added warning for duplicate @RG tag in header

[bamtools.git] / bamtools_utilities.h

diff --git a/bamtools_utilities.h b/bamtools_utilities.h
index 79462c7be3ac428c15b51761f1c06d7bc7910c5f..7d655e69fe2b089bdd97ca90d4a7b92a2273288a 100644 (file)
--- a/bamtools_utilities.h
+++ b/bamtools_utilities.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 27 May 2010
+// Last modified: 2 June 2010
 // ---------------------------------------------------------------------------
 // Provides general utilities used by BamTools sub-tools.
 // ***************************************************************************
@@ -11,89 +11,29 @@
 #ifndef BAMTOOLS_UTILITIES_H
 #define BAMTOOLS_UTILITIES_H
 
-#include <cstdlib>
-#include <iostream>
 #include <string>
 
 namespace BamTools {
 
-// Parses a REGION string, stores in (startChrom, startPos, stopChrom, stopPos) variables
-// Returns successful parse (true/false)
-static inline
-bool ParseRegionString(const std::string& regionString, std::string& startChrom, int& startPos, std::string& stopChrom, int& stopPos) {
-    
-    // shouldn't call this function with empty string but worth checking 
-    // checked first for clarity purposes later on, since we can assume at least some content in the string
-    if ( regionString.empty() ) { 
-        std::cerr << "Empty REGION. Usual format (e.g. chr2:1000..2000). See README for more detailed uses." << std::endl;
-        return false; 
-    }
-  
-    // non-empty string, look for a colom
-    size_t foundFirstColon = regionString.find(':');
-    
-    // no colon found
-    // going to use entire contents of requested chromosome 
-    // just store entire region string as startChrom name
-    // use BamReader methods to check if its valid for current BAM file
-    if ( foundFirstColon == std::string::npos ) {
-        startChrom = regionString;
-        startPos   = -1;                                                        // ** not sure about these defaults (should stopChrom == startChrom if same?)
-        stopChrom  = "";
-        stopPos    = -1;
-        return true;
-    }
-    
-    // colon found, so we at least have some sort of startPos requested
-    else {
-      
-        // store start chrom from beginning to first colon
-        startChrom = regionString.substr(0,foundFirstColon);
-        
-        // look for ".." after the colon
-        size_t foundRangeDots = regionString.find("..", foundFirstColon+1);
-        
-        // no dots found
-        // so we have a startPos but no range
-        // store contents before colon as startChrom, after as startPos
-        if ( foundRangeDots == std::string::npos ) {
-            startPos   = atoi( regionString.substr(foundFirstColon+1).c_str() ); 
-            stopChrom  = "";
-            stopPos    = -1;
-            return true;
-        } 
-        
-        // ".." found, so we have some sort of range selected
-        else {
-          
-            // store startPos between first colon and range dots ".."
-            startPos = atoi( regionString.substr(foundFirstColon+1, foundRangeDots-foundFirstColon-1).c_str() );
-          
-            // look for second colon
-            size_t foundSecondColon = regionString.find(':', foundRangeDots+1);
-            
-            // no second colon found
-            // so we have a "standard" chrom:start..stop input format (on single chrom)
-            if ( foundSecondColon == std::string::npos ) {
-                stopChrom  = "";
-                stopPos    = atoi( regionString.substr(foundRangeDots+2).c_str() );
-                return true;
-            }
-            
-            // second colon found
-            // so we have a range requested across 2 chrom's
-            else {
-                stopChrom  = regionString.substr(foundRangeDots+2, regionString.length()-foundSecondColon-1);
-                stopPos    = atoi( regionString.substr(foundSecondColon+1).c_str() );
-                return true;
-            }
-        }
-    }
+class BamReader;
+class BamMultiReader;
+
+struct Region {
+    int StartChromID;
+    int StopChromID;
+    int StartPosition;
+    int StopPosition;
+};
+
+class Utilities {
   
-    // shouldn't get here - any code path that does?
-    // if not, what does true/false really signify?
-    return false;
-}
+    public:                          
+        // Parses a region string, uses reader to do validation (valid ID's, positions), stores in Region struct
+        // Returns success (true/false)
+        static bool ParseRegionString(const std::string& regionString, const BamReader& reader, Region& region);
+        // Same as above, but accepts a BamMultiReader
+        static bool ParseRegionString(const std::string& regionString, const BamMultiReader& reader, Region& region);
+};
 
 } // namespace BamTools