+struct diffPair {
+ float prob;
+ float reverseProb;
+
+ diffPair() {
+ prob = 0; reverseProb = 0;
+ }
+ diffPair(float p, float rp) {
+ prob = p;
+ reverseProb = rp;
+ }
+};
+
+/**********************************************************/
+struct CommonHeader {
+ unsigned int magicNumber;
+ string version;
+ unsigned long long indexOffset;
+ unsigned int indexLength;
+ unsigned int numReads;
+ unsigned short headerLength;
+ unsigned short keyLength;
+ unsigned short numFlowsPerRead;
+ int flogramFormatCode;
+ string flowChars; //length depends on number flow reads
+ string keySequence; //length depends on key length
+
+ CommonHeader(){ magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; }
+ ~CommonHeader() { }
+};
+/**********************************************************/
+struct Header {
+ unsigned short headerLength;
+ unsigned short nameLength;
+ unsigned int numBases;
+ unsigned short clipQualLeft;
+ unsigned short clipQualRight;
+ unsigned short clipAdapterLeft;
+ unsigned short clipAdapterRight;
+ string name; //length depends on nameLength
+ string timestamp;
+ string region;
+ string xy;
+
+ Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
+ ~Header() { }
+};
+/**********************************************************/
+struct seqRead {
+ vector<unsigned short> flowgram;
+ vector<unsigned int> flowIndex;
+ string bases;
+ vector<unsigned int> qualScores;
+
+ seqRead() { }
+ ~seqRead() { }
+};
+
+/***********************************************************************/
+struct PDistCell{
+ ull index;
+ float dist;
+ PDistCell() : index(0), dist(0) {};
+ PDistCell(ull c, float d) : index(c), dist(d) {}
+};
+/***********************************************************************/
+struct consTax{
+ string name;
+ string taxonomy;
+ int abundance;
+ consTax() : name(""), taxonomy("unknown"), abundance(0) {};
+ consTax(string n, string t, int a) : name(n), taxonomy(t), abundance(a) {}
+};
+/***********************************************************************/
+struct consTax2{
+ string taxonomy;
+ int abundance;
+ consTax2() : taxonomy("unknown"), abundance(0) {};
+ consTax2(string t, int a) : taxonomy(t), abundance(a) {}
+};