Allowed > 2^31 hits

[rsem.git] / HitContainer.h

diff --git a/HitContainer.h b/HitContainer.h
index b051ed40ef3fefbde00f7c3892f23e8b71f0e78d..5dfbf7ea6b401d6e1fbfa52959f28f70d849fbfc 100644 (file)
--- a/HitContainer.h
+++ b/HitContainer.h
@@ -4,8 +4,9 @@
 #include<cassert>
 #include<iostream>
 #include<vector>
-
 #include<algorithm>
+
+#include "utils.h"
 #include "GroupInfo.h"
 
 template<class HitType>
@@ -39,32 +40,32 @@ public:
                }
        }
 
-       int getN() { return n; }
+       READ_INT_TYPE getN() { return n; }
 
-       int getNHits() { return nhits; }
+       HIT_INT_TYPE getNHits() { return nhits; }
 
-       int calcNumGeneMultiReads(const GroupInfo&);
-       int calcNumIsoformMultiReads();
+       READ_INT_TYPE calcNumGeneMultiReads(const GroupInfo&);
+       READ_INT_TYPE calcNumIsoformMultiReads();
 
-       int getSAt(int pos) { assert(pos >= 0 && pos <= n); return s[pos]; }
+       HIT_INT_TYPE getSAt(READ_INT_TYPE pos) { assert(pos >= 0 && pos <= n); return s[pos]; }
 
-       HitType& getHitAt(int pos) { assert(pos >= 0 && pos < nhits); return hits[pos]; }
+       HitType& getHitAt(HIT_INT_TYPE pos) { assert(pos >= 0 && pos < nhits); return hits[pos]; }
 
 private:
-       int n; // n reads in total
-       int nhits; // # of hits
-       std::vector<int> s;
+       READ_INT_TYPE n; // n reads in total
+       HIT_INT_TYPE nhits; // # of hits
+       std::vector<HIT_INT_TYPE> s;
        std::vector<HitType> hits;
 };
 
 //Each time only read one read's hits. If you want to start over, must call clear() first!
 template<class HitType>
 bool HitContainer<HitType>::read(std::istream& in) {
-       int tot;
+       HIT_INT_TYPE tot;
 
        if (!(in>>tot)) return false;
        assert(tot > 0);
-       for (int i = 0; i < tot; i++) {
+       for (HIT_INT_TYPE i = 0; i < tot; i++) {
                HitType hit;
                if (!hit.read(in)) return false;
                hits.push_back(hit);
@@ -80,9 +81,9 @@ bool HitContainer<HitType>::read(std::istream& in) {
 template<class HitType>
 void HitContainer<HitType>::write(std::ostream& out) {
        if (n <= 0) return;
-       for (int i = 0; i < n; i++) {
+       for (READ_INT_TYPE i = 0; i < n; i++) {
                out<<s[i + 1] - s[i];
-               for (int j = s[i]; j < s[i + 1]; j++) {
+               for (HIT_INT_TYPE j = s[i]; j < s[i + 1]; j++) {
                        hits[j].write(out);
                }
                out<<std::endl;
@@ -90,14 +91,14 @@ void HitContainer<HitType>::write(std::ostream& out) {
 }
 
 template<class HitType>
-int HitContainer<HitType>::calcNumGeneMultiReads(const GroupInfo& gi) {
-       int res = 0;
+READ_INT_TYPE HitContainer<HitType>::calcNumGeneMultiReads(const GroupInfo& gi) {
+       READ_INT_TYPE res = 0;
        int *sortgids = NULL;
 
-       for (int i = 0; i < n; i++) {
-               int num = s[i + 1] - s[i];
+       for (READ_INT_TYPE i = 0; i < n; i++) {
+               HIT_INT_TYPE num = s[i + 1] - s[i];
                sortgids = new int[num];
-               for (int j = s[i]; j < s[i + 1]; j++) sortgids[j] = gi.gidAt(hits[j].getSid());
+               for (HIT_INT_TYPE j = s[i]; j < s[i + 1]; j++) sortgids[j] = gi.gidAt(hits[j].getSid());
                std::sort(sortgids, sortgids + num);
                if (std::unique(sortgids, sortgids + num) - sortgids > 1) ++res;
                delete[] sortgids;
@@ -107,9 +108,9 @@ int HitContainer<HitType>::calcNumGeneMultiReads(const GroupInfo& gi) {
 }
 
 template<class HitType>
-int HitContainer<HitType>::calcNumIsoformMultiReads() {
-       int res = 0;
-       for (int i = 0; i < n; i++)
+READ_INT_TYPE HitContainer<HitType>::calcNumIsoformMultiReads() {
+       READ_INT_TYPE res = 0;
+       for (READ_INT_TYPE i = 0; i < n; i++)
                if (s[i + 1] - s[i] > 1) ++res;
        return res;
 }