-void PairedEndReadQ::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 PairedEndReadQ::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();