Mercurial > repos > chrisd > testshed
view gene_fraction/src/Sam.cpp @ 0:0fd352f62446 draft default tip
planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
author | chrisd |
---|---|
date | Sun, 21 Feb 2016 06:05:24 -0500 |
parents | |
children |
line wrap: on
line source
#include "Sam.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) { std::cerr << "Could not open sam file " << sam_fp << std::endl; 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(); }