# named as $spe.genome

trf genome.fasta 2 7 7 80 10 50 500 -f -d -m
perl trfRepeatMask.pl

# named as $spe.trf 

RepeatMasker -pa 36 -q -no_is -norna -nolow -div 40 -lib $TE_library -cutoff 225 -gff genome.fasta

# named as $spe.genome.out.gff 

nucmer --mum -l 50 -c 100 ref.fa query.fa
delta-filter -m -i 90 $delta > $delta.filtered
show-coords -THrd $delta.filtered > $delta.filtered.coords 
syri  -c $delta.filtered.coords -r $ref -q $query -d $delta --all --no-chrmatch

# named by $spe.syri.out 

input = $spe.syri.out
perl SyRI_Parse.pl $input
perl Covert_CPV.pl $input.SV.bed

for i in $(ls *.syri.out.SV.bed.mergeDel.CPV2InDel);do awk '{len1=0;if($7=="Insertion"){len1=$6-$5+1}else{len1=$3-$2+1};if(len1>=50 || len1<=-50){print}}' $i >$i.50.bp;done

perl Merge_SyRI_SV_spe.pl 

# out file is : Merge_Syri_bed.result.0.9.0.9.tag
perl Add_spe_column.pl Merge_Syri_bed.result.0.9.0.9 

perl Infer_1.pl
perl Intersect.pl
perl Infer_2.pl 

perl ChangeSV_sampleID.pl
awk '{if($1!~/Undefined/){print}}'  Merge_Syri_bed.result.0.9.0.9.rename.tag.infer_1.infer_2.Add >Merge_Syri_bed.result.0.9.0.9.rename.tag.infer_1.infer_2.Add.Defined
 
#split SV for VNTR :
perl split_Merged_SV_For_VNTR.pl 

#infer SV for spe: 
for i in $(ls *.syri.out.SV.bed.mergeDel.CPV2InDel);do perl infer_SV_for_mechanism.pl $i Merge_Syri_bed.result.0.9.0.9.tag.infer_1.infer_2.Add.vntr ;done 

# filter ambiguous SVs
for i in $(ls *.syri.out.SV.bed.mergeDel.CPV2InDel.infered);do perl Filter_overlaped_SV.pl  $i;done

# Check TE and tandem repeat : 
for i in $(ls *.syri.out.SV.bed.mergeDel.CPV2InDel.infered.uniq);do perl Combine_TE_TRF_SV.pl  $i;done

# call SV cluster type :
for i in $(ls *.syri.out.SV.bed.mergeDel.CPV2InDel.infered.uniq);do a=${i%%\.*};perl Call_SV_Mechanism1.pl  $i $a 1 ; done

# Check SV breakpoint homology: 
for i in $(ls *.syri.out.SV.bed.mergeDel.CPV2InDel.infered.uniq.TRF_TE);do perl Check_Homology.pl $i;done

# call SV mechanism :
for i in $(ls *.syri.out.SV.bed.mergeDel.CPV2InDel.infered.uniq.TRF_TE.homo);do a=${i%.syri.out.SV.bed.mergeDel.CPV2InDel.infered.uniq.TRF_TE.homo};echo $a;perl Call_SV_Mechanism_new.pl   $i $a.syri.out.SV.bed.mergeDel.CPV2InDel.infered.uniq.ref.Cluster_Type $a.syri.out.SV.bed.mergeDel.CPV2InDel.infered.uniq.query.Cluster_Type;done