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1 #!/usr/bin/perl -w
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2
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3 use strict;
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4 use warnings;
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5
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6 while (<>) {
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7 if (/\tXA:Z:(\S+)/) {
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8 my $l = $1;
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9 print;
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10 my @t = split("\t");
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11 while ($l =~ /([^,;]+),([-+]\d+),([^,]+),(\d+);/g) {
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12 my $mchr = ($t[6] eq $1)? '=' : $t[6]; # FIXME: TLEN/ISIZE is not calculated!
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13 my $seq = $t[9];
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14 my $phred = $t[10];
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15 # if alternative alignment has other orientation than primary,
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16 # then print the reverse (complement) of sequence and phred string
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17 if ((($t[1]&0x10)>0) xor ($2<0)) {
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18 $seq = reverse $seq;
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19 $seq =~ tr/ACGTacgt/TGCAtgca/;
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20 $phred = reverse $phred;
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21 }
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22 print(join("\t", $t[0], 0x100|($t[1]&0x6e9)|($2<0?0x10:0), $1, abs($2), 0, $3, @t[6..7], 0, $seq, $phred, "NM:i:$4"), "\n");
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23 }
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24 } else { print; }
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25 }
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