1 #ifndef SFFINFOCOMMAND_H
2 #define SFFINFOCOMMAND_H
8 * Created by westcott on 7/7/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
16 /**********************************************************/
18 unsigned int magicNumber;
20 unsigned long int indexOffset;
21 unsigned int indexLength;
22 unsigned int numReads;
23 unsigned short headerLength;
24 unsigned short keyLength;
25 unsigned short numFlowsPerRead;
26 int flogramFormatCode;
27 string flowChars; //length depends on number flow reads
28 string keySequence; //length depends on key length
30 CommonHeader(){ magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; }
33 /**********************************************************/
35 unsigned short headerLength;
36 unsigned short nameLength;
37 unsigned int numBases;
38 unsigned short clipQualLeft;
39 unsigned short clipQualRight;
40 unsigned short clipAdapterLeft;
41 unsigned short clipAdapterRight;
42 string name; //length depends on nameLength
47 Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
50 /**********************************************************/
52 vector<unsigned short> flowgram;
53 vector<unsigned int> flowIndex;
55 vector<unsigned int> qualScores;
60 /**********************************************************/
62 class SffInfoCommand : public Command {
65 SffInfoCommand(string);
68 vector<string> getRequiredParameters();
69 vector<string> getValidParameters();
70 vector<string> getRequiredFiles();
71 map<string, vector<string> > getOutputFiles() { return outputTypes; }
76 string sffFilename, sfftxtFilename, outputDir, accnosName;
77 vector<string> filenames, outputNames, accnosFileNames;
78 bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
80 map<string, vector<string> > outputTypes;
82 //extract sff file functions
83 int extractSffInfo(string, string);
84 int readCommonHeader(ifstream&, CommonHeader&);
85 int readHeader(ifstream&, Header&);
86 int readSeqData(ifstream&, seqRead&, int, int);
87 int decodeName(string&, string&, string&, string);
89 int printCommonHeader(ofstream&, CommonHeader&);
90 int printHeader(ofstream&, Header&);
91 int printSffTxtSeqData(ofstream&, seqRead&, Header&);
92 int printFlowSeqData(ofstream&, seqRead&, Header&);
93 int printFastaSeqData(ofstream&, seqRead&, Header&);
94 int printQualSeqData(ofstream&, seqRead&, Header&);
95 int readAccnosFile(string);
98 //parsesfftxt file functions
99 int parseHeaderLineToInt(ifstream&);
100 vector<unsigned short> parseHeaderLineToFloatVector(ifstream&, int);
101 vector<unsigned int> parseHeaderLineToIntVector(ifstream&, int);
102 string parseHeaderLineToString(ifstream&);
105 /**********************************************************/