diff snp_caller/src/Alignment.cpp @ 0:0fd352f62446 draft default tip

planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snp_caller/src/Alignment.cpp	Sun Feb 21 06:05:24 2016 -0500
@@ -0,0 +1,96 @@
+#include "Alignment.h"
+#include "int_util.h"
+
+#include <boost/algorithm/string.hpp>
+
+#include <iostream>
+#include <sstream>
+#include <algorithm>
+
+#define READ_PAIRED                         1
+#define READ_MAPPED_IN_PROPER_PAIR          2
+#define READ_UNMAPPED                       4
+#define MATE_UNMAPPED                       8
+#define READ_REVERSE_STRAND                 16
+#define MATE_REVERSE_STRAND                 32
+#define FIRST_IN_PAIR                       64
+#define SECOND_IN_PAIR                      128
+#define NOT_PRIMARY_ALIGNMENT               256
+#define READ_FAILS_VENDOR_QUALITY_CHECKS    512
+#define READ_IS_PCR_OR_OPTICAL_DUPLICATE    1024
+#define SUPPLEMENTARY_ALIGNMENT             2048
+
+Alignment::Alignment(std::string alignment) : _alignment(alignment) {
+	fill_alignment_fields(alignment);
+	fill_bit_flag(field.FLAG);
+	fill_xa_field(alignment);
+}
+
+void Alignment::fill_alignment_fields(const std::string &alignment) {
+	std::istringstream ss(alignment);
+	ss >> field.QNAME >> field.FLAG >> field.RNAME >> field.POS >>
+              field.MAPQ >> field.CIGAR >> field.RNEXT >> field.PNEXT >>
+              field.TLEN >> field.SEQ >> field.QUAL;
+}
+
+void Alignment::fill_bit_flag(const int &flag) {
+    if( (flag & READ_PAIRED) == 1)                     b_flag.read_paired = true;
+    if( (flag & READ_MAPPED_IN_PROPER_PAIR) > 1)       b_flag.read_mapped_in_proper_pair = true;
+    if( (flag & READ_UNMAPPED) > 1)                    b_flag.read_unmapped = true;
+    if( (flag & MATE_UNMAPPED) > 1)                    b_flag.mate_unmapped = true;
+    if( (flag & READ_REVERSE_STRAND) > 1)              b_flag.read_reverse_strand = true;
+    if( (flag & MATE_REVERSE_STRAND) > 1)              b_flag.mate_reverse_strand = true;
+    if( (flag & FIRST_IN_PAIR) > 1)                    b_flag.first_in_pair = true;
+    if( (flag & SECOND_IN_PAIR) > 1)                   b_flag.second_in_pair = true;
+}
+
+// XA:Z:mef(A)_10_AF376746,+81,92M,2;
+bool Alignment::fill_xa_field(const std::string &alignment) {
+	xa_fields hits;
+	std::string alt_fields;
+	int offset = 5;
+	std::size_t alt_index = alignment.find("XA:Z:");
+	
+	if(alt_index != std::string::npos) {
+		alt_fields = alignment.substr(alt_index+offset, alignment.length());		
+	}
+	else {
+		return false;
+	}
+
+	std::string field;
+	std::istringstream ss(alt_fields);
+
+	while(std::getline(ss, field, ',')) {
+		hits.rname = field;
+		//std::cout << hits.rname << std::endl;
+		getline(ss, field, ',');
+		hits.pos = strand_to_i(field);
+		//std::cout << hits.pos << std::endl;
+		getline(ss, field, ',');
+		hits.cigar = field;
+		//std::cout << hits.cigar << std::endl;
+		getline(ss, field, ';');
+		hits.edit = 0;
+		alternate_hits.push_back(hits);
+	}
+		
+	return true;	
+}
+
+std::vector<std::pair<int,char> > Alignment::get_cigar() {
+	return get_cigar_operations(field.CIGAR);
+}
+
+std::vector<std::pair<int,char> > Alignment::get_cigar_operations(const std::string &cigar) {
+	std::vector<std::pair<int,char>> p;
+	int count;
+	char operation;
+	
+	std::istringstream ss(cigar);
+	while(ss >> count >> operation) {
+		p.push_back(std::make_pair(count,operation));
+	}
+
+	return p;
+}