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

[bamtools.git] / src / api / internal / SamFormatPrinter_p.cpp

diff --git a/src/api/internal/SamFormatPrinter_p.cpp b/src/api/internal/SamFormatPrinter_p.cpp
new file mode 100644 (file)
index 0000000..dcde46e
--- /dev/null
+++ b/src/api/internal/SamFormatPrinter_p.cpp
@@ -0,0 +1,185 @@
+// ***************************************************************************
+// SamFormatPrinter.cpp (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 23 December 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides functionality for printing formatted SAM header to string
+// ***************************************************************************
+
+#include <api/SamConstants.h>
+#include <api/SamHeader.h>
+#include <api/internal/SamFormatPrinter_p.h>
+using namespace BamTools;
+using namespace BamTools::Internal;
+
+#include <iostream>
+#include <sstream>
+#include <vector>
+using namespace std;
+
+SamFormatPrinter::SamFormatPrinter(const SamHeader& header)
+    : m_header(header)
+{ }
+
+SamFormatPrinter::~SamFormatPrinter(void) { }
+
+const string SamFormatPrinter::FormatTag(const string &tag, const string &value) const {
+    return string(Constants::SAM_TAB + tag + Constants::SAM_COLON + value);
+}
+
+const string SamFormatPrinter::ToString(void) const {
+
+    // clear out stream
+    stringstream out("");
+
+    // generate formatted header text
+    PrintHD(out);
+    PrintSQ(out);
+    PrintRG(out);
+    PrintPG(out);
+    PrintCO(out);
+
+    // return result
+    return out.str();
+}
+
+void SamFormatPrinter::PrintHD(std::stringstream& out) const {
+
+    // if header has @HD data
+    if ( m_header.HasVersion() ) {
+
+        // @HD VN:<Version>
+        out << Constants::SAM_HD_BEGIN_TOKEN
+            << FormatTag(Constants::SAM_HD_VERSION_TAG, m_header.Version);
+
+        // SO:<SortOrder>
+        if ( m_header.HasSortOrder() )
+            out << FormatTag(Constants::SAM_HD_SORTORDER_TAG, m_header.SortOrder);
+
+        // GO:<GroupOrder>
+        if ( m_header.HasGroupOrder() )
+            out << FormatTag(Constants::SAM_HD_GROUPORDER_TAG, m_header.GroupOrder);
+
+        // newline
+        out << endl;
+    }
+}
+
+void SamFormatPrinter::PrintSQ(std::stringstream& out) const {
+
+    // iterate over sequence entries
+    SamSequenceConstIterator seqIter = m_header.Sequences.ConstBegin();
+    SamSequenceConstIterator seqEnd  = m_header.Sequences.ConstEnd();
+    for ( ; seqIter != seqEnd; ++seqIter ) {
+        const SamSequence& seq = (*seqIter);
+
+        // @SQ SN:<Name> LN:<Length>
+        out << Constants::SAM_SQ_BEGIN_TOKEN
+            << FormatTag(Constants::SAM_SQ_NAME_TAG, seq.Name)
+            << FormatTag(Constants::SAM_SQ_LENGTH_TAG, seq.Length);
+
+        // AS:<AssemblyID>
+        if ( seq.HasAssemblyID() )
+            out << FormatTag(Constants::SAM_SQ_ASSEMBLYID_TAG, seq.AssemblyID);
+
+        // M5:<Checksum>
+        if ( seq.HasChecksum() )
+            out << FormatTag(Constants::SAM_SQ_CHECKSUM_TAG, seq.Checksum);
+
+        // UR:<URI>
+        if ( seq.HasURI() )
+            out << FormatTag(Constants::SAM_SQ_URI_TAG, seq.URI);
+
+        // SP:<Species>
+        if ( seq.HasSpecies() )
+            out << FormatTag(Constants::SAM_SQ_SPECIES_TAG, seq.Species);
+
+        // newline
+        out << endl;
+    }
+}
+
+void SamFormatPrinter::PrintRG(std::stringstream& out) const {
+
+    // iterate over read group entries
+    SamReadGroupConstIterator rgIter = m_header.ReadGroups.ConstBegin();
+    SamReadGroupConstIterator rgEnd  = m_header.ReadGroups.ConstEnd();
+    for ( ; rgIter != rgEnd; ++rgIter ) {
+        const SamReadGroup& rg = (*rgIter);
+
+        // @RG ID:<ID> SM:<Sample>
+        out << Constants::SAM_RG_BEGIN_TOKEN
+            << FormatTag(Constants::SAM_RG_ID_TAG, rg.ID)
+            << FormatTag(Constants::SAM_RG_SAMPLE_TAG, rg.Sample);
+
+        // LB:<Library>
+        if ( rg.HasLibrary() )
+            out << FormatTag(Constants::SAM_RG_LIBRARY_TAG, rg.Library);
+
+        // DS:<Description>
+        if ( rg.HasDescription() )
+            out << FormatTag(Constants::SAM_RG_DESCRIPTION_TAG, rg.Description);
+
+        // PU:<PlatformUnit>
+        if ( rg.HasPlatformUnit() )
+            out << FormatTag(Constants::SAM_RG_PLATFORMUNIT_TAG, rg.PlatformUnit);
+
+        // PI:<PredictedInsertSize>
+        if ( rg.HasPredictedInsertSize() )
+            out << FormatTag(Constants::SAM_RG_PREDICTEDINSERTSIZE_TAG, rg.PredictedInsertSize);
+
+        // CN:<SequencingCenter>
+        if ( rg.HasSequencingCenter() )
+            out << FormatTag(Constants::SAM_RG_SEQCENTER_TAG, rg.SequencingCenter);
+
+        // DT:<ProductionDate>
+        if ( rg.HasProductionDate() )
+            out << FormatTag(Constants::SAM_RG_PRODUCTIONDATE_TAG, rg.ProductionDate);
+
+        // PL:<SequencingTechnology>
+        if ( rg.HasSequencingTechnology() )
+            out << FormatTag(Constants::SAM_RG_SEQTECHNOLOGY_TAG, rg.SequencingTechnology);
+
+        // newline
+        out << endl;
+    }
+}
+
+void SamFormatPrinter::PrintPG(std::stringstream& out) const {
+
+    // if header has @PG data
+    if ( m_header.HasProgramName() ) {
+
+        // @PG ID:<ProgramName>
+        out << Constants::SAM_PG_BEGIN_TOKEN
+            << FormatTag(Constants::SAM_PG_NAME_TAG, m_header.ProgramName);
+
+        // VN:<ProgramVersion>
+        if ( m_header.HasProgramVersion() )
+            out << FormatTag(Constants::SAM_PG_VERSION_TAG, m_header.ProgramVersion);
+
+        // CL:<ProgramCommandLine>
+        if ( m_header.HasProgramCommandLine() )
+            out << FormatTag(Constants::SAM_PG_COMMANDLINE_TAG, m_header.ProgramCommandLine);
+
+        // newline
+        out << endl;
+    }
+}
+
+void SamFormatPrinter::PrintCO(std::stringstream& out) const {
+
+    // iterate over comments
+    vector<string>::const_iterator commentIter = m_header.Comments.begin();
+    vector<string>::const_iterator commentEnd  = m_header.Comments.end();
+    for ( ; commentIter != commentEnd; ++commentIter ) {
+
+        // @CO <Comment>
+        out << Constants::SAM_CO_BEGIN_TOKEN
+            << Constants::SAM_TAB
+            << (*commentIter)
+            << endl;
+    }
+}