20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,94 @@
+package CIGAR;
+
+use strict;
+use warnings;
+
+use Nuc_translator;
+
+####
+sub construct_cigar {
+	my ($genome_coords_aref, $query_coords_aref, $read_length, # required
+		$genome_seq_sref, $strand # optional
+		) = @_;
+
+	my $cigar = "";
+		
+
+	for (my $i = 0; $i <= $#$genome_coords_aref; $i++) {
+		
+		my ($curr_genome_lend, $curr_genome_rend) = @{$genome_coords_aref->[$i]};
+		my ($curr_query_lend, $curr_query_rend) = @{$query_coords_aref->[$i]};
+
+		if ($i == 0) {
+
+			if ($curr_query_lend > 1) {
+				$cigar .= ($curr_query_lend - 1) . "S";
+			}
+		}
+		else {
+			my ($prev_genome_lend, $prev_genome_rend) = @{$genome_coords_aref->[$i-1]};
+			my ($prev_query_lend, $prev_query_rend) = @{$query_coords_aref->[$i-1]};
+			
+			if ( (my $delta_genome = $curr_genome_lend - $prev_genome_rend) > 1) {
+				my $deletion_intron_char = ($genome_seq_sref && $strand) ? &_check_intron_consensus($prev_genome_rend, $curr_genome_lend, $genome_seq_sref, $strand) : 'D'; # intron or deletion?
+				$cigar .= ($delta_genome-1) . $deletion_intron_char;
+			}
+			if ( (my $delta_query = $curr_query_lend - $prev_query_rend) > 1) {
+				$cigar .= ($delta_query-1) . "I";
+			}
+		}
+		
+
+		my $len = $curr_genome_rend - $curr_genome_lend + 1;
+		
+		$cigar .= "$len" . "M";
+		
+		if ($i == $#$genome_coords_aref) {
+			
+			if ($curr_query_rend < $read_length) {
+				$cigar .= ($read_length - $curr_query_rend) . "S";
+			}
+		}
+		
+	}
+
+	return($cigar);
+}
+
+
+####
+sub _check_intron_consensus {
+	my ($left_segment_bound, $right_segment_bound, $genome_sref, $strand) = @_;
+
+	my $left_dinuc = uc substr($$genome_sref, $left_segment_bound, 2);
+
+	my $right_dinuc = uc substr($$genome_sref, $right_segment_bound-3, 2);
+
+	if ($strand eq '-') {
+		$left_dinuc = &reverse_complement($right_dinuc);
+		$right_dinuc = &reverse_complement($left_dinuc);
+	}
+
+	if (  
+		( ($left_dinuc eq "GT" || $left_dinuc eq "GC") && $right_dinuc eq "AG")
+		||
+		($left_dinuc eq "CT" && $right_dinuc eq "AC")
+		) {
+
+		return("N"); # got splice pair
+	}
+	else {
+		return("D"); # deletion
+	}
+	
+
+}
+
+
+
+
+
+
+
+
+1; #EOM