ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/gclib/tophat_cpp/reads.h

#	Line 13 | Line 13
13		#include <sstream>
14		#include <seqan/sequence.h>
15		#include "common.h"
16	+	#include <queue>
17
18		using std::string;
19
20	<	static const int max_read_bp = 64;
20	>	static const int max_read_bp = 256;
21
22		// Note: qualities are not currently used by TopHat
23		struct Read
#	Line 68 | Line 69
69		}
70
71		class ReadTable;
72	<
72	>	/*
73		bool get_read_from_stream(uint64_t insert_id,
74		FILE* reads_file,
75		ReadFormat reads_format,
#	Line 76 | Line 77
77		char read_name [],
78		char read_seq  [],
79		char read_alt_name [],
80	<	char read_qual []);
80	>	char read_qual [],
81	>	FILE* um_out=NULL); //unmapped reads output
82	>	*/
83	>	bool get_read_from_stream(uint64_t insert_id,
84	>	FILE* reads_file,
85	>	ReadFormat reads_format,
86	>	bool strip_slash,
87	>	Read& read,
88	>	FILE* um_out=NULL, //unmapped reads output
89	>	bool um_write_found=false);
90
91		class FLineReader { //simple text line reader class, buffering last line read
92		int len;
#	Line 130 | Line 140
140		}
141		};
142
143	+
144		void skip_lines(FLineReader& fr);
145		bool next_fasta_record(FLineReader& fr, string& defline, string& seq, ReadFormat reads_format);
146		bool next_fastq_record(FLineReader& fr, const string& seq, string& alt_name, string& qual, ReadFormat reads_format);
147	<	bool next_fastx_read(FLineReader& fr, Read& read, ReadFormat reads_format,
147	>	bool next_fastx_read(FLineReader& fr, Read& read, ReadFormat reads_format=FASTQ,
148		FLineReader* frq=NULL);
149
150	+
151	+
152	+	class ReadStream {
153	+	protected:
154	+	struct ReadOrdering
155	+	{
156	+	bool operator()(std::pair<uint64_t, Read>& lhs, std::pair<uint64_t, Read>& rhs)
157	+	{
158	+	return (lhs.first > rhs.first);
159	+	}
160	+	};
161	+	FZPipe fstream;
162	+	std::priority_queue< std::pair<uint64_t, Read>,
163	+	std::vector<std::pair<uint64_t, Read> >,
164	+	ReadOrdering > read_pq;
165	+	uint64_t last_id; //keep track of last requested ID, for consistency check
166	+	bool r_eof;
167	+	bool next_read(Read& read, ReadFormat read_format); //get top read from the queue
168	+
169	+	public:
170	+	ReadStream():fstream(), read_pq(), last_id(0), r_eof(false) {   }
171	+
172	+	ReadStream(string& fname):fstream(fname, false),
173	+	read_pq(), last_id(0), r_eof(false) {   }
174	+
175	+	void init(string& fname) {
176	+	fstream.openRead(fname, false);
177	+	}
178	+	const char* filename() {
179	+	return fstream.filename.c_str();
180	+	}
181	+	//read_ids must ALWAYS be requested in increasing order
182	+	bool getRead(uint64_t read_id, Read& read,
183	+	ReadFormat read_format=FASTQ,
184	+	bool strip_slash=false,
185	+	FILE* um_out=NULL, //unmapped reads output
186	+	bool um_write_found=false);
187	+
188	+	void rewind() {
189	+	fstream.rewind();
190	+	clear();
191	+	}
192	+	FILE* file() {
193	+	return fstream.file;
194	+	}
195	+	void clear() {
196	+	/* while (read_pq.size()) {
197	+	const std::pair<uint64_t, Read>& t = read_pq.top();
198	+	//free(t.second);
199	+	read_pq.pop();
200	+	} */
201	+	read_pq=std::priority_queue< std::pair<uint64_t, Read>,
202	+	std::vector<std::pair<uint64_t, Read> >,
203	+	ReadOrdering > ();
204	+	}
205	+	void close() {
206	+	clear();
207	+	fstream.close();
208	+	}
209	+	~ReadStream() {
210	+	close();
211	+	}
212	+	};
213		#endif

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines