Added posterior standard deviation of counts as output if either '--calc-pme' or...

[rsem.git] / ReadReader.h

diff --git a/ReadReader.h b/ReadReader.h
index d244efa4236807871dcdda49c4b1f942d224f3ef..141585aa5cfe78ff3cd1aca0899f227f092928af 100644 (file)
--- a/ReadReader.h
+++ b/ReadReader.h
@@ -7,6 +7,7 @@
 #include<iostream>
 #include<cassert>
 #include<fstream>
+#include<vector>
 
 #include "utils.h"
 #include "SingleRead.h"
@@ -27,7 +28,7 @@ public:
                this->indices = indices;
        }
 
-       bool locate(long); // You should guarantee that indices exist and rid is valid, otherwise return false; If it fails, you should reset it manually!
+       bool locate(READ_INT_TYPE); // You should guarantee that indices exist and rid is valid, otherwise return false; If it fails, you should reset it manually!
        void reset();
 
        bool next(ReadType& read, int flags = 7) {
@@ -78,15 +79,15 @@ ReadReader<ReadType>::~ReadReader() {
 }
 
 template<class ReadType>
-bool ReadReader<ReadType>::locate(long rid) {
-       long crid = -1;
+bool ReadReader<ReadType>::locate(READ_INT_TYPE rid) {
+       READ_INT_TYPE crid = -1;
        ReadType read;
 
        if (indices == NULL) return false;
 
        //We should make sure that crid returned by each indices is the same
        for (int i = 0; i < s; i++) {
-               long val = indices[i]->locate(rid, *arr[i]);
+               READ_INT_TYPE val = indices[i]->locate(rid, *arr[i]);
                if (i == 0) { crid = val; } else { assert(crid == val); }
        }
        assert(crid <= rid);
@@ -94,7 +95,7 @@ bool ReadReader<ReadType>::locate(long rid) {
 
        if (crid < rid) return false;
 
-       std::streampos tmp[s];
+       std::vector<std::streampos> tmp(s);
        for (int i = 0; i < s; i++) { tmp[i] = arr[i]->tellg(); }
 
        if (!read.read(s, (std::istream**)arr, 0)) return false;