X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=PairedEndRead.h;h=01d3d007a36669ac4292b777f97132ae9c747012;hp=6504e610141e9db33d027bdb47cff33fb2af95a9;hb=da57529b92adbb7ae74a89861cb39fb35ac7c62d;hpb=946f9a6adb2a82048c8453d44693cd3838d32939

diff --git a/PairedEndRead.h b/PairedEndRead.h
index 6504e61..01d3d00 100644
--- a/PairedEndRead.h
+++ b/PairedEndRead.h
@@ -9,30 +9,28 @@
 #include "SingleRead.h"
 
 class PairedEndRead : public Read {
- public:
-  PairedEndRead() : mate1(), mate2() {}
-  PairedEndRead(const SingleRead& mate1, const SingleRead& mate2) {
-	  this->mate1 = mate1;
-	  this->mate2 = mate2;
-	  this->name = mate1.getName();
-
-	  calc_lq();
-  }
-
-  bool read(int argc, std::istream* argv[], int flags = 7);
-  void write(int argc, std::ostream* argv[]);
-
-  const SingleRead& getMate1() const { return mate1; }
-  const SingleRead& getMate2() const { return mate2; }
-  const SingleRead& getMate(int i) const {
-	  if (i == 1) return mate1;
-	  else return mate2;
-  }
-
- private:
-  SingleRead mate1, mate2;
-
-  void calc_lq();
+public:
+	PairedEndRead() : mate1(), mate2() {}
+	PairedEndRead(const SingleRead& mate1, const SingleRead& mate2) {
+		this->mate1 = mate1;
+		this->mate2 = mate2;
+		this->name = mate1.getName();
+	}
+
+	bool read(int argc, std::istream* argv[], int flags = 7);
+	void write(int argc, std::ostream* argv[]);
+
+	const SingleRead& getMate1() const { return mate1; }
+	const SingleRead& getMate2() const { return mate2; }
+	const SingleRead& getMate(int i) const {
+		if (i == 1) return mate1;
+		else return mate2;
+	}
+
+	void calc_lq(bool, int); // calculate if this read is low quality. Without calling this function, isLowQuality() will always be false
+
+private:
+	SingleRead mate1, mate2;
 };
 
 bool PairedEndRead::read(int argc, std::istream* argv[], int flags) {
@@ -45,8 +43,6 @@ bool PairedEndRead::read(int argc, std::istream* argv[], int flags) {
 	name = "";
 	if (flags & 4) { name = mate1.getName(); } //May chop 1 char later if we want
 
-	if (flags & 1) calc_lq();
-
 	return success;
 }
 
@@ -59,9 +55,13 @@ void PairedEndRead::write(int argc, std::ostream *argv[]) {
 	mate2.write(1, outMate2);
 }
 
-void PairedEndRead::calc_lq() {
-	low_quality = mate1.isLowQuality() && mate2.isLowQuality();
-	if (mate1.getReadLength() < OLEN || mate2.getReadLength() < OLEN) low_quality = true;
+//calculate if this read is low quality
+void PairedEndRead::calc_lq(bool hasPolyA, int seedLen) {
+	low_quality = false;
+	mate1.calc_lq(hasPolyA, seedLen);
+	mate2.calc_lq(hasPolyA, seedLen);
+	if (mate1.getReadLength() < seedLen || mate2.getReadLength() < seedLen) low_quality = true;
+	else low_quality = mate1.isLowQuality() && mate2.isLowQuality();
 }
 
 #endif