Added SAM header-handling classes for read/write/validate.

[bamtools.git] / src / api / SamHeader.cpp

diff --git a/src/api/SamHeader.cpp b/src/api/SamHeader.cpp
new file mode 100644 (file)
index 0000000..405033f
--- /dev/null
+++ b/src/api/SamHeader.cpp
@@ -0,0 +1,102 @@
+// ***************************************************************************
+// SamHeader.cpp (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 23 December 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides functionality for querying/manipulating SAM header data
+// **************************************************************************
+
+#include <api/SamHeader.h>
+#include <api/internal/SamFormatParser_p.h>
+#include <api/internal/SamFormatPrinter_p.h>
+#include <api/internal/SamHeaderValidator_p.h>
+using namespace BamTools;
+using namespace BamTools::Internal;
+using namespace std;
+
+SamHeader::SamHeader(const string& headerText)
+    : Version("")
+    , SortOrder("")
+    , GroupOrder("")
+    , ProgramName("")
+    , ProgramVersion("")
+    , ProgramCommandLine("")
+{
+    SamFormatParser parser(*this);
+    parser.Parse(headerText);
+}
+
+SamHeader::~SamHeader(void) {
+    Clear();
+}
+
+void SamHeader::Clear(void) {
+    Version.clear();
+    SortOrder.clear();
+    GroupOrder.clear();
+    Sequences.Clear();
+    ReadGroups.Clear();
+    ProgramName.clear();
+    ProgramVersion.clear();
+    ProgramCommandLine.clear();
+    Comments.clear();
+}
+
+// retrieve the SAM header, with any local modifications
+string SamHeader::ToString(void) const {
+    SamFormatPrinter printer(*this);
+    return printer.ToString();
+}
+
+// query if header contains @HD ID:<Version>
+bool SamHeader::HasVersion(void) const {
+    return (!Version.empty());
+}
+
+// query if header contains @HD SO:<SortOrder>
+bool SamHeader::HasSortOrder(void) const {
+    return (!SortOrder.empty());
+}
+
+// query if header contains @HD GO:<GroupOrder>
+bool SamHeader::HasGroupOrder(void) const {
+    return (!GroupOrder.empty());
+}
+
+// query if header contains @SQ entries
+bool SamHeader::HasSequences(void) const {
+    return (!Sequences.IsEmpty());
+}
+
+// query if header contains @RG entries
+bool SamHeader::HasReadGroups(void) const {
+    return (!ReadGroups.IsEmpty());
+}
+
+// query if header contains @PG ID:<ProgramName>
+bool SamHeader::HasProgramName(void) const {
+    return (!ProgramName.empty());
+}
+
+// query if header contains @HD VN:<ProgramVersion>
+bool SamHeader::HasProgramVersion(void) const {
+    return (!ProgramVersion.empty());
+}
+
+// query if header contains @HD CL:<ProgramCommandLine>
+bool SamHeader::HasProgramCommandLine(void) const {
+    return (!ProgramCommandLine.empty());
+}
+
+// query if header contains @CO entries
+bool SamHeader::HasComments(void) const {
+    return (!Comments.empty());
+}
+
+// validation
+bool SamHeader::IsValid(bool verbose) const {
+    SamHeaderValidator validator(*this);
+    return validator.Validate(verbose);
+}