ViewVC Help

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

root/gclib/tophat_cpp/reads.h

#	Line 11 | Line 11
11
12		#include <string>
13		#include <sstream>
14	+	#include <queue>
15	+	#include <limits>
16		#include <seqan/sequence.h>
17		#include "common.h"
18	<	#include <queue>
18	>
19
20		using std::string;
21
#	Line 69 | Line 71
71		}
72
73		class ReadTable;
72	–	/*
73	–	bool get_read_from_stream(uint64_t insert_id,
74	–	FILE* reads_file,
75	–	ReadFormat reads_format,
76	–	bool strip_slash,
77	–	char read_name [],
78	–	char read_seq  [],
79	–	char read_alt_name [],
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);
74
75		class FLineReader { //simple text line reader class, buffering last line read
76		int len;
#	Line 97 | Line 81
81		bool is_pipe;
82		bool pushed; //pushed back
83		int lcount; //counting all lines read by the object
84	+
85	+	public:
86	+	// daehwan - this is not a good place to store the last read ...
87	+	Read last_read;
88	+	bool pushed_read;
89	+
90		public:
91		char* chars() { return buf; }
92		char* line() { return buf; }
#	Line 107 | Line 97
97		FILE* fhandle() { return file; }
98		void pushBack() { if (lcount>0) pushed=true; } // "undo" the last getLine request
99		// so the next call will in fact return the same line
100	+	void pushBack_read() { if(!last_read.name.empty()) pushed_read=true;}
101		FLineReader(FILE* stream=NULL) {
102		len=0;
103		isEOF=false;
#	Line 117 | Line 108
108		buf[0]=0;
109		file=stream;
110		pushed=false;
111	+	pushed_read=false;
112		}
121	–
113		FLineReader(FZPipe& fzpipe) {
114		len=0;
115		isEOF=false;
#	Line 129 | Line 120
120		file=fzpipe.file;
121		is_pipe=!fzpipe.pipecmd.empty();
122		pushed=false;
123	+	pushed_read=false;
124		}
125		void close() {
126		if (file==NULL) return;
127		if (is_pipe) pclose(file);
128		else fclose(file);
129		}
130	+
131		~FLineReader() {
132		free(buf); //does not call close() -- we might reuse the file handle
133		}
134		};
135
136	+	bool get_read_from_stream(uint64_t insert_id,
137	+	FLineReader& fr,
138	+	ReadFormat reads_format,
139	+	bool strip_slash,
140	+	Read& read,
141	+	FILE* um_out=NULL, //unmapped reads output
142	+	bool um_write_found=false);
143
144		void skip_lines(FLineReader& fr);
145		bool next_fasta_record(FLineReader& fr, string& defline, string& seq, ReadFormat reads_format);
#	Line 147 | Line 147
147		bool next_fastx_read(FLineReader& fr, Read& read, ReadFormat reads_format=FASTQ,
148		FLineReader* frq=NULL);
149
150	–
151	–
150		class ReadStream {
151		protected:
152		struct ReadOrdering
#	Line 169 | Line 167
167		public:
168		ReadStream():fstream(), read_pq(), last_id(0), r_eof(false) {   }
169
170	<	ReadStream(string& fname):fstream(fname, false),
170	>	ReadStream(const string& fname):fstream(fname, false),
171		read_pq(), last_id(0), r_eof(false) {   }
172
173		void init(string& fname) {
#	Line 180 | Line 178
178		}
179		//read_ids must ALWAYS be requested in increasing order
180		bool getRead(uint64_t read_id, Read& read,
181	<	ReadFormat read_format=FASTQ,
182	<	bool strip_slash=false,
183	<	FILE* um_out=NULL, //unmapped reads output
184	<	bool um_write_found=false);
181	>	ReadFormat read_format=FASTQ,
182	>	bool strip_slash=false,
183	>	FILE* um_out=NULL, //unmapped reads output
184	>	bool um_write_found=false,
185	>	uint64_t begin_id = 0,
186	>	uint64_t end_id=std::numeric_limits<uint64_t>::max());
187
188		void rewind() {
189		fstream.rewind();
190		clear();
191		}
192	+	void seek(int64_t offset) {
193	+	clear();
194	+	fstream.seek(offset);
195	+	}
196		FILE* file() {
197		return fstream.file;
198		}

Diff Legend

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