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#ifndef READS_H |
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#define READS_H |
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/* |
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* reads.h |
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* TopHat |
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* |
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* Created by Cole Trapnell on 9/2/08. |
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* Copyright 2008 Cole Trapnell. All rights reserved. |
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* |
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*/ |
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|
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#include <string> |
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#include <sstream> |
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#include <seqan/sequence.h> |
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#include "common.h" |
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|
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using std::string; |
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|
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static const int max_read_bp = 64; |
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|
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// Note: qualities are not currently used by TopHat |
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struct Read |
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{ |
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Read() |
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{ |
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seq.reserve(max_read_bp); |
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qual.reserve(max_read_bp); |
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} |
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|
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string name; |
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string seq; |
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string alt_name; |
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string qual; |
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|
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bool lengths_equal() { return seq.length() == qual.length(); } |
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void clear() |
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{ |
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name.clear(); |
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seq.clear(); |
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qual.clear(); |
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alt_name.clear(); |
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} |
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}; |
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|
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void reverse_complement(string& seq); |
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string convert_color_to_bp(const string& color); |
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seqan::String<char> convert_color_to_bp(char base, const seqan::String<char>& color); |
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|
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string convert_bp_to_color(const string& bp, bool remove_primer = false); |
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seqan::String<char> convert_bp_to_color(const seqan::String<char>& bp, bool remove_primer = false); |
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|
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/* |
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This is a dynamic programming to decode a colorspace read, which is from BWA paper. |
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|
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Heng Li and Richard Durbin |
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Fast and accurate short read alignment with Burrows-Wheeler transform |
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*/ |
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void BWA_decode(const string& color, const string& qual, const string& ref, string& decode); |
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|
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|
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template <class Type> |
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string DnaString_to_string(const Type& dnaString) |
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{ |
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std::string result; |
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std::stringstream ss(std::stringstream::in | std::stringstream::out); |
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ss << dnaString >> result; |
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return result; |
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} |
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|
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class ReadTable; |
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|
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bool get_read_from_stream(uint64_t insert_id, |
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FILE* reads_file, |
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ReadFormat reads_format, |
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bool strip_slash, |
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char read_name [], |
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char read_seq [], |
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char read_alt_name [], |
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char read_qual []); |
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|
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class FLineReader { //simple text line reader class, buffering last line read |
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int len; |
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int allocated; |
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char* buf; |
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bool isEOF; |
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FILE* file; |
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bool is_pipe; |
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bool pushed; //pushed back |
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int lcount; //counting all lines read by the object |
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public: |
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char* chars() { return buf; } |
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char* line() { return buf; } |
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int readcount() { return lcount; } //number of lines read |
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int length() { return len; } //length of the last line read |
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bool isEof() {return isEOF; } |
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char* nextLine(); |
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FILE* fhandle() { return file; } |
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void pushBack() { if (lcount>0) pushed=true; } // "undo" the last getLine request |
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// so the next call will in fact return the same line |
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FLineReader(FILE* stream=NULL) { |
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len=0; |
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isEOF=false; |
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is_pipe=false; |
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allocated=512; |
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buf=(char*)malloc(allocated); |
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lcount=0; |
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buf[0]=0; |
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file=stream; |
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pushed=false; |
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} |
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|
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FLineReader(FZPipe& fzpipe) { |
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len=0; |
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isEOF=false; |
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allocated=512; |
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buf=(char*)malloc(allocated); |
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lcount=0; |
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buf[0]=0; |
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file=fzpipe.file; |
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is_pipe=!fzpipe.pipecmd.empty(); |
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pushed=false; |
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} |
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void close() { |
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if (file==NULL) return; |
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if (is_pipe) pclose(file); |
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else fclose(file); |
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} |
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~FLineReader() { |
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free(buf); //does not call close() -- we might reuse the file handle |
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} |
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}; |
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|
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void skip_lines(FLineReader& fr); |
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bool next_fasta_record(FLineReader& fr, string& defline, string& seq, ReadFormat reads_format); |
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bool next_fastq_record(FLineReader& fr, const string& seq, string& alt_name, string& qual, ReadFormat reads_format); |
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bool next_fastx_read(FLineReader& fr, Read& read, ReadFormat reads_format, |
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FLineReader* frq=NULL); |
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|
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#endif |