20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,93 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib ("$FindBin::RealBin/../../PerlLib");
+use SAM_reader;
+use SAM_entry;
+use Overlap_piler;
+
+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);
+
+    my %core_to_coords;
+    
+	while ($sam_reader->has_next()) {
+
+		my $sam_entry = $sam_reader->get_next();
+
+		if ($sam_entry->is_query_unmapped()) {
+			next;
+		}
+
+		my $read_name = $sam_entry->get_read_name();
+		my $scaff_name = $sam_entry->get_scaffold_name();
+		
+		my $strand = $sam_entry->get_query_strand();
+
+		my ($genome_coords_aref, $query_coords_aref) = $sam_entry->get_alignment_coords();
+
+        
+        my $core_scaff = join("$;", $sam_entry->get_core_read_name(), $scaff_name);
+
+		my @coords;
+		foreach my $segment (@$genome_coords_aref) {
+			my ($lend, $rend) = @$segment;
+            
+            push (@{$core_to_coords{$core_scaff}}, [$lend, $rend]);
+		}
+
+    }
+    
+    foreach my $core_scaff (keys %core_to_coords) {
+
+        my @coords = @{$core_to_coords{$core_scaff}};
+        my ($read_core_name, $scaff_name) = split(/$;/, $core_scaff);
+        
+		@coords = sort {$a<=>$b} @coords;
+		@coords = &Overlap_piler::simple_coordsets_collapser(@coords);
+        
+
+        my $span_lend = $coords[0]->[0];
+		my $span_rend = $coords[$#coords]->[1];
+        
+		my @lengths;
+		my @starts;
+		my $num_segments = 0;
+		foreach my $segment (@coords) {
+			my ($lend, $rend) = @$segment;
+			
+			my $length = $rend - $lend + 1;
+			push (@lengths, $length);
+			push (@starts, $lend - $span_lend);
+			$num_segments++;
+		}
+        
+		$span_lend--; # coordinate is zero-based, and rend is exclusive
+
+		print join("\t", 
+				   $scaff_name,
+				   $span_lend,
+				   $span_rend,
+				   $read_core_name,
+				   0,
+				   "+",
+				   $span_lend,
+				   $span_rend,
+				   ".",
+				   $num_segments,
+				   join(",", @lengths),
+				   join(",", @starts),
+				   ) . "\n";
+	}
+
+
+	exit(0);
+}