SimpleSparse.h - bitseq (run/dbbbc957-dc5a-4047-b0fb-65756349c57e/main)

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_release_Makefile
ArgumentParser.cpp
ArgumentParser.h
biocUpdate.sh
changeList
checkTR.py
CollapsedSampler.cpp
CollapsedSampler.h
common.cpp
common.h
convertSamples.cpp
estimateDE.cpp
estimateExpression.cpp
estimateHyperPar.cpp
estimateVBExpression.cpp
extractSamples.cpp
extractTranscriptInfo.py
FileHeader.cpp
FileHeader.h
getCounts.py
getFoldChange.cpp
getGeneExpression.cpp
getPPLR.cpp
getVariance.cpp
getWithinGeneExpression.cpp
GibbsParameters.cpp
GibbsParameters.h
GibbsSampler.cpp
GibbsSampler.h
lowess.cpp
lowess.h
Makefile
misc.cpp
misc.h
MyTimer.cpp
MyTimer.h
parameters1.txt
parseAlignment.cpp
parseAlignment.py
PosteriorSamples.cpp
PosteriorSamples.h
ReadDistribution.cpp
ReadDistribution.h
README.md
releaseDo.sh
releaseList
Sampler.cpp
Sampler.h
SimpleSparse.cpp
SimpleSparse.h
tagAlignment.h
TagAlignments.cpp
TagAlignments.h
TranscriptExpression.cpp
TranscriptExpression.h
TranscriptInfo.cpp
TranscriptInfo.h
TranscriptSequence.cpp
TranscriptSequence.h
transposeFiles.cpp
transposeFiles.h
transposeLargeFile.cpp
VariationalBayes.cpp
VariationalBayes.h

SimpleSparse.h @run/dbbbc957-dc5a-4047-b0fb-65756349c57e/main — raw · history · blame

#ifndef SIMPLESPARSE_H
#define SIMPLESPARSE_H

#include<stdint.h>

//#define setVal(x,i,y) {for(i=0;i<x->T;i++)x->val[i]=y;}

class SimpleSparse {
   private:
   bool base;
   public:
   long N,M,T; // reads, transcripts, total
   int_least32_t *rowStart,*colStart,*col;
   double *val;

   SimpleSparse(long n,long m, long t);
   SimpleSparse(SimpleSparse *m0);
   ~SimpleSparse();
   void softmax(SimpleSparse *res) const;
   void softmaxInplace(SimpleSparse *res);
   long countAboveDelta(double delta = 0.99) const;
   void sumCols(double res[]) const;
   void sumRows(double res[]) const;
   double logSumExpVal(long st, long en) const;
};

#endif