diff snp_caller/src/Sam.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/Sam.cpp	Sun Feb 21 06:05:24 2016 -0500
@@ -0,0 +1,57 @@
+#include "Sam.h"
+#include "alignment_util.h"
+
+#include <string>
+#include <vector>
+#include <fstream>
+#include <iostream>
+
+Sam::Sam(std::string sam_fp) : _sam_fp(sam_fp) {}
+
+void Sam::read_se_sam(const std::string &sam_fp, bool best) {
+	std::ifstream in(sam_fp.c_str());
+	if(!in) {
+		std::cerr << "Could not open sam file " << sam_fp << std::endl;
+		exit(EXIT_FAILURE);
+	}
+
+	std::string alignment;
+	while(getline(in, alignment)) {
+		if(alignment[0] == '@')
+			continue;
+		//std::vector<std::string> parts = split_alignment(alignment);
+		if(se_fields_are_good(alignment, best)) {
+			alignments.push_back(alignment);
+		}
+	}
+	sort_by_qname(alignments);
+}
+
+void Sam::read_pe_sam(const std::string &sam_fp, bool best) {
+	std::ifstream in(sam_fp.c_str());
+	if(!in)	{
+		std::cerr << "Could not open sam file " << sam_fp << std::endl;
+		exit(EXIT_FAILURE);
+	}
+
+	std::string alignment;
+	while(getline(in, alignment)) {
+		if(alignment[0] == '@')
+			continue;
+		//std::vector<std::string> parts = split_alignment(alignment);
+		if(pe_fields_are_good(alignment, best)) {
+			alignments.push_back(alignment);
+		}
+	}
+	sort_by_qname(alignments);
+}
+
+void Sam::sort_by_qname(std::vector<Alignment> &v) {
+	sort(v.begin(), v.end(),
+	     [](const Alignment &a, const Alignment &b)
+	     { return a.qname() < b.qname(); });
+}
+
+
+
+