diff snp_caller/src/main.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/main.cpp	Sun Feb 21 06:05:24 2016 -0500
@@ -0,0 +1,46 @@
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include "args.h"
+#include "Fasta.h"
+#include "FastaRecord.h"
+#include "Sam.h"
+#include "SnipDriver.h"
+
+using namespace std;
+
+void print_fasta(const Fasta &f) {
+	for(const auto &record: f.records) {
+		cout << record.gene_id() << endl;
+		cout << record.gene() << endl;
+	}
+}
+
+void print_sam(const Sam &s) {
+	for(const auto &alignment: s.alignments) {
+		cout << alignment.alignment() << endl;
+	}
+}
+
+int main(int argc, const char *argv[]) {
+	cmd_args arg;
+	arg = parse_command_line(argc, argv);		
+
+	Fasta f(arg.amr_fp);
+	f.read_fasta(arg.amr_fp);	
+
+	Sam s(arg.sam_fp);
+	if(arg.samse) {
+		s.read_se_sam(arg.sam_fp, arg.best);
+	}
+	else {
+		s.read_pe_sam(arg.sam_fp, arg.best);
+	}
+
+	run(f.records, s.alignments, arg);
+	write_snips(f.records, arg.out_fp);
+
+
+	return 0;
+}