 && chrq==$15 && endr<$1+50) {startr=$1; endr=$2; startq=$3; endq=$4; sense=$13} \
{if(chrr==$14 && chrq!=$15) {chrq=$15; startr=$1; endr=$2; startq=$3; endq=$4; sense=$13} \
{if(chrr!=$14) {chrr=$14; chrq=$15; startr=$1; endr=$2; startq=$3; endq=$4; sense=$13}}}}}}' |\
awk '{if($22!="INVERTED" && $13==-1 && $21==-1) \
{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12"\t"$13"\t"$14"\t"$15"\t"$16"\t"$17"\t"$18"\t"$19"\t"$20"\t"$21"\t"$22*-1"\t"$23}\
else {print $0}}' > ""$prefix"_query".coords_matched_subtelofilt2
##remove rDNA##
if [[ $rDNA_filter == "yes" ]]
then
cat ""$prefix"_query".coords_matched_subtelofilt2 |\
awk '{if($14=="chrXII" && $1<=445500) {print$0} \
{if($14=="chrXII" && $2>=485500) {print $0}\
{if($14!="chrXII") {print $0}}}}' > ""$prefix"_query".coords_overlaps
else
cp ""$prefix"_query".coords_matched_subtelofilt2 ""$prefix"_query".coords_overlaps
fi
##list of pure clean, less than 50bp overlaps or gaps in the query and with an overlap in the reference##
cat ""$prefix"_query".coords_overlaps | awk '{if($22!="INVERTED" && $22<=50 && $22>=-50) {print $0"\tclean"}}' > ""$prefix"_query".coords_overlaps_clean
##list of positive gaps with and without corresponding deletion##
cat ""$prefix"_query".coords_overlaps | awk '{if($22!="INVERTED" && $22>50) {print $0}}' > ""$prefix"_query".coords_overlaps_pos
##Only print those overlaps, with a gap following the overlap, with those that match locations of insertions in the 50bp calls in both senses##
awk 'FNR==NR{c[$2, $3, $4]++;next} (($15, $17, $1) in c) > 0' ""$prefix"_ref".gaps_50 ""$prefix"_query".coords_overlaps_pos > ""$prefix"_query".coords_overlaps_pos_tempforward
awk 'FNR==NR{c[$2, $3, $4]++;next} (($15, $1, $17) in c) > 0' ""$prefix"_ref".gaps_50 ""$prefix"_query".coords_overlaps_pos > ""$prefix"_query".coords_overlaps_pos_tempreverse
cat ""$prefix"_query".coords_overlaps_pos_tempforward ""$prefix"_query".coords_overlaps_pos_tempreverse > ""$prefix"_query".coords_overlaps_pos_match
cat ""$prefix"_query".coords_overlaps_pos_match ""$prefix"_query".coords_overlaps_clean |\
sort -k1,1 -k3V |\
awk '{print $15"\t"$14"\t"$19"\t"$3"\t"$20*-1"\tcontraction\t"$1"\t"$17}' > ""$prefix"_query".coords_dups_50
cat ""$prefix"_query".coords_dups_50 | awk '$5>=1000{print $0}' > ""$prefix"_query".coords_dups_1000
rm ""$prefix"_query".coords_matched_subtelofilt2
rm ""$prefix"_query".coords_overlaps
rm ""$prefix"_query".coords_overlaps_clean
rm ""$prefix"_query".coords_overlaps_pos
rm ""$prefix"_query".coords_overlaps_pos_tempforward
rm ""$prefix"_query".coords_overlaps_pos_tempreverse
rm ""$prefix"_query".coords_overlaps_pos_match
##############################################
########COMBINING CALLS FOR FILTERING#########
##############################################
echo ""
echo ""
echo "##############################################################################################################"
echo "Combining both deletions, insertion, inversions and duplications and identifying regions of more than one call"
echo "##############################################################################################################"
echo ""
echo ""
echo "Filtering clean inversions using deletion and insertion information"
echo ""
####Inversions will take precedance if previously both an insertion and deletion was labelled at the same location####
####This is due to the global alignment filter removing them and therefore they are missing only due to this fault####
##only using 1kb for now, joining DELs, INSs, and INVs##
#cat ""$prefix"_ref".gaps_1000 ""$prefix"_query".gaps_1000 ""$prefix"_ref".inv_1000_neighbours_agg ""$prefix"_ref".fragments_more500concat | sort -k1,1 -k3V > $prefix.1000bp_invfilt
cat ""$prefix"_ref".gaps_1000 ""$prefix"_query".gaps_1000 ""$prefix"_ref".inv_1000_neighbours_agg $prefix.transloc_candidate_alignments7_fragments10000 | sort -k1,1 -k3V > $prefix.1000bp_invfilt
##filter out rDNA section##
if [[ $rDNA_filter == "yes" ]]
then
cat $prefix.1000bp_invfilt | awk '{if($1=="chrXII" && $3<=445500) {print$0} \
{if($1=="chrXII" && $4>=485500) {print $0}\
{if($1!="chrXII") {print $0}}}}' \
> $prefix.1000bp_invfilt_r
else
cp $prefix.1000bp_invfilt $prefix.1000bp_invfilt_r
fi
##index all matching SV calls and label them with numbers, so each group has a unique value, then filter only those with assigned values##
##then in groups with inversion, deletion and insertion, take inversion as the call and deletion as the position##
rows3=$(wc -l $prefix.1000bp_invfilt_r | awk '{print $1}')
cat $prefix.1000bp_invfilt_r | awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8}' | \
awk -v rowss="$rows3" 'BEGIN{all=""; num=0; chrr=""; chrq=""; startr=0; endr=0; cont=0} \
{if(rowss!=NR && chrr==$1 && chrq==$2 && startr>=$3-500 && startr<=$3+500 || rowss!=NR && chrr==$1 && chrq==$2 && endr>=$4-500 && endr<=$4+500 || rowss!=NR && chrr==$1 && chrq==$2 && startr<=$3 && endr>=$4 || rowss!=NR && chrr==$1 && chrq==$2 && startr>=$3 && endr<=$4) \
{print all"\t"num; startr=$3; endr=$4; all=$0; cont=1} \
{if(rowss!=NR && chrr==$1 && chrq==$2 && cont==0 && startr<$3-500 && endr<$4-500 || rowss!=NR && chrr==$1 && chrq==$2 && cont==0 && startr>=$3+500 && endr<=$4+500) \
{print all; startr=$3; endr=$4; all=$0} \
{if(rowss!=NR && chrr==$1 && chrq==$2 && cont==1 && startr<$3-500 && endr<$4-500 || rowss!=NR && chrr==$1 && chrq==$2 && cont==1 && startr>=$3+500 && endr<=$4+500) \
{print all"\t"num; startr=$3; endr=$4; all=$0; num=num+1; cont=0} \
{if(chrr=="") {chrr=$1; chrq=$2; startr=$3; endr=$4; all=$0; num=1} \
{if(rowss!=NR && chrr==$1 && chrq!=$2 && cont==0) \
{print all; chrr=$1; chrq=$2; startr=$3; endr=$4; all=$0} \
{if(rowss!=NR && chrr==$1 && chrq!=$2 && cont==1) \
{print all"\t"num; chrr=$1; chrq=$2; startr=$3; endr=$4; all=$0; num=num+1; cont=0} \
{if(rowss!=NR && chrr!=$1 && cont==0) \
{print all; chrr=$1; chrq=$2; startr=$3; endr=$4; all=$0} \
{if(rowss!=NR && chrr!=$1 && cont==1) \
{print all"\t"num; chrr=$1; chrq=$2; startr=$3; endr=$4; all=$0; num=num+1} \
{if(rowss==NR && chrr==$1 && chrq==$2 && startr>=$3-500 && startr<=$3+500 || rowss==NR && chrr==$1 && chrq==$2 && endr>=$4-500 && endr<=$4+500 || rowss==NR && chrr==$1 && chrq==$2 && startr<=$3 && endr>=$4 ||rowss==NR && chrr==$1 && chrq==$2 && startr>=$3 && endr<=$4) \
{print all"\t"num"\n"$0"\t"num} \
{if(rowss==NR && chrr==$1 && chrq==$2 && cont==0 && startr<$3-500 && endr<$4-500 || rowss==NR && chrr==$1 && chrq==$2 && cont==0 && startr>=$3+500 && endr<=$4+500) \
{print all"\n"$0} \
{if(rowss==NR && chrr==$1 && chrq==$2 && cont==1 && startr<$3-500 && endr<$4-500 || rowss==NR && chrr==$1 && chrq==$2 && cont==1 && startr>=$3+500 && endr<=$4+500) \
{print all"\t"num"\n"$0} \
{if(rowss==NR && chrr!=$1 && cont==0) \
{print all"\n"$0} \
{if(rowss==NR && chrr!=$1 && cont==1) \
{print all"\t"num"\n"$0}}}}}}}}}}}}}}' |\
awk '$9!="" {print $0}' |\
sort -k9,9V -k6 > $prefix.1000bp_invfilt_r_groups
##remove any value that only had it once, generally for those that have been linked to translocations##
awk -F'\t' 'NR==FNR { dup[$0]; next; } $9 in dup' <(awk -F'\t' '{print $9}' $prefix.1000bp_invfilt_r_groups | sort | uniq -d) $prefix.1000bp_invfilt_r_groups > $prefix.1000bp_invfilt_r_groups2
##if inversion has insertion and deletion alongside it attach the deletion values##
##or if inversion is greater than 30kb use it anyway, it will be translocation associated
cat $prefix.1000bp_invfilt_r_groups2 | awk 'BEGIN{del=0; ins=0; inv=0; dex=1; sv=""; count=0} \
{if($9==dex && $6=="deletion" && count==0) {print $0; count=1; alldel=$0} \
{if($9==dex && $6=="insertion" && count==1) {print $0; count=2} \
{if($9==dex && $6=="insertion" && count==0) {print $0} \
{if($9==dex && $6=="inversion" && count==0 && $5 < 30000) {print $0; count=0} \
{if($9==dex && $6=="inversion" && count==1 && $5 < 30000) {print $0; count=0} \
{if($9==dex && $6=="inversion" && count==0 && $5 >= 30000) {print $0"\t"$0; count=0} \
{if($9==dex && $6=="inversion" && count==1 && $5 >= 30000) {print $0"\t"$0; count=0} \
{if($9==dex && $6=="inversion" && count==2) {print $0"\t"alldel; count=0} \
{if($9!=dex && $6=="deletion" && count==0) {print $0; count=1; alldel=$0; dex=$9} \
{if($9!=dex && $6=="deletion" && count==1) {print $0; count=1; alldel=$0; dex=$9} \
{if($9!=dex && $6=="deletion" && count==2) {print $0; count=1; alldel=$0; dex=$9} \
{if($9!=dex && $6=="inversion" && $5 >= 30000) {print $0"\t"$0; count=1; alldel=$0; dex=$9}}}}}}}}}}}}}'\
> $prefix.1000bp_invfilt_r_groups3
##only take those INVs that have the deletion values alongside it##
maxdex=$(sort -k9 -n $prefix.1000bp_invfilt_r_groups3 | tail -1 | awk '{print $9}')
tac $prefix.1000bp_invfilt_r_groups3 | awk -v maxdexx="$maxdex" 'BEGIN{inv=0; dex=maxdexx} \
{if(dex==$9 && $10=="" && inv==0) {} \
{if(dex==$9 && $10=="" && inv==1) {} \
{if(dex==$9 && $10!=""){print $1"\t"$2"\t"$12"\t"$13"\t"$14"\t"$6"\t"$16"\t"$17"\t"$18; inv=1}
{if(dex!=$9 && $10=="") {dex=$9; inv=0} \
{if(dex!=$9 && $10!=""){print $1"\t"$2"\t"$12"\t"$13"\t"$14"\t"$6"\t"$16"\t"$17"\t"$18; inv=1; dex=$9}}}}}}' |\
sort -k9,9V -k6 |\
awk 'BEGIN{FS=OFS="\t"} NF{--NF};1' > $prefix.1000bp_inversionsclean
rm $prefix.1000bp_invfilt
rm $prefix.1000bp_invfilt_r
rm $prefix.1000bp_invfilt_r_groups
rm $prefix.1000bp_invfilt_r_groups2
rm $prefix.1000bp_invfilt_r_groups3
#######################################################################
########COMBINING CALLS AND REMOVING ALIGNMENT SPECIFIC ISSUES#########
#######################################################################
echo ""
echo "Combining all called SVs"
echo ""
#####50bp-1kb######
##remove insertions and deletion due to mummer3 alignment gaps issue which occur exactly the same in both ref and query yet don't correspond to an inversion##
##therefore remove any deletion or insertion calls with exactly the same coords in ref and query##
tac ""$prefix"_ref".gaps_50 ""$prefix"_query".gaps_50 |\
sort -k1,1 -k3V |\
awk 'BEGIN{startr=""; endr=""; startq=""; endq=""} {if(startr==$3 && endr==$4 && startq==$7 && endq==$8 || startr==$3 && endr==$4 && startq==$8 && endq==$7 || startr==$4 && endr==$3 && startq==$7 && endq==$8 || startr==$4 && endr==$3 && startq==$8 && endq==$7) {print $0"\texact\t"size} else {print $0; startr=$3; endr=$4; startq=$7; endq=$8; size=$5}}' > $prefix.gaps_50filter_temp
tac $prefix.gaps_50filter_temp |\
awk 'BEGIN{startr=""; endr=""; startq=""; endq=""} {if(startr==$3 && endr==$4 && startq==$7 && endq==$8 || startr==$3 && endr==$4 && startq==$8 && endq==$7 || startr==$4 && endr==$3 && startq==$7 && endq==$8 || startr==$4 && endr==$3 && startq==$8 && endq==$7) {print $0"\texact\t"size} else {print $0; startr=$3; endr=$4; startq=$7; endq=$8; size=$5}}' |\
awk '{if($9=="exact" && $5 > $10) {print $0"\t"$5-$10} else if($9=="exact" && $10 > $5) {print $0"\t"$10-$5} else {print $0}}' |\
awk '{if($11>5000) {print $0} else if($9!="exact"){print $0}}' |\
awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8}' |\
sort -k1,1 -k3V > $prefix.gaps_50filtered
##50bp calls do not have inversions YET, need to filter them using INDEL info as before MAYBE....##
cat $prefix.gaps_50filtered ${prefix}_ref.coords_dups_50 ${prefix}_query.coords_dups_50 | sort -V -k1 -k3 | sort -V -k1 |\
awk '{if($5<1000) print $0}'> $prefix.50bp
##filter out rDNA section##
if [[ $rDNA_filter == "yes" ]]
then
cat $prefix.50bp | awk '{if($1=="chrXII" && $3<=445500) {print$0} \
{if($1=="chrXII" && $4>=485500) {print $0}\
{if($1!="chrXII") {print $0}}}}' \
>$prefix.50bp_r
else
cp $prefix.50bp $prefix.50bp_r
fi
##removes doubles, more important for 50bp as it appears more, possibly marker for inversions....Could do as is done with 1kb inversions##
cat $prefix.50bp_r | awk 'BEGIN{start=0; end=0} {if(start==$3 || end==$4) {print $0"\tdouble" ; start=$3; end=$4} \
{if(start==0 && end ==0 || start!=$3 || end!=$4) {print $0; start=$3; end=$4}}}' > $prefix.50bp_doubles
#####1kb->######
##remove insertions and deletions due to mummer3 alignment gaps issue which occur exactly the same in both ref and query yet don't correspond to an inversion##
##therefore remove any deletion or insertion calls with exactly the same coords in ref and query##
tac ""$prefix"_ref".gaps_1000 ""$prefix"_query".gaps_1000 |\
sort -k1,1 -k3V |\
awk 'BEGIN{startr=""; endr=""; startq=""; endq=""} {if(startr==$3 && endr==$4 && startq==$7 && endq==$8 || startr==$3 && endr==$4 && startq==$8 && endq==$7 || startr==$4 && endr==$3 && startq==$7 && endq==$8 || startr==$4 && endr==$3 && startq==$8 && endq==$7) {print $0"\texact\t"size} else {print $0; startr=$3; endr=$4; startq=$7; endq=$8; size=$5}}' > $prefix.gaps_1000filter_temp
tac $prefix.gaps_1000filter_temp |\
awk 'BEGIN{startr=""; endr=""; startq=""; endq=""} {if(startr==$3 && endr==$4 && startq==$7 && endq==$8 || startr==$3 && endr==$4 && startq==$8 && endq==$7 || startr==$4 && endr==$3 && startq==$7 && endq==$8 || startr==$4 && endr==$3 && startq==$8 && endq==$7) {print $0"\texact\t"size} else {print $0; startr=$3; endr=$4; startq=$7; endq=$8; size=$5}}' |\
awk '{if($9=="exact" && $5 > $10) {print $0"\t"$5-$10} else if($9=="exact" && $10 > $5) {print $0"\t"$10-$5} else {print $0}}' |\
awk '{if($11>5000) {print $0} else if($9!="exact"){print $0}}' |\
awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8}' |\
sort -k1,1 -k3V > $prefix.gaps_1000filtered
cat $prefix.gaps_1000filtered ""$prefix"_ref".coords_dups_1000 ""$prefix"_query".coords_dups_1000 $prefix.transloc_candidate_alignments7_fragments10000 $prefix.1000bp_inversionsclean | sort -k1,1 -k3V > $prefix.1000bp
##filter out rDNA section##
if [[ $rDNA_filter == "yes" ]]
then
cat $prefix.1000bp | awk '{if($1=="chrXII" && $3<=445500) {print$0} \
{if($1=="chrXII" && $4>=485500) {print $0}\
{if($1!="chrXII") {print $0}}}}' \
>$prefix.1000bp_r
else
cp $prefix.1000bp $prefix.1000bp_r
fi
##labelling those that overlap or are very close to the other, seperately defining if an inversion is involved or not##
##then perform it in the opposite sense and once more##
tac $prefix.1000bp_r | awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8}' | \
awk 'BEGIN{start=0; end=0; sv=""} \
{if(start>=$3-500 && start<=$3+500 && sv=="inversion" || end>=$4-500 && end<=$4+500 && sv=="inversion" || start<=$3 && end>=$4 && sv=="inversion" || start>=$3 && end<=$4 && sv=="inversion") \
{print $0"\tdouble_inversion"; start=$3; end=$4} \
{if(start>=$3-500 && start<=$3+500 && $6=="inversion" || end>=$4-500 && end<=$4+500 && $6=="inversion" || start<=$3 && end>=$4 && $6=="inversion" || start>=$3 && end<=$4 && $6=="inversion") \
{print $0"\tdouble_inversion"; start=$3; end=$4; sv=$6} \
{if(start>=$3-500 && start<=$3+500 && sv!="inversion" || end>=$4-500 && end<=$4+500 && sv!="inversion" || start<=$3 && end>=$4 && sv!="inversion" || start>=$3 && end<=$4 && sv!="inversion") \
{print $0"\tdouble"; start=$3; end=$4; sv=$6} \
{if(start<=$3-500 || start>=$3+500 || end<=$4-500 || end>=$4+500) {print $0; start=$3; end=$4; sv=$6} \
{if(start==0 && end==0) {print $0; start=$3; end=$4; sv=$6}}}}}}' \
> $prefix.1000bp_r_doubles
tac $prefix.1000bp_r_doubles | \
awk 'BEGIN{start=0; end=0; sv=""} \
{if(start>=$3-500 && start<=$3+500 && sv=="inversion" || end>=$4-500 && end<=$4+500 && sv=="inversion" || start<=$3 && end>=$4 && sv=="inversion" || start>=$3 && end<=$4 && sv=="inversion") \
{print $0"\tdouble_inversion"; start=$3; end=$4} \
{if(start>=$3-500 && start<=$3+500 && $6=="inversion" || end>=$4-500 && end<=$4+500 && $6=="inversion" || start<=$3 && end>=$4 && $6=="inversion" || start>=$3 && end<=$4 && $6=="inversion") \
{print $0"\tdouble_inversion"; start=$3; end=$4; sv=$6} \
{if(start>=$3-500 && start<=$3+500 && sv!="inversion" || end>=$4-500 && end<=$4+500 && sv!="inversion" || start<=$3 && end>=$4 && sv!="inversion" || start>=$3 && end<=$4 && sv!="inversion") \
{print $0"\tdouble"; start=$3; end=$4; sv=$6} \
{if(start<=$3-500 || start>=$3+500 || end<=$4-500 || end>=$4+500) {print $0; start=$3; end=$4; sv=$6} \
{if(start==0 && end==0) {print $0; start=$3; end=$4; sv=$6}}}}}}' \
> $prefix.1000bp_r_doubles2
cat $prefix.1000bp_r_doubles2 | awk '{if($6!="transloc" && $9=="double" && $10=="double_inversion") {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$10} \
{if($6!="transloc" && $9=="double_inversion" && $10=="double" || $6!="transloc" && $9=="double_inversion" && $10=="" || $9=="double_inversion" && $10=="double_inversion") {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9} \
{if($6!="transloc" && $9=="double" && $10=="") {print $0}\
{if($6=="transloc" || $9=="") {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8}\
{if($6!="transloc" && $9=="double" && $10=="double") {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9}}}}}}' \
> $prefix.1000bp_r_doubles3