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Merge pull request #17 from sanger-tol/dp24_treeval_parity
Updating everything
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| awk 'BEGIN{OFS="\t"}{if($1 ~ /^\@/) {print($0)} else {$2=and($2,compl(2048)); print(substr($0,2))}}' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,109 @@ | ||
| #!/usr/bin/perl | ||
| use strict; | ||
| use warnings; | ||
|
|
||
| my $prev_id = ""; | ||
| my @five; | ||
| my @three; | ||
| my @unmap; | ||
| my @mid; | ||
| my @all; | ||
| my $counter = 0; | ||
|
|
||
| while (<STDIN>){ | ||
| chomp; | ||
| if (/^@/){ | ||
| print $_."\n"; | ||
| next; | ||
| } | ||
| my ($id, $flag, $chr_from, $loc_from, $mapq, $cigar, $d1, $d2, $d3, $read, $read_qual, @rest) = split /\t/; | ||
| my $bin = reverse(dec2bin($flag)); | ||
| my @binary = split(//,$bin); | ||
| if ($prev_id ne $id && $prev_id ne ""){ | ||
| if ($counter == 1){ | ||
| if (@five == 1){ | ||
| print $five[0]."\n"; | ||
| } | ||
| else{ | ||
| my ($id_1, $flag_1, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1) = split /\t/, $all[0]; | ||
| my $bin_1 = reverse(dec2bin($flag_1)); | ||
| my @binary_1 = split(//,$bin_1); | ||
| $binary_1[2] = 1; | ||
| my $bin_1_new = reverse(join("",@binary_1)); | ||
| my $flag_1_new = bin2dec($bin_1_new); | ||
| print(join("\t",$id_1, $flag_1_new, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1)."\n"); | ||
| } | ||
| } | ||
| elsif ($counter == 2 && @five == 1){ | ||
| print $five[0]."\n"; | ||
| } | ||
| else{ | ||
| my ($id_1, $flag_1, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1) = split /\t/, $all[0]; | ||
| my $bin_1 = reverse(dec2bin($flag_1)); | ||
| my @binary_1 = split(//,$bin_1); | ||
| $binary_1[2] = 1; | ||
| my $bin_1_new = reverse(join("",@binary_1)); | ||
| my $flag_1_new = bin2dec($bin_1_new); | ||
| print(join("\t",$id_1, $flag_1_new, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1)."\n"); | ||
| } | ||
|
|
||
| $counter = 0; | ||
| undef @unmap; | ||
| undef @five; | ||
| undef @three; | ||
| undef @mid; | ||
| undef @all; | ||
| } | ||
|
|
||
| $counter++; | ||
| $prev_id = $id; | ||
| push @all,$_; | ||
| if ($binary[2]==1){ | ||
| push @unmap,$_; | ||
| } | ||
| elsif ($binary[4]==0 && $cigar =~ m/^[0-9]*M/ || $binary[4]==1 && $cigar =~ m/.*M$/){ | ||
| push @five, $_; | ||
| } | ||
| elsif ($binary[4]==1 && $cigar =~ m/^[0-9]*M/ || $binary[4]==0 && $cigar =~ m/.*M$/){ | ||
| push @three, $_; | ||
| } | ||
| elsif ($cigar =~ m/^[0-9]*[HS].*M.*[HS]$/){ | ||
| push @mid, $_; | ||
| } | ||
| } | ||
|
|
||
| if ($counter == 1){ | ||
| if (@five == 1){ | ||
| print $five[0]."\n"; | ||
| } | ||
| else{ | ||
| my ($id_1, $flag_1, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1) = split /\t/, $all[0]; | ||
| my $bin_1 = reverse(dec2bin($flag_1)); | ||
| my @binary_1 = split(//,$bin_1); | ||
| $binary_1[2] = 1; | ||
| my $bin_1_new = reverse(join("",@binary_1)); | ||
| my $flag_1_new = bin2dec($bin_1_new); | ||
| print(join("\t",$id_1, $flag_1_new, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1)."\n"); | ||
| } | ||
| } | ||
| elsif ($counter == 2 && @five == 1){ | ||
| print $five[0]."\n"; | ||
| } | ||
| else{ | ||
| my ($id_1, $flag_1, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1) = split /\t/, $all[0]; | ||
| my $bin_1 = reverse(dec2bin($flag_1)); | ||
| my @binary_1 = split(//,$bin_1); | ||
| $binary_1[2] = 1; | ||
| my $bin_1_new = reverse(join("",@binary_1)); | ||
| my $flag_1_new = bin2dec($bin_1_new); | ||
| print(join("\t",$id_1, $flag_1_new, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1)."\n"); | ||
| } | ||
|
|
||
| sub dec2bin { | ||
| my $str = unpack("B32", pack("N", shift)); | ||
| return $str; | ||
| } | ||
|
|
||
| sub bin2dec { | ||
| return unpack("N", pack("B32", substr("0" x 32 . shift, -32))); | ||
| } |
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