X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=ReadReader.h;h=141585aa5cfe78ff3cd1aca0899f227f092928af;hp=f1bd1f59a8395c5938a034199e7cd48b70d6a9fb;hb=da57529b92adbb7ae74a89861cb39fb35ac7c62d;hpb=a95154919f950f86de9104b2b9dcf1f0c7e83387

diff --git a/ReadReader.h b/ReadReader.h
index f1bd1f5..141585a 100644
--- a/ReadReader.h
+++ b/ReadReader.h
@@ -7,6 +7,7 @@
 #include<iostream>
 #include<cassert>
 #include<fstream>
+#include<vector>
 
 #include "utils.h"
 #include "SingleRead.h"
@@ -19,19 +20,21 @@
 template<class ReadType>
 class ReadReader {
 public:
-	ReadReader() { s = 0; indices = NULL; arr = NULL; }
-	ReadReader(int s, char readFs[][STRLEN]);
+	ReadReader() { s = 0; indices = NULL; arr = NULL; hasPolyA = false; seedLen = -1; }
+	ReadReader(int s, char readFs[][STRLEN], bool hasPolyA = false, int seedLen = -1);
 	~ReadReader();
 
 	void setIndices(ReadIndex** indices) {
 		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) {
-		return read.read(s, (std::istream**)arr, flags);
+		bool success = read.read(s, (std::istream**)arr, flags);
+		if (success && seedLen > 0) { read.calc_lq(hasPolyA, seedLen); }
+		return success;
 	}
 
 private:
@@ -39,10 +42,13 @@ private:
 	ReadIndex **indices;
 	std::ifstream** arr;
 	std::streampos *locations;
+
+	bool hasPolyA;
+	int seedLen;
 };
 
 template<class ReadType>
-ReadReader<ReadType>::ReadReader(int s, char readFs[][STRLEN]) {
+ReadReader<ReadType>::ReadReader(int s, char readFs[][STRLEN], bool hasPolyA, int seedLen) {
 	assert(s > 0);
 	this->s = s;
 	arr = new std::ifstream*[s];
@@ -53,6 +59,8 @@ ReadReader<ReadType>::ReadReader(int s, char readFs[][STRLEN]) {
 		if (!arr[i]->is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", readFs[i]); exit(-1); }
 		locations[i] = arr[i]->tellg();
 	}
+	this->hasPolyA = hasPolyA;
+	this->seedLen = seedLen;
 }
 
 template<class ReadType>
@@ -71,15 +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);
@@ -87,7 +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;