--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2.4/src/Check_integration.sh	Sat May 31 11:23:36 2014 -0400
@@ -0,0 +1,86 @@
+#!/bin/sh
+#$ -V
+#$ -cwd
+#$ -q 1-day
+#$ -m ae
+#$ -M hart.steven@mayo.edu
+#$ -l h_vmem=8G
+#$ -l h_stack=10M
+VCF_FILE=$1
+x=$2
+#VIRAL_SEQDB=/data2/bsi/tertiary/m110344/SoftTile/Mia/BLAST_DB/OBrien/Virus_PCGS.fasta #must me indexed by bwasw
+VIRAL_SEQDB=$3
+VCF_FILE=$4
+#VCF_FILE=final.vcf
+
+set -x 
+
+perl -ane '$dist=100;
+$mate=$F[4];
+$mate=~s/[A-Z]|\[|\]//g;
+@mate=split(/:/,$mate);
+$end1a=@F[1]-$dist;
+$end1b=@F[1]+$dist;
+$end2a=$dist+@mate[1];
+$end2b=$dist+@mate[1];
+print "@F[0]\t$end1a\t$end1b\n@mate[0]\t$end2a\t$end2b\n"' $VCF_FILE|
+sortBed > targets.bed
+
+
+#100 min
+time samtools view -h $x -L targets.bed |awk '(($9==0)&&($11!~/#/)&&($3!~/^chrGL/)&&($3!~/^chrM/))'|perl -ane 'print "\@@F[0]\n@F[9]\n+\n@F[10]\n"' >${x%%.bam}.res.fq
+#23 min
+time bwa mem -t 4 $VIRAL_SEQDB ${x%%.bam}.res.fq |samtools view -S - |grep gi > ${x%%.bam}.tmp.sam
+
+#find out how many hits there are
+cut -f3 ${x%%.bam}.tmp.sam|perl -ne '@_=split(":",$_);@res=split(/_/,@_[1],2);print "@res[1]"' | sort|uniq -c|sort -k1nr|tee ${x%%.bam}.Viral_maps.out |head
+#Get the reads mapping to those hits to find out where the integration site is
+
+#Read in the viruses until there is a significant drop off in number of reads (i.e. contributing less than 10%)
+perl -ne '@_=split(" ",$_);$i=$_[0]+$i;$j=$_[0];$res=$j/$i;if($res>.1){print "@_[1]\n"}' ${x%%.bam}.Viral_maps.out >${x%%.bam}.to.keep
+fgrep -f ${x%%.bam}.to.keep ${x%%.bam}.tmp.sam |cut -f1 >${x%%.bam}.reads
+
+#75min+
+
+time samtools view $x -L targets.bed |
+fgrep -f ${x%%.bam}.reads|
+awk '{if(($9==0)&&($11!~/#/)&&($3!~/^chrGL/)&&($3!~/^chrM/)&&($3!~/^\*/)){print $3"\t"$4"\t"$4"\t"$1}}'|
+tee ${x%%.bam}.unsorted.bed|
+sortBed | mergeBed -nms -d 1000|
+perl -e 'open (FILE,"$ARGV[0]") or die "cant open file\n\n";
+ $SAM="$ARGV[1]";
+ $SAM=~chomp;
+ while(<FILE>){
+chomp;
+  @_=split(/\t/,$_);
+  @reads=split(/;/,@_[3]);
+#print "LINE=$_\nRES=grep $reads[0] $SAM\n";
+  $res=`grep $reads[0] $SAM` ;
+#  print "AFTER GREP, RES=$res\n";
+  if($res){
+   @res=split(/\t/,$res);
+   print join("\t",@_[0..2],@res[2])."\n"
+   }
+  };
+ close FILE' - ${x%%.bam}.tmp.sam |
+perl -ne 's/\|/\t/g;@_=split("\t",$_);print join ("\t",@_[0..2,7])'|
+perl -pne 's/_/\t/'|  cut -f4 --complement |
+perl -e '
+ open (FILE,"$ARGV[0]") or die "cant open file\n\n";
+ $SAM="$ARGV[1]";
+ while(<FILE>){
+  chomp;
+  @_=split(/\t/,$_);
+  $res=`grep $_[3] $SAM`;
+  if($res){
+   @res=split(" ",$res);
+   $reads[0]=chomp;
+   print join("\t",@_[0..4],@res[0])."\n";
+  }
+ }
+close FILE;
+' - ${x%%.bam}.Viral_maps.out|
+perl -pne 's/_/ /g'> ${x%%.bam}.Virus.integrated.bed
+
+rm ${x%%.bam}.reads ${x%%.bam}.to.keep ${x%%.bam}.tmp.sam ${x%%.bam}.res.fq
+echo "DONE with $x"