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#!/usr/bin/env perl
#
$argc = @ARGV;
if ($argc == 0) {
print "usage: cat aln1.sam | sam_add_rg.pl <read group id> <sample name>\n";
print "changes all alignments to have RG tags matching the new sample name.\n";
print "prints SAM format out stdout\n";
exit(0);
}
$ID = $ARGV[0];
$SM = $ARGV[1];
$in_header = 1;
while (<STDIN>) {
if ($_ =~ /^@/) {
print $_;
next;
} else {
# add the new RG group to the end of the header
if ($in_header) {
print "\@RG\tID:$ID\tSM:$SM\n";
$in_header = 0;
}
if ($_ =~ /\tRG:Z:(.+?)/) {
$_ =~ s/\tRG:Z:.+?([\t\n])/\tRG:Z:$ID$1/;
} else {
$_ =~ s/\n/\tRG:Z:$ID\n/;
}
print $_;
}
}
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