35 lines
700 B
Perl
35 lines
700 B
Perl
#!/usr/bin/env perl
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use strict;
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use warnings;
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use FindBin;
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use lib ("$FindBin::RealBin/../../PerlLib");
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use SAM_reader;
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use SAM_entry;
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use Nuc_translator;
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my $usage = "usage: $0 file.sam\n\n";
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my $sam_file = $ARGV[0] or die $usage;
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main: {
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my $sam_reader = new SAM_reader($sam_file);
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while (my $sam_entry = $sam_reader->get_next()) {
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my $read_name = $sam_entry->reconstruct_full_read_name();
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my $sequence = $sam_entry->get_sequence();
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if ((! $sam_entry->is_query_unmapped()) && $sam_entry->get_query_strand() eq '-') {
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$sequence = &reverse_complement($sequence);
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}
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print ">$read_name\n$sequence\n";
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}
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exit(0);
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}
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