annotate scripts/pickOverlapPair.ex_MEM.pl @ 18:e198b686bfe4 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit edf843bf10fa262f075980626a9201078f868757
author mvdbeek
date Wed, 17 Aug 2016 11:49:25 -0400
parents ca36262102d8
children 9672fe07a232
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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1 #!/share/bin/perl
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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2 use Bio::Seq;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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3 use List::Util qw(sum);
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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4
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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5 die "perl $0 <*.excision.cluster.rpmk.refined.bp>\n" if @ARGV<0;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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7 my $title=$ARGV[0];
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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8 if ($title =~ /annotation/) {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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9 $title =~ s/excision.cluster.annotation.refined.bp/sorted.bam/;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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10 }
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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11 else {$title =~ s/excision.cluster.rpmk.refined.bp/sorted.bam/;}
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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12 #system("samtools index /home/wangj2/scratch/bill/bill_genomic/$title");
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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13
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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14 my %chrs=();
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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15 system("samtools view -H $title > header");
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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16 open (input, "<header") or die "Can't open header since $!\n";
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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17 while (my $line=<input>) {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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18 if ($line =~ /^\@SQ/) {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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19 my @a=split(/\t/, $line);
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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20 for my $j (0..$#a) {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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21 if ($a[$j] =~ /^SN:/) {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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22 $a[$j] =~ s/^SN://;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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23 $chrs{$a[$j]}=1;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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24 }
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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25 }
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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26 }
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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27 }
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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28 close input;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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29 system("rm header");
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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30
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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31 open (input, "<$ARGV[0]") or die "Can't open $ARGV[0] since $!\n";
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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32 my $header=<input>;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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33 while (my $line=<input>) {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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34 chomp($line);
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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35 my @a=split(/\t/, $line);
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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36
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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37 my $left=0;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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38 my $right=0;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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39 if ($a[4] eq "") {$left=$a[1];}
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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40 else {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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41 my @t=split(/\,/, $a[4]);
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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42 my @p=split(/\(/, $t[$#t]);
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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43 $left=$p[0];
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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44 }
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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45 if ($a[5] eq "") {$right=$a[2];}
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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46 else {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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47 my @t=split(/\,/, $a[5]);
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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48 my @p=split(/\(/, $t[0]);
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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49 $right=$p[0];
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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50 }
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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51
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52 my $leftlower=$left-500;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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53 my $leftupper=$left+500;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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54 my $rightlower=$right-500;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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55 my $rightupper=$right+500;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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56 my $chr_num=$a[0];
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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57 $chr_num =~ s/chr//;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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58 if (($chrs{$a[0]} == 1) && (! defined $chrs{$chr_num})) {$chr_num=$a[0];}
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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59 system("samtools view -Xf 0x2 $title $chr_num\:$leftlower\-$leftupper $chr_num\:$rightlower\-$rightupper > temp.sam");
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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60
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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61 open in,"temp.sam";
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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62 my %ps=();
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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63 my %me=();
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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64 my %uniqp=();
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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65 my %uniqm=();
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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66 my $ref_sup=0;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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67
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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68 while(<in>)
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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69 {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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70 chomp;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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71 my @f=split/\t/,$_,12;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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72 ## read number 1 or 2
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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73 my ($rnum)=$f[1]=~/(\d)$/;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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74
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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75 ## XT:A:*
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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76 my $xt="";
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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77 my @a=split(/\s+/, $_);
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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78 my $as=0;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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79 my $xs=0;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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80 for my $i (11..$#a) {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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81 if ($a[$i] =~ /^AS:i:/) {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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82 $a[$i] =~ s/AS:i://;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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83 $as=$a[$i];
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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84 }
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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85 elsif ($a[$i] =~ /^XS:i:/) {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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86 $a[$i] =~ s/XS:i://;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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87 $xs=$a[$i];
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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88 }
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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89 if (($xs > 0) && ($as-$xs <= $ARGV[2])) {$xt="R";}
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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90 elsif ($as > 0) {$xt="U";}
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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91 }
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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92
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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93 ## Coordinate
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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94 my $coor=$f[3];
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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95 if ($f[1]=~/r/)
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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96 {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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97 if ($xt eq "U") {$uniqm{$f[0]}=1;}
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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98 my (@cigar_m)=$f[5]=~/(\d+)M/g;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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99 my (@cigar_d)=$f[5]=~/(\d+)D/g;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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100 my (@cigar_s)=$f[5]=~/(\d+)S/g;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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101 my (@cigar_i)=$f[5]=~/(\d+)I/g;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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102 my $aln_ln=sum(@cigar_m,@cigar_d);
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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103 $me{$f[0]}=$f[3]+$aln_ln-1;
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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104 }
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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105 elsif ($f[1]=~/R/) {
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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106 $ps{$f[0]}=$f[3];
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107 if ($xt eq "U") {$uniqp{$f[0]}=1;}
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108 }
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109
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110 # ${$pe{$f[0]}}[$rnum-1]=[$xt,$coor];
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111 }
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112 close in;
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113
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114 foreach my $id (keys %ps)
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115 {
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116 # my @rid=@{$pe{$id}};
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117
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118 # if(($rid[0][0] eq "U" && $rid[1][0] eq "M") || ($rid[0][0] eq "M" && $rid[1][0] eq "U"))
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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119 # {
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120 # $soft_clip++;
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121 # print "$id\n";
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122 # }
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123
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124 if ((defined $me{$id})&&((defined $uniqp{$id})||(defined $uniqm{$id})))
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125 {
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126 if (((($ps{$id}+5)<=$right)&&($me{$id}>$right)&&($uniqm{$id}==1)) || ((($me{$id}-5)>=$left)&&($ps{$id}<$left)&&($uniqp{$id}==1))) {
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127 $ref_sup++;
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128 }
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129 }
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130 }
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131
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132 print "$a[0]\t$a[1]\t$a[2]\t$a[3]\t$left\t$right\t$ref_sup\n";
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133 system("rm temp.sam");
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134 }
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135