- // ---------------------------------------------
- // ConvertTool constants
-
- // supported conversion format command-line names
- static const string FORMAT_BED = "bed";
- static const string FORMAT_FASTA = "fasta";
- static const string FORMAT_FASTQ = "fastq";
- static const string FORMAT_JSON = "json";
- static const string FORMAT_SAM = "sam";
- static const string FORMAT_PILEUP = "pileup";
- static const string FORMAT_YAML = "yaml";
-
- // other constants
- static const unsigned int FASTA_LINE_MAX = 50;
-
- // ---------------------------------------------
- // ConvertPileupFormatVisitor declaration
-
- class ConvertPileupFormatVisitor : public PileupVisitor {
-
- // ctor & dtor
- public:
- ConvertPileupFormatVisitor(const RefVector& references,
- const string& fastaFilename,
- const bool isPrintingMapQualities,
- ostream* out);
- ~ConvertPileupFormatVisitor(void);
-
- // PileupVisitor interface implementation
- public:
- void Visit(const PileupPosition& pileupData);
-
- // data members
- private:
- Fasta m_fasta;
- bool m_hasFasta;
- bool m_isPrintingMapQualities;
- ostream* m_out;
- RefVector m_references;
- };
+// ---------------------------------------------
+// ConvertTool constants
+
+// supported conversion format command-line names
+static const string FORMAT_BED = "bed";
+static const string FORMAT_FASTA = "fasta";
+static const string FORMAT_FASTQ = "fastq";
+static const string FORMAT_JSON = "json";
+static const string FORMAT_SAM = "sam";
+static const string FORMAT_PILEUP = "pileup";
+static const string FORMAT_YAML = "yaml";
+
+// other constants
+static const unsigned int FASTA_LINE_MAX = 50;
+
+// ---------------------------------------------
+// ConvertPileupFormatVisitor declaration
+
+class ConvertPileupFormatVisitor : public PileupVisitor {
+
+ // ctor & dtor
+ public:
+ ConvertPileupFormatVisitor(const RefVector& references,
+ const string& fastaFilename,
+ const bool isPrintingMapQualities,
+ ostream* out);
+ ~ConvertPileupFormatVisitor(void);
+
+ // PileupVisitor interface implementation
+ public:
+ void Visit(const PileupPosition& pileupData);
+
+ // data members
+ private:
+ Fasta m_fasta;
+ bool m_hasFasta;
+ bool m_isPrintingMapQualities;
+ ostream* m_out;
+ RefVector m_references;
+};