feat: sets trim-poly-G as True for one-color-system too (iSeq 100)

README.md

@@ -270,15 +270,15 @@ Please note that the trimming for `--max_len` limitation will be applied at the
 4, quality pruning at 5' (--cut_front)
 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)
+7, trim polyG (--trim_poly_g, enabled by default for NovaSeq/NextSeq/iSeq data)
 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)
 ```
 
 # polyG tail trimming
-For Illumina NextSeq/NovaSeq data, `polyG` can happen in read tails since `G` means no signal in the Illumina two-color systems. `fastp` can detect the polyG in read tails and trim them. This feature is enabled for NextSeq/NovaSeq data by default, and you can specify `-g` or `--trim_poly_g` to enable it for any data, or specify `-G` or `--disable_trim_poly_g` to disable it. NextSeq/NovaSeq data is detected by the machine ID in the FASTQ records.  
+For Illumina NextSeq/NovaSeq data, `polyG` can happen in read tails since `G` means no signal in the Illumina two-color systems. `fastp` can detect the polyG in read tails and trim them. This feature is enabled for NextSeq/NovaSeq data by default, and you can specify `-g` or `--trim_poly_g` to enable it for any data, or specify `-G` or `--disable_trim_poly_g` to disable it. NextSeq/NovaSeq/iSeq data is detected by the machine ID in the FASTQ records.  
 
 A minimum length can be set with `<poly_g_min_len>` for `fastp` to detect polyG. This value is 10 by default.
 

src/evaluator.cpp

@@ -13,16 +13,17 @@ Evaluator::Evaluator(Options* opt){
 Evaluator::~Evaluator(){
 }
 
-bool Evaluator::isTwoColorSystem() {
+bool Evaluator::isOneOrTwoColorSystem() {
     FastqReader reader(mOptions->in1);
 
     Read* r = reader.read();
 
     if(!r)
         return false;
 
-    // NEXTSEQ500, NEXTSEQ 550/550DX, NOVASEQ
-    if(starts_with(r->mName, "@NS") || starts_with(r->mName, "@NB") || starts_with(r->mName, "@NDX") || starts_with(r->mName, "@A0")) {
+    // NEXTSEQ500, NEXTSEQ 550/550DX, NOVASEQ [2-color-system]
+    // iSeq 100 [1-color-system]
+    if(starts_with(r->mName, "@NS") || starts_with(r->mName, "@NB") || starts_with(r->mName, "@NDX") || starts_with(r->mName, "@A0") || starts_with(r->mName, "@FS")) {
         delete r;
         return true;
     }

src/evaluator.h

@@ -18,7 +18,7 @@ class Evaluator{
     void evaluateReadNum(long& readNum);
     string evalAdapterAndReadNumDepreciated(long& readNum);
     string evalAdapterAndReadNum(long& readNum, bool isR2);
-    bool isTwoColorSystem();
+    bool isOneOrTwoColorSystem();
     void evaluateSeqLen();
     void evaluateOverRepSeqs();
     void computeOverRepSeq(string filename, map<string, long>& hotseqs, int seqLen);

src/main.cpp

@@ -73,9 +73,9 @@ int main(int argc, char* argv[]){
     cmd.add("dont_eval_duplication", 0, "don't evaluate duplication rate to save time and use less memory.");
 
     // polyG tail trimming
-    cmd.add("trim_poly_g", 'g', "force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data");
+    cmd.add("trim_poly_g", 'g', "force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq/iSeq data");
     cmd.add<int>("poly_g_min_len", 0, "the minimum length to detect polyG in the read tail. 10 by default.", false, 10);
-    cmd.add("disable_trim_poly_g", 'G', "disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data");
+    cmd.add("disable_trim_poly_g", 'G', "disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq/iSeq data");
 
     // polyX tail trimming
     cmd.add("trim_poly_x", 'x', "enable polyX trimming in 3' ends.");
@@ -498,8 +498,8 @@ int main(int argc, char* argv[]){
 
     // using evaluator to check if it's two color system
     if(!cmd.exist("trim_poly_g") && !cmd.exist("disable_trim_poly_g") && supportEvaluation) {
-        bool twoColorSystem = eva.isTwoColorSystem();
-        if(twoColorSystem){
+        bool oneOrTwoColorSystem = eva.isOneOrTwoColorSystem();
+        if(oneOrTwoColorSystem){
             opt.polyGTrim.enabled = true;
         }
     }