Mercurial > repos > portiahollyoak > temp
annotate scripts/mergeTagsWithGap.pl @ 17:e7d3dc3e0ec9 draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit 22724a75342e3097cd0976e4bfcfe7a19308ac4f-dirty
author | portiahollyoak |
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date | Wed, 15 Jun 2016 10:30:06 -0400 |
parents | 28d1a6f8143f |
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rev | line source |
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28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
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1 #!/share/bin/perl |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
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2 #chr2L 114333 114409 FBgn0003055_P-element harwich,1; + antisense |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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3 #chr2L 114443 114567 FBgn0003055_P-element harwich,3; + antisense |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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4 #chr2L 114636 114712 FBgn0003055_P-element harwich,1; - antisense |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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5 #chr2L 131640 131929 FBgn0003055_P-element harwich,42; + sense |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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6 #chr2L 131948 132274 FBgn0003055_P-element harwich,18; - sense |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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7 #chr2L 132027 132103 FBgn0003055_P-element harwich,1; - antisense |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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8 |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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9 use warnings; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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10 use strict; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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11 use List::Util qw(max min); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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12 |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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13 if(scalar(@ARGV)<2 || grep {/^-h/} @ARGV) |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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14 { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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15 die " |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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16 usage: mergeOverlapBed4.pl inputFile |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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17 Expects BED input with at least 4 fields. For each {chr,name} pair, |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
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18 merges overlapping ranges and prints out sorted BED4 to stdout. |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
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19 inputFile can be - or stdin to read from stdin. |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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20 "; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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21 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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22 |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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23 my $input=shift @ARGV; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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24 my $maxgap=shift @ARGV; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
portiahollyoak
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25 grep {s/^stdin$/-/i} $input; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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26 |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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27 my %item2coords; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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28 open IN,$input; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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29 while (<IN>) |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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30 { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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31 chomp; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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32 my ($chrom,$start,$end,$transposonName,$count,$strand,$transposonStrand)=split/\t/; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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33 push @{$item2coords{"$chrom;$transposonName;$transposonStrand"}},[$start,$end,$count,$strand]; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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34 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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35 close IN; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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36 |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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37 my @results; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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38 foreach my $item (keys %item2coords) |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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39 { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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40 my @sortedCoords=sort{ $a->[0]<=>$b->[0] } @{$item2coords{$item}}; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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41 my ($chrom,$tName,$tStrand)=split(/;/,$item); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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42 my ($mergeStart,$mergeEnd,$mergeCounts,$mergeStrand)=@{shift @sortedCoords}; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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43 my %sampleCounts=(); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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44 my ($breakStart,$breakEnd)=0; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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45 foreach my $sa (split/;/,$mergeCounts) |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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46 { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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47 my ($s,$c)=split/,/,$sa; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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48 $sampleCounts{$s}{$mergeStrand}=$c; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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49 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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50 foreach my $rangeRef (@sortedCoords) |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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51 { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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52 my ($rangeStart,$rangeEnd,$rangeCounts,$rangeStrand)=@{$rangeRef}; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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53 if($mergeStrand=~/\Q$rangeStrand\E$/) |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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54 { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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55 if($rangeStart>=$mergeEnd+$maxgap) |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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56 { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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57 $mergeCounts=""; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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58 foreach my $s (keys %sampleCounts) |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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59 { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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60 $mergeCounts.=$s; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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61 $mergeCounts.=",".$_.$sampleCounts{$s}{$_} foreach keys %{$sampleCounts{$s}}; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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62 $mergeCounts.=";"; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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63 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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64 if($mergeStrand eq "+") |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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65 { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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66 $breakStart=$mergeEnd; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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67 $breakEnd=$mergeEnd+$maxgap; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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68 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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69 if($mergeStrand eq "-") |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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70 { |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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71 $breakStart=$mergeStart-$maxgap; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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72 $breakEnd=$mergeStart; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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73 } |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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74 push @results,[$chrom,$mergeStart,$mergeEnd,$tName,$mergeCounts,$mergeStrand,$tStrand,"$chrom:$breakStart.$breakEnd"]; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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75 ($mergeStart,$mergeEnd,$mergeStrand)=($rangeStart,$rangeEnd,$rangeStrand); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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76 %sampleCounts=(); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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77 foreach my $sa (split/;/,$rangeCounts) |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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78 { |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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79 my ($s,$c)=split/,/,$sa; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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80 $sampleCounts{$s}{$rangeStrand}=$c; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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81 } |
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82 } |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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83 else |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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84 { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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85 $mergeEnd=max($rangeEnd,$mergeEnd); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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86 foreach my $sa (split/;/,$rangeCounts) |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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87 { |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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88 my ($s,$c)=split/,/,$sa; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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89 $sampleCounts{$s}{$rangeStrand}+=$c; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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90 } |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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91 } |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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92 } |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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93 elsif($rangeStrand eq "+") |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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94 { |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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95 $mergeCounts=""; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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96 foreach my $s (keys %sampleCounts) |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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97 { |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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98 $mergeCounts.=$s; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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99 $mergeCounts.=",".$_.$sampleCounts{$s}{$_} foreach keys %{$sampleCounts{$s}}; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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100 $mergeCounts.=";"; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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101 } |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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102 if($mergeStrand eq "+") |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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103 { |
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104 $breakStart=$mergeEnd; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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105 $breakEnd=$mergeEnd+$maxgap; |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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106 } |
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107 if($mergeStrand eq "-") |
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108 { |
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109 $breakStart=$mergeStart-$maxgap; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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110 $breakEnd=$mergeStart; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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111 } |
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112 push @results,[$chrom,$mergeStart,$mergeEnd,$tName,$mergeCounts,$mergeStrand,$tStrand,"$chrom:$breakStart.$breakEnd"]; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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113 ($mergeStart,$mergeEnd,$mergeStrand)=($rangeStart,$rangeEnd,$rangeStrand); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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114 %sampleCounts=(); |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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115 foreach my $sa (split/;/,$rangeCounts) |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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116 { |
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117 my ($s,$c)=split/,/,$sa; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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118 $sampleCounts{$s}{$rangeStrand}=$c; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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119 } |
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120 } |
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121 else |
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122 { |
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123 if($rangeStart>=$mergeEnd+$maxgap*2) |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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124 { |
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125 $mergeCounts=""; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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126 foreach my $s (keys %sampleCounts) |
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127 { |
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128 $mergeCounts.=$s; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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129 $mergeCounts.=",".$_.$sampleCounts{$s}{$_} foreach keys %{$sampleCounts{$s}}; |
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130 $mergeCounts.=";"; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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131 } |
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132 if($mergeStrand eq "+") |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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133 { |
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134 $breakStart=$mergeEnd; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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135 $breakEnd=$mergeEnd+$maxgap; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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136 } |
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137 if($mergeStrand eq "-") |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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138 { |
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139 $breakStart=$mergeStart-$maxgap; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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140 $breakEnd=$mergeStart; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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141 } |
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142 push @results,[$chrom,$mergeStart,$mergeEnd,$tName,$mergeCounts,$mergeStrand,$tStrand,"$chrom:$breakStart.$breakEnd"]; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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143 ($mergeStart,$mergeEnd,$mergeStrand)=($rangeStart,$rangeEnd,$rangeStrand); |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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144 %sampleCounts=(); |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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145 foreach my $sa (split/;/,$rangeCounts) |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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146 { |
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147 my ($s,$c)=split/,/,$sa; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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148 $sampleCounts{$s}{$rangeStrand}=$c; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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149 } |
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150 } |
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151 else |
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152 { |
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153 $breakStart=$mergeEnd; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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154 $mergeEnd=max($rangeEnd,$mergeEnd); |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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155 $breakEnd=$rangeStart; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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156 foreach my $sa (split/;/,$rangeCounts) |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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157 { |
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158 my ($s,$c)=split/,/,$sa; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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159 $sampleCounts{$s}{$rangeStrand}+=$c; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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160 } |
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161 $mergeStrand.=$rangeStrand; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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162 } |
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163 } |
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164 } |
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165 $mergeCounts=""; |
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166 foreach my $s (keys %sampleCounts) |
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167 { |
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168 $mergeCounts.=$s; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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169 $mergeCounts.=",".$_.$sampleCounts{$s}{$_} foreach keys %{$sampleCounts{$s}}; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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170 $mergeCounts.=";"; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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171 } |
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172 if($mergeStrand eq "+") |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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173 { |
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174 $breakStart=$mergeEnd; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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175 $breakEnd=$mergeEnd+$maxgap; |
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176 } |
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177 if($mergeStrand eq "-") |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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178 { |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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179 $breakStart=$mergeStart-$maxgap; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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180 $breakEnd=$mergeStart; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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181 } |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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182 push @results,[$chrom,$mergeStart,$mergeEnd,$tName,$mergeCounts,$mergeStrand,$tStrand,"$chrom:$breakStart.$breakEnd"] if $mergeEnd; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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183 } |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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184 |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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185 sub bed4Cmp |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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186 { |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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187 # For sorting by chrom, chromStart, and names -- reverse order for names |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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188 return $a->[0] cmp $b->[0] || |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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189 $a->[1] <=> $b->[1] || |
28d1a6f8143f
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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190 $b->[3] cmp $a->[3]; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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191 } |
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192 |
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193 foreach my $r (sort bed4Cmp @results) |
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194 { |
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195 print join("\t",@{$r}),"\n"; |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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196 } |