added mergesfffiles command. added current directories to get.current commands output...

[mothur.git] / sffinfocommand.h

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 1909e2d43e6d83b3d48ef06922b2d369a0e104d5..12f0180db565edf8818455648eadcc19107ec5ab 100644 (file)
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -13,50 +13,6 @@
 #include "command.hpp"
 #include "groupmap.h"
 
-/**********************************************************/
-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() { } 
-};
 /**********************************************************/
 
 class SffInfoCommand : public Command {