51 lines
1.0 KiB
Perl
51 lines
1.0 KiB
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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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 = $sam_reader->get_next()) {
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my ($genome_coords_aref, $read_coords_aref) = $sam_entry->get_alignment_coords();
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my $read_name = $sam_entry->get_read_name();
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my $scaffold = $sam_entry->get_scaffold_name();
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print join("\t", $scaffold, &get_coord_string($genome_coords_aref),
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$read_name, &get_coord_string($read_coords_aref)) . "\n";
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}
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exit(0);
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}
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####
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sub get_coord_string {
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my ($coords_aref) = @_;
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my $text = "";
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foreach my $coordset (@$coords_aref) {
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my ($lend, $rend) = @$coordset;
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if ($text) {
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$text .= ",";
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}
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$text .= "$lend-$rend";
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}
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return($text);
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}
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