X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=PairedEndModel.h;h=0d2c9b3f216db8df91fa47a85c57065123fe2331;hp=70d14c9de9a97680eb9a683715f887a1d2a1e16f;hb=HEAD;hpb=fc69cf6af24c0550e55447fc82f01cb6f90c1c42

diff --git a/PairedEndModel.h b/PairedEndModel.h
index 70d14c9..0d2c9b3 100644
--- a/PairedEndModel.h
+++ b/PairedEndModel.h
@@ -8,8 +8,11 @@
 #include<string>
 #include<algorithm>
 #include<sstream>
+#include<iostream>
+#include<vector>
 
 #include "utils.h"
+#include "my_assert.h"
 #include "Orientation.h"
 #include "LenDist.h"
 #include "RSPD.h"
@@ -99,7 +102,15 @@ public:
 		int fpos = (dir == 0 ? pos : totLen - pos - insertLen); // the aligned position reported in SAM file, should be a coordinate in forward strand
 		int effL = std::min(fullLen, totLen - insertLen + 1);
 		
-		assert(fpos >= 0 && fpos + insertLen <= totLen && insertLen <= totLen);
+		general_assert(fpos >= 0, "The alignment of fragment " + read.getName() + " to transcript " + itos(sid) + " starts at " + itos(fpos) + \
+				" from the forward direction, which should be a non-negative number! " + \
+				"It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
+		general_assert(fpos + insertLen <= totLen,"Fragment " + read.getName() + " is hung over the end of transcript " + itos(sid) + "! " \
+				+ "It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
+		general_assert(insertLen <= totLen, "Fragment " + read.getName() + " has length " + itos(insertLen) + ", but it is aligned to transcript " \
+				+ itos(sid) + ", whose length (" + itos(totLen) + ") is shorter than the fragment's length!");
+
+
 		if (fpos >= fullLen || ref.getMask(fpos)) return 0.0; // For paired-end model, fpos is the seedPos
 
 		prob = ori->getProb(dir) * gld->getAdjustedProb(insertLen, totLen) *
@@ -183,12 +194,12 @@ public:
 
 	const LenDist& getGLD() { return *gld; }
 
-	void startSimulation(simul*, double*);
-	bool simulate(int, PairedEndRead&, int&);
+	void startSimulation(simul*, const std::vector<double>&);
+	bool simulate(READ_INT_TYPE, PairedEndRead&, int&);
 	void finishSimulation();
 
 	//Use it after function 'read' or 'estimateFromReads'
-	double* getMW() { 
+	const double* getMW() { 
 	  assert(mw != NULL);
 	  return mw;
 	}
@@ -200,7 +211,7 @@ private:
 	static const int read_type = 2;
 
 	int M;
-	int N[3];
+	READ_INT_TYPE N[3];
 	Refs *refs;
 	int seedLen;
 
@@ -232,7 +243,7 @@ void PairedEndModel::estimateFromReads(const char* readFN) {
     		genReadFileNames(readFN, i, read_type, s, readFs);
     		ReadReader<PairedEndRead> reader(s, readFs, refs->hasPolyA(), seedLen); // allow calculation of calc_lq() function
 
-    		int cnt = 0;
+    		READ_INT_TYPE cnt = 0;
     		while (reader.next(read)) {
     			SingleRead mate1 = read.getMate1();
     			SingleRead mate2 = read.getMate2();
@@ -247,14 +258,14 @@ void PairedEndModel::estimateFromReads(const char* readFN) {
     				}
     			}
     			else if (verbose && (mate1.getReadLength() < seedLen || mate2.getReadLength() < seedLen)) {
-    				printf("Warning: Read %s is ignored due to at least one of the mates' length < seed length %d!\n", read.getName().c_str(), seedLen);
+				std::cout<< "Warning: Read "<< read.getName()<< " is ignored due to at least one of the mates' length < seed length "<< seedLen<< "!"<< std::endl;
     			}
 
     			++cnt;
-    			if (verbose && cnt % 1000000 == 0) { printf("%d READS PROCESSED\n", cnt); }
+    			if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< " READS PROCESSED"<< std::endl; }
     		}
 
-    		if (verbose) { printf("estimateFromReads, N%d finished.\n", i); }
+    		if (verbose) { std::cout<< "estimateFromReads, N"<< i<< " finished."<< std::endl; }
     	}
 
     mld->finish();
@@ -339,7 +350,7 @@ void PairedEndModel::write(const char* outF) {
 	fclose(fo);
 }
 
-void PairedEndModel::startSimulation(simul* sampler, double* theta) {
+void PairedEndModel::startSimulation(simul* sampler, const std::vector<double>& theta) {
 	this->sampler = sampler;
 
 	theta_cdf = new double[M + 1];
@@ -353,7 +364,7 @@ void PairedEndModel::startSimulation(simul* sampler, double* theta) {
 	npro->startSimulation();
 }
 
-bool PairedEndModel::simulate(int rid, PairedEndRead& read, int& sid) {
+bool PairedEndModel::simulate(READ_INT_TYPE rid, PairedEndRead& read, int& sid) {
 	int dir, pos;
 	int insertL, mateL1, mateL2;
 	std::string name;