Fixed a bug causing crashed introduced in the previous patch.

source/BAMbinSortByCoordinate.cpp

@@ -7,15 +7,21 @@ void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, st
 
     if (binS==0) return; //nothing to do for empty bins
     //allocate arrays
-    char *bamIn=new char[binS];
+    char *bamIn=new char[binS+1];
     uint *startPos=new uint[binN*3];
 
     uint bamInBytes=0;
     //load all aligns
     for (uint it=0; it<nThreads; it++) {
         string bamInFile=dirBAMsort+to_string(it)+"/"+to_string((uint) iBin);
-        ifstream bamInStream (bamInFile.c_str());
-        bamInStream.read(bamIn+bamInBytes,binS);//read the whole file
+        ifstream bamInStream;
+        bamInStream.open(bamInFile.c_str(),std::ios::binary | std::ios::ate);//open at the end to get file size
+        uint s1=bamInStream.tellg();
+        if (s1>0)
+        {
+            bamInStream.seekg(std::ios::beg);
+            bamInStream.read(bamIn+bamInBytes,s1);//read the whole file
+        };
         bamInBytes += bamInStream.gcount();
         bamInStream.close();
         remove(bamInFile.c_str());

source/ReadAlign_outputAlignments.cpp

@@ -109,7 +109,7 @@ void ReadAlign::outputAlignments() {
             {//write all transcripts         
                 //mate mapped = true if a mate was present in one of the trancsripts
                 mateMapped[trMult[iTr]->exons[0][EX_iFrag]]=true;
-                mateMapped[trMult[iTr]->exons[trBest->nExons-1][EX_iFrag]]=true; 
+                mateMapped[trMult[iTr]->exons[trMult[iTr]->nExons-1][EX_iFrag]]=true; 
 
                 //mateMapped1 = true if a mate is present in this transcript
                 bool mateMapped1[2]={false,false};

source/parametersDefault

@@ -331,17 +331,17 @@ outFilterMismatchNmax           10
     int: alignment will be output only if it has no more mismatches than this value.
 
 outFilterMismatchNoverLmax      0.3
-    int: alignment will be output only if its ratio of mismatches to *mapped* length is less than or equal to this value.
+    float: alignment will be output only if its ratio of mismatches to *mapped* length is less than or equal to this value.
 
-outFilterMismatchNoverReadLmax  1
-    int: alignment will be output only if its ratio of mismatches to *read* length is less than or equal to this value.
+outFilterMismatchNoverReadLmax  1.0
+    float: alignment will be output only if its ratio of mismatches to *read* length is less than or equal to this value.
 
 
 outFilterScoreMin               0
     int: alignment will be output only if its score is higher than or equal to this value.
 
 outFilterScoreMinOverLread      0.66
-        float: same as outFilterScoreMin, but  normalized to read length (sum of mates' lengths for paired-end reads)
+    float: same as outFilterScoreMin, but  normalized to read length (sum of mates' lengths for paired-end reads)
 
 outFilterMatchNmin              0
     int: alignment will be output only if the number of matched bases is higher than or equal to this value.