update the order of polyX trimming and adapter trimming to support polyA trimming for RNA Seq

#132

Author: sfchen

README.md

@@ -182,9 +182,9 @@ Please note that the trimming for `--max_len` limitation will be applied at the
 5, quality pruning by sliding window (--cut_right)
 6, quality pruning at 3' (--cut_tail)
 7, trim polyG (--trim_poly_g, enabled by default for NovaSeq/NextSeq data)
-8, trim polyX (--trim_poly_x)
-9, trim adapter by overlap analysis (enabled by default for PE data)
-10, trim adapter by adapter sequence (--adapter_sequence, --adapter_sequence_r2. For PE data, this step is skipped if last step succeeded)
+8, trim adapter by overlap analysis (enabled by default for PE data)
+9, trim adapter by adapter sequence (--adapter_sequence, --adapter_sequence_r2. For PE data, this step is skipped if last step succeeded)
+10, trim polyX (--trim_poly_x)
 11, trim to max length (---max_len)
 ```
 

src/peprocessor.cpp

@@ -264,8 +264,6 @@ bool PairEndProcessor::processPairEnd(ReadPairPack* pack, ThreadConfig* config){
         if(r1 != NULL && r2!=NULL) {
             if(mOptions->polyGTrim.enabled)
                 PolyX::trimPolyG(r1, r2, config->getFilterResult(), mOptions->polyGTrim.minLen);
-            if(mOptions->polyXTrim.enabled)
-                PolyX::trimPolyX(r1, r2, config->getFilterResult(), mOptions->polyXTrim.minLen);
         }
         bool isizeEvaluated = false;
         if(r1 != NULL && r2!=NULL && (mOptions->adapter.enabled || mOptions->correction.enabled)){
@@ -295,6 +293,11 @@ bool PairEndProcessor::processPairEnd(ReadPairPack* pack, ThreadConfig* config){
             isizeEvaluated = true;
         }
 
+        if(r1 != NULL && r2!=NULL) {
+            if(mOptions->polyXTrim.enabled)
+                PolyX::trimPolyX(r1, r2, config->getFilterResult(), mOptions->polyXTrim.minLen);
+        }
+
         if(r1 != NULL && r2!=NULL) {
             if( mOptions->trim.maxLen1 > 0 && mOptions->trim.maxLen1 < r1->length())
                 r1->resize(mOptions->trim.maxLen1);

src/seprocessor.cpp

@@ -207,14 +207,17 @@ bool SingleEndProcessor::processSingleEnd(ReadPack* pack, ThreadConfig* config){
         if(r1 != NULL) {
             if(mOptions->polyGTrim.enabled)
                 PolyX::trimPolyG(r1, config->getFilterResult(), mOptions->polyGTrim.minLen);
-            if(mOptions->polyXTrim.enabled)
-                PolyX::trimPolyX(r1, config->getFilterResult(), mOptions->polyXTrim.minLen);
         }
 
         if(r1 != NULL && mOptions->adapter.enabled && mOptions->adapter.hasSeqR1){
             AdapterTrimmer::trimBySequence(r1, config->getFilterResult(), mOptions->adapter.sequence);
         }
 
+        if(r1 != NULL) {
+            if(mOptions->polyXTrim.enabled)
+                PolyX::trimPolyX(r1, config->getFilterResult(), mOptions->polyXTrim.minLen);
+        }
+
         if(r1 != NULL) {
             if( mOptions->trim.maxLen1 > 0 && mOptions->trim.maxLen1 < r1->length())
                 r1->resize(mOptions->trim.maxLen1);