Major update to BamTools version 1.0

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

diff --git a/src/api/internal/BamIndexFactory_p.cpp b/src/api/internal/BamIndexFactory_p.cpp
new file mode 100644 (file)
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+++ b/src/api/internal/BamIndexFactory_p.cpp
@@ -0,0 +1,110 @@
+// ***************************************************************************
+// BamIndexFactory_p.cpp (c) 2011 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 21 March 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides interface for generating BamIndex implementations
+// ***************************************************************************
+
+#include <api/BamAux.h>
+#include <api/internal/BamIndexFactory_p.h>
+#include <api/internal/BamStandardIndex_p.h>
+#include <api/internal/BamToolsIndex_p.h>
+using namespace BamTools;
+using namespace BamTools::Internal;
+
+#include <cstdio>
+using namespace std;
+
+// generates index filename from BAM filename (depending on requested type)
+// if type is unknown, returns empty string
+const string BamIndexFactory::CreateIndexFilename(const string& bamFilename,
+                                                  const BamIndex::IndexType& type)
+{
+    switch ( type ) {
+        case ( BamIndex::STANDARD ) : return ( bamFilename + BAI_EXTENSION );
+        case ( BamIndex::BAMTOOLS ) : return ( bamFilename + BTI_EXTENSION );
+        default :
+            fprintf(stderr, "BamIndexFactory ERROR: unknown index type %u\n", type);
+            return string();
+    }
+}
+
+// creates a new BamIndex object, depending on extension of @indexFilename
+BamIndex* BamIndexFactory::CreateIndexFromFilename(const string& indexFilename) {
+
+    // if file doesn't exist, return null index
+    if ( !BamTools::FileExists(indexFilename) )
+        return 0;
+
+    // get file extension from index filename, including dot (".EXT")
+    // if can't get file extension, return null index
+    const string extension = FileExtension(indexFilename);
+    if ( extension.empty() )
+        return 0;
+
+    // create index based on extension
+    if      ( extension == BAI_EXTENSION ) return new BamStandardIndex;
+    else if ( extension == BTI_EXTENSION ) return new BamToolsIndex;
+    else                                   return 0;
+}
+
+// creates a new BamIndex, object of requested @type
+BamIndex* BamIndexFactory::CreateIndexOfType(const BamIndex::IndexType& type) {
+    switch ( type ) {
+        case ( BamIndex::STANDARD ) : return new BamStandardIndex;
+        case ( BamIndex::BAMTOOLS ) : return new BamToolsIndex;
+        default :
+            fprintf(stderr, "BamIndexFactory ERROR: unknown index type %u\n", type);
+            return 0;
+    }
+}
+
+// retrieves file extension (including '.')
+const string BamIndexFactory::FileExtension(const string& filename) {
+
+    // if filename cannot contain valid path + extension, return empty string
+    if ( filename.empty() || filename.length() <= 4 )
+        return string();
+
+    // look for last dot in filename
+    size_t lastDotPosition = filename.find_last_of('.');
+
+    // if none found, return empty string
+    if ( lastDotPosition == string::npos )
+        return string();
+
+    // return substring from last dot position
+    return filename.substr(lastDotPosition);
+}
+
+// returns name of existing index file that corresponds to @bamFilename
+// will defer to @preferredType if possible, if not will attempt to load any supported type
+// returns empty string if not found
+const string BamIndexFactory::FindIndexFilename(const string& bamFilename,
+                                                const BamIndex::IndexType& preferredType)
+{
+    // try to find index of preferred type first
+    // return index filename if found
+    string indexFilename = CreateIndexFilename(bamFilename, preferredType);
+    if ( !indexFilename.empty() && BamTools::FileExists(indexFilename) )
+        return indexFilename;
+
+    // couldn't find preferred type, try the other supported types
+    // return index filename if found
+    if ( preferredType != BamIndex::STANDARD ) {
+        indexFilename = CreateIndexFilename(bamFilename, BamIndex::STANDARD);
+        if ( !indexFilename.empty() && BamTools::FileExists(indexFilename) )
+            return indexFilename;
+    }
+    if ( preferredType != BamIndex::BAMTOOLS ) {
+        indexFilename = CreateIndexFilename(bamFilename, BamIndex::BAMTOOLS);
+        if ( !indexFilename.empty() && BamTools::FileExists(indexFilename) )
+            return indexFilename;
+    }
+
+    // otherwise couldn't find any index matching this filename
+    return string();
+}