diff gene_fraction/src/Sam.cpp @ 0:f95150c37d38 draft default tip

planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_fraction/src/Sam.cpp	Sun Feb 21 23:31:55 2016 -0500
@@ -0,0 +1,41 @@
+#include "Sam.h"
+#include "args.h"
+#include "dir_util.h"
+#include "alignment_util.h"
+
+#include <iostream>
+#include <fstream>
+
+Sam::Sam(std::string sam_fp) : _sam_fp(sam_fp) {}
+
+void Sam::read_sam(cmd_args args) {
+	if(args.bam_stream) read_from_stdin();
+	else read_from_file(args.sam_fp);
+}
+
+void Sam::read_from_stdin() {
+	std::string line;
+	while(std::getline(std::cin, line)) {
+		if(line[0] == '@') continue;
+		alignment.push_back(line);
+	}
+}
+
+void Sam::read_from_file(const std::string &sam_fp) {
+	std::ifstream in(sam_fp.c_str());
+	if(!in) {
+		usage();
+		exit(EXIT_FAILURE);
+	}
+
+	std::string line;
+	while(getline(in, line)) {
+		if(line[0] == '@') continue;
+		if(is_good_alignment(line))
+			alignment.push_back(line);
+	}
+
+	in.close();
+}
+
+