X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=EBSeq%2FcalcClusteringInfo.cpp;h=27357b23f757298bc2e3a3794318ee5a5e432cb4;hb=cee60cca5d914c7e6e880cb8276cdb5b129458c7;hp=2103f6169db7f27f4b636f12c62bdea9d1f054c7;hpb=9c2e46183a19d661f0a618a8eabe8ce1f6a8e2d6;p=rsem.git

diff --git a/EBSeq/calcClusteringInfo.cpp b/EBSeq/calcClusteringInfo.cpp
index 2103f61..27357b2 100644
--- a/EBSeq/calcClusteringInfo.cpp
+++ b/EBSeq/calcClusteringInfo.cpp
@@ -10,21 +10,19 @@
 #include<algorithm>
 using namespace std;
 
-typedef unsigned int INTEGER;
-
 const int STRLEN = 1005;
 
-INTEGER M;
+int M;
 int k; // k-mer size
 vector<string> names;
 vector<string> seqs;
-vector<INTEGER> effL;
+vector<int> effL;
 
 // tid starts from 1
 struct ReadType {
-  INTEGER tid, pos;
+  int tid, pos;
 
-  ReadType(INTEGER tid, INTEGER pos) {
+  ReadType(int tid, int pos) {
     this->tid = tid;
     this->pos = pos;
   }
@@ -65,18 +63,17 @@ string convert(const string& rawseq) {
 void loadRef(char* inpF) {
   ifstream fin(inpF);
   string tag, line, rawseq;
-  void *pt;
 
   assert(fin.is_open());
 
   names.clear(); names.push_back("");
   seqs.clear(); seqs.push_back("");
   
-  pt = getline(fin, line);
-  while (pt != 0 && line[0] == '>') {
+  getline(fin, line);
+  while ((fin) && (line[0] == '>')) {
     tag = line.substr(1);
     rawseq = "";
-    while((pt = getline(fin, line)) && line[0] != '>') {
+    while((getline(fin, line)) && (line[0] != '>')) {
       rawseq += line;
     }
     if (rawseq.size() <= 0) {
@@ -105,10 +102,10 @@ int main(int argc, char* argv[]) {
 
   cands.clear();
   effL.assign(M + 1, 0);
-  for (INTEGER i = 1; i <= M; i++) {
-    effL[i] = seqs[i].length() - k + 1;
+  for (int i = 1; i <= M; i++) {
+    effL[i] = int(seqs[i].length()) - k + 1;
     if (effL[i] <= 0) effL[i] = 0; // effL should be non-negative
-    for (INTEGER j = 0; j < effL[i]; j++) 
+    for (int j = 0; j < effL[i]; j++) 
       cands.push_back(ReadType(i, j));
   }
   printf("All possbile %d mers are generated.\n", k);
@@ -134,7 +131,7 @@ int main(int argc, char* argv[]) {
       p = i;
     }
 
-  for (INTEGER i = 1; i <= M; i++) 
+  for (int i = 1; i <= M; i++) 
     if (effL[i] == 0) clusteringInfo[i] = -1.0;
     else clusteringInfo[i] /= effL[i];
 
@@ -142,7 +139,7 @@ int main(int argc, char* argv[]) {
 
 
   ofstream fout(argv[3]);
-  for (INTEGER i = 1; i <= M; i++) fout<<names[i]<<"\t"<<setprecision(6)<<clusteringInfo[i]<<endl;
+  for (int i = 1; i <= M; i++) fout<<names[i]<<"\t"<<setprecision(6)<<clusteringInfo[i]<<endl;
   fout.close();
 
   return 0;