tweaks to bamtofastq

src/bamToFastq/bamToFastq.cpp

@@ -176,6 +176,8 @@ void BamToFastq::PairedFastqUseTags() {
             // since the info for both ends are contained in each BAM record,
             // we only need to process one of the two records (bam1) in order
             // to produce FASTQ entries for both ends.
+            // NOTE: Assumes that R2 and Q2 have already been rev 
+            //      and revcomped if necessary
             if (bam1.IsFirstMate() == true) {
                 // end1
                 fq1 << "@" << bam1.Name << "/1" << endl;

src/bamToFastq/bamToFastq.h

@@ -30,26 +30,26 @@ class BamToFastq {
 
 public:
 
-	// constructor 
-	BamToFastq(string bamFile, string fastq1, string fastq2, bool useMateTags, bool pairedEnd);
+    // constructor 
+    BamToFastq(string bamFile, string fastq1, string fastq2, bool useMateTags, bool pairedEnd);
 
-	// destructor
-	~BamToFastq(void);
+    // destructor
+    ~BamToFastq(void);
 
-		
+        
 private:
-		
-	void SingleFastq();
-	void PairedFastq();
-	void PairedFastqUseTags();
+        
+    void SingleFastq();
+    void PairedFastq();
+    void PairedFastqUseTags();
 
-	string _bamFile;
+    string _bamFile;
 
-	BamAlignment _end1;
-	BamAlignment _end2;
+    BamAlignment _end1;
+    BamAlignment _end2;
 
-	string _fastq1, _fastq2;	// the names of the fastq output files
-	bool _useMateTags;			// whether or not the mate sequence should be 
-								// extracted from the R2 BAM tag.
+    string _fastq1, _fastq2;    // the names of the fastq output files
+    bool _useMateTags;          // whether or not the mate sequence should be 
+                                // extracted from the R2 BAM tag.
     bool _pairedEnd;
 };

src/bamToFastq/bamToFastqMain.cpp

@@ -127,7 +127,8 @@ void bamtofastq_help(void) {
     cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <BAM> -fq <FQ> " << endl << endl;
 
     cerr << "Options:" << endl;
-    cerr << "\t-fq2\tFASTQ for second end.  Use if BAM contains paired-end data." << endl << endl;
+    cerr << "\t-fq2\tFASTQ for second end.  Used if BAM contains paired-end data." << endl;
+    cerr << "\t\tBAM should be sorted by query name is creating paired FASTQ." << endl << endl;
     
     cerr << "\t-tags\tCreate FASTQ based on the mate info" << endl;
     cerr << "\t\tin the BAM R2 and Q2 tags." << endl << endl;