20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,103 @@
+#!/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 = $read->get_core_read_name();
+        
+        if ($scaff_name ne $prev_scaff_name ||  $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 @left_reads;
+    my @right_reads;
+
+    foreach my $read (@reads) {
+        if ($read->is_first_in_pair()) {
+            push (@left_reads, $read);
+        }
+        elsif ($read->is_second_in_pair()) {
+            push (@right_reads, $read);
+        }
+    }
+
+    unless (@left_reads && @right_reads) {
+        die "Error, dont have pairs!";
+    }
+    
+    my $left_read = shift @left_reads;
+    my $aligned_pos = $left_read->get_aligned_position();
+
+    my $right_read = undef;
+    while ((! defined($right_read)) && @right_reads) {
+        my $read = shift @right_reads;
+        if ($read->get_mate_scaffold_position() == $aligned_pos) {
+            $right_read = $read;
+            last;
+        }
+    }
+
+    unless ($left_read && $right_read) {
+        die "Error, couldn't match pairs.";
+    }
+
+    print $left_read->toString() . "\n";
+    print $right_read->toString() . "\n";
+    
+
+    return;
+}
+
+
+    
+
+        
+