For genome BAM, modified MD tag accordingly

[rsem.git] / SingleReadQ.h

diff --git a/SingleReadQ.h b/SingleReadQ.h
index 976637fc269d79fa484cb0033421e7f7a0769c49..9fd3dd18156b74674e5f19a43a50e937403181df 100644 (file)
--- a/SingleReadQ.h
+++ b/SingleReadQ.h
@@ -12,50 +12,46 @@
 #include "Read.h"
 
 class SingleReadQ : public Read {
- public:
-  SingleReadQ() { readseq = qscore = ""; len = 0; }
-  SingleReadQ(const std::string& name, const std::string& readseq, const std::string& qscore) {
-         this->name = name;
-         this->readseq = readseq;
-         this->qscore = qscore;
-         this->len = readseq.length();
-
-         calc_lq();
-  }
-
-  bool read(int argc, std::istream* argv[], int flags = 7);
-  void write(int argc, std::ostream* argv[]);
-
-  int getReadLength() const { return len; }
-  const std::string& getReadSeq() const { return readseq; }
-  const std::string& getQScore() const { return qscore; }
-
- private:
-  int len; // read length
-  std::string readseq, qscore; // qscore : quality scores
-
-  void calc_lq();
+public:
+       SingleReadQ() { readseq = qscore = ""; len = 0; }
+       SingleReadQ(const std::string& name, const std::string& readseq, const std::string& qscore) {
+               this->name = name;
+               this->readseq = readseq;
+               this->qscore = qscore;
+               this->len = readseq.length();
+       }
+
+       bool read(int argc, std::istream* argv[], int flags = 7);
+       void write(int argc, std::ostream* argv[]);
+
+       int getReadLength() const { return len; }
+       const std::string& getReadSeq() const { return readseq; }
+       const std::string& getQScore() const { return qscore; }
+
+       void calc_lq(bool, int); // calculate if this read is low quality. Without calling this function, isLowQuality() will always be false
+
+private:
+       int len; // read length
+       std::string readseq, qscore; // qscore : quality scores
 };
 
 bool SingleReadQ::read(int argc, std::istream* argv[], int flags) {
-  std::string line;
-
-  assert(argc == 1);
-  if (!getline((*argv[0]), line)) return false;
-  if (line[0] != '@') { fprintf(stderr, "Read file does not look like a FASTQ file!\n"); exit(-1); }
-  name = "";
-  if (flags & 4) { name = line.substr(1); }
-  if (!getline((*argv[0]), readseq)) return false;
-  len = readseq.length();
-  if (!(flags & 1)) { readseq = ""; }
-  if (!getline((*argv[0]), line)) return false;
-  if (line[0] != '+') { fprintf(stderr, "Read file does not look like a FASTQ file!\n"); exit(-1); }
-  if (!getline((*argv[0]), qscore)) return false;
-  if (!(flags & 2)) { qscore = ""; }
-
-  if (flags & 1) calc_lq();
-
-  return true;
+       std::string line;
+
+       assert(argc == 1);
+       if (!getline((*argv[0]), line)) return false;
+       if (line[0] != '@') { fprintf(stderr, "Read file does not look like a FASTQ file!\n"); exit(-1); }
+       name = "";
+       if (flags & 4) { name = line.substr(1); }
+       if (!getline((*argv[0]), readseq)) return false;
+       len = readseq.length();
+       if (!(flags & 1)) { readseq = ""; }
+       if (!getline((*argv[0]), line)) return false;
+       if (line[0] != '+') { fprintf(stderr, "Read file does not look like a FASTQ file!\n"); exit(-1); }
+       if (!getline((*argv[0]), qscore)) return false;
+       if (!(flags & 2)) { qscore = ""; }
+
+       return true;
 }
 
 void SingleReadQ::write(int argc, std::ostream* argv[]) {
@@ -63,32 +59,39 @@ void SingleReadQ::write(int argc, std::ostream* argv[]) {
        (*argv[0])<<"@"<<name<<std::endl<<readseq<<std::endl<<"+\n"<<qscore<<std::endl;
 }
 
-void SingleReadQ::calc_lq() {
-  int numA = 0, numT = 0, numAO = 0, numTO = 0; // numAO : number of A in overlap seed region
-  int threshold_1, threshold_2;
-
-  if (len < OLEN) { low_quality = true; return; }
-
-  threshold_1 = int(0.9 * len - 1.5 * sqrt(len * 1.0) + 0.5);
-  threshold_2 = (OLEN - 1) / 2 + 1;
-  for (int i = 0; i < len; i++) {
-    if (readseq[i] == 'A') { 
-      ++numA;
-      if (i < OLEN) ++numAO;
-    }
-    if (readseq[i] == 'T') {
-      ++numT;
-      if (i >= len - OLEN) ++numTO; 
-    }
-  }
-  
-  if (numA >= threshold_1) {
-    low_quality = (numAO >= threshold_2);
-  }
-  else if (numT >= threshold_1) {
-    low_quality = (numTO >= threshold_2);
-  }
-  else low_quality = false;
+//calculate if this read is low quality
+void SingleReadQ::calc_lq(bool hasPolyA, int seedLen) {
+       low_quality = false;
+       if (len < seedLen) { low_quality = true; return; }
+
+       // if no polyA, no need to do the following calculation
+       if (!hasPolyA) return;
+
+       assert(readseq != "");
+
+       int numA = 0, numT = 0, numAO = 0, numTO = 0; // numAO : number of A in overlap seed region
+       int threshold_1, threshold_2;
+
+       threshold_1 = int(0.9 * len - 1.5 * sqrt(len * 1.0) + 0.5);
+       threshold_2 = (OLEN - 1) / 2 + 1;
+       for (int i = 0; i < len; i++) {
+               if (readseq[i] == 'A') {
+                       ++numA;
+                       if (i < OLEN) ++numAO;
+               }
+               if (readseq[i] == 'T') {
+                       ++numT;
+                       if (i >= len - OLEN) ++numTO;
+               }
+       }
+
+       if (numA >= threshold_1) {
+               low_quality = (numAO >= threshold_2);
+       }
+       else if (numT >= threshold_1) {
+               low_quality = (numTO >= threshold_2);
+       }
+       else low_quality = false;
 }
 
 #endif