20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,50 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib ("$FindBin::RealBin/../../PerlLib");
+use SAM_reader;
+use SAM_entry;
+
+my $usage = "usage: $0 file.sam\n\n";
+
+my $sam_file = $ARGV[0] or die $usage;
+
+
+main: {
+    my $sam_reader = new SAM_reader($sam_file);
+    
+    while (my $sam_entry = $sam_reader->get_next()) {
+        my ($genome_coords_aref, $read_coords_aref) = $sam_entry->get_alignment_coords();
+        
+        my $read_name = $sam_entry->get_read_name();
+        my $scaffold = $sam_entry->get_scaffold_name();
+        
+        print join("\t", $scaffold, &get_coord_string($genome_coords_aref),
+                   $read_name, &get_coord_string($read_coords_aref)) . "\n";
+    }
+    
+    exit(0);
+}
+
+
+####
+sub get_coord_string {
+    my ($coords_aref) = @_;
+
+    my $text = "";
+    
+    foreach my $coordset (@$coords_aref) {
+        my ($lend, $rend) = @$coordset;
+        
+        if ($text) {
+            $text .= ",";
+        }
+        
+        $text .= "$lend-$rend";
+    }
+
+    return($text);
+}