20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,138 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib ("$FindBin::RealBin/../../PerlLib");
+use SAM_reader;
+use SAM_entry;
+
+my $usage = "\n\nusage: name_sorted_paired_reads.sam\n\n";
+
+my $sam_file = $ARGV[0] or die $usage;
+
+main: {
+
+
+    my $prev_read_name = "";
+    my $prev_scaff_name = "";
+
+    my @reads;
+
+    my $sam_reader = new SAM_reader($sam_file);
+    while ($sam_reader->has_next()) {
+
+        my $read = $sam_reader->get_next();
+        
+        my $scaff_name = $read->get_scaffold_name();
+        my $core_read_name = $read->get_core_read_name();
+
+        
+        if ($core_read_name ne $prev_read_name) {
+
+            if (@reads) {
+                &process_pairs(@reads);
+                @reads = ();
+            }
+        }
+        
+        push (@reads, $read);
+        
+
+        $prev_read_name = $core_read_name;
+        $prev_scaff_name = $scaff_name;
+        
+        
+    }
+    
+    &process_pairs(@reads);
+
+
+    exit(0);
+}
+
+####
+sub process_pairs {
+    my (@reads) = @_;
+
+    my %scaffold_to_reads;
+    foreach my $read (@reads) {
+        my $scaff_name = $read->get_scaffold_name();
+        push (@{$scaffold_to_reads{$scaff_name}}, $read);
+    }
+
+    foreach my $scaff (keys  %scaffold_to_reads) {
+        
+        my @scaff_reads = @{$scaffold_to_reads{$scaff}};
+
+        &process_scaffold_pairs(@scaff_reads);
+    }
+
+
+    return;
+}
+
+
+
+
+sub process_scaffold_pairs {
+    my @reads = @_;
+    
+    my @left_reads;
+    my @right_reads;
+
+    foreach my $read (@reads) {
+        
+        my $read_name = $read->get_read_name();
+
+        #print "processing: $read_name\n";
+
+        if ($read_name =~ m|/1$|) {
+            push (@left_reads, $read);
+        }
+        elsif ($read_name =~ m|/2$|) {
+            push (@right_reads, $read);
+        }
+    }
+
+    unless (@left_reads && @right_reads) {
+        #print "\t** no pairs...\n";
+        return;
+    }
+    
+    my $left_read = shift @left_reads;
+    my $left_aligned_pos = $left_read->get_aligned_position();
+    my $scaffold_name = $left_read->get_scaffold_name();
+        
+    my $right_read = shift @right_reads;
+    my $right_aligned_pos = $right_read->get_aligned_position();
+    
+    $left_read->set_mate_scaffold_name($scaffold_name);
+    $left_read->set_mate_scaffold_position($right_aligned_pos);
+    
+    $right_read->set_mate_scaffold_name($scaffold_name);
+    $right_read->set_mate_scaffold_position($left_aligned_pos);
+
+    $left_read->set_paired(1);
+    $right_read->set_paired(1);
+
+    $left_read->set_proper_pair(1);
+    $right_read->set_proper_pair(1);
+
+    $left_read->set_first_in_pair(1);
+    $right_read->set_second_in_pair(1);
+
+
+    print $left_read->toString() . "\n";
+    print $right_read->toString() . "\n";
+    
+
+    return;
+}
+
+
+    
+
+        
+