20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,34 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin;
+use lib ("$FindBin::RealBin/../../PerlLib");
+use SAM_reader;
+use SAM_entry;
+use Nuc_translator;
+
+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 $read_name = $sam_entry->reconstruct_full_read_name();
+        my $sequence = $sam_entry->get_sequence();
+        
+        if ((! $sam_entry->is_query_unmapped()) && $sam_entry->get_query_strand() eq '-') {
+            $sequence = &reverse_complement($sequence);
+        }
+
+        print ">$read_name\n$sequence\n";
+    }
+
+
+    exit(0);
+}
+