Include full header lines with FASTA/FASTQ output

BenLangmead · Dec 14, 2014 · 86c9cc3 · 86c9cc3
1 parent 7730317
commit 86c9cc3
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/src/classify.cpp b/src/classify.cpp
@@ -254,13 +254,13 @@ void classify_sequence(DNASequence &dna, ostringstream &koss,
     bool print = call ? Print_classified : Print_unclassified;
     if (print) {
       if (Fastq_input) {
-        (*oss_ptr) << "@" << dna.id << endl
+        (*oss_ptr) << "@" << dna.header_line << endl
             << dna.seq << endl
             << "+" << endl
             << dna.quals << endl;
       }
       else {
-        (*oss_ptr) << ">" << dna.id << endl
+        (*oss_ptr) << ">" << dna.header_line << endl
             << dna.seq << endl;
       }
     }

diff --git a/src/seqreader.cpp b/src/seqreader.cpp
@@ -53,7 +53,8 @@ namespace kraken {
       valid = false;
       return dna;
     }
-    istringstream seq_id(line.substr(1));
+    dna.header_line = line.substr(1);
+    istringstream seq_id(dna.header_line);
     seq_id >> dna.id;
 
     ostringstream seq_ss;
@@ -111,7 +112,8 @@ namespace kraken {
       valid = false;
       return dna;
     }
-    istringstream line_ss(line.substr(1));
+    dna.header_line = line.substr(1);
+    istringstream line_ss(dna.header_line);
 
     line_ss >> dna.id;
     getline(file, dna.seq);

diff --git a/src/seqreader.hpp b/src/seqreader.hpp
@@ -25,6 +25,7 @@
 namespace kraken {
   typedef struct {
     std::string id;
+    std::string header_line;  // id + optional description
     std::string seq;
     std::string quals;
   } DNASequence;