Added a second Utilities::ParseRegionString() that accepts BamMultiReader

diff --git a/bamtools_utilities.cpp b/bamtools_utilities.cpp
index e3ab868178bccb3ef8e8e756fafdde860f703714..fcbabdf48d8ac19717b89580298bec1c6a3cae60 100644 (file)
--- a/bamtools_utilities.cpp
+++ b/bamtools_utilities.cpp
@@ -11,11 +11,13 @@
 #include <cstdlib>
 #include "bamtools_utilities.h"
 #include "BamReader.h"
+#include "BamMultiReader.h"
 
 using namespace std;
 using namespace BamTools;
 
 // Parses a region string, does validation (valid ID's, positions), stores in Region struct
+// Returns success (true/false)
 bool Utilities::ParseRegionString(const std::string& regionString, const BamReader& reader, Region& region) {
   
     // -------------------------------
@@ -110,7 +112,7 @@ bool Utilities::ParseRegionString(const std::string& regionString, const BamRead
     if ( stopPos > stopReference.RefLength ) return false;
     
     // if no stopPosition specified, set to reference end
-    if ( stopPos == -1 )stopPos = stopReference.RefLength;  
+    if ( stopPos == -1 ) stopPos = stopReference.RefLength;  
     
     // -------------------------------
     // set up Region struct & return
@@ -122,3 +124,109 @@ bool Utilities::ParseRegionString(const std::string& regionString, const BamRead
     return true;
 }
 
+// Same as ParseRegionString() above, but accepts a BamMultiReader
+bool Utilities::ParseRegionString(const std::string& regionString, const BamMultiReader& reader, Region& region) {
+  
+    // -------------------------------
+    // parse region string
+  
+    // check first for empty string
+    if ( regionString.empty() ) 
+        return false;   
+    
+    // non-empty string, look for a colom
+    size_t foundFirstColon = regionString.find(':');
+    
+    // store chrom strings, and numeric positions
+    string startChrom;
+    string stopChrom;
+    int startPos;
+    int stopPos;
+    
+    // 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 == string::npos ) {
+        startChrom = regionString;
+        startPos   = 0;
+        stopChrom  = regionString;
+        stopPos    = -1;
+    }
+    
+    // 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 == string::npos ) {
+            startPos   = atoi( regionString.substr(foundFirstColon+1).c_str() ); 
+            stopChrom  = startChrom;
+            stopPos    = -1;
+        } 
+        
+        // ".." 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 == string::npos ) {
+                stopChrom  = startChrom;
+                stopPos    = atoi( regionString.substr(foundRangeDots+2).c_str() );
+            }
+            
+            // second colon found
+            // so we have a range requested across 2 chrom's
+            else {
+                stopChrom  = regionString.substr(foundRangeDots+2, foundSecondColon-(foundRangeDots+2));
+                stopPos    = atoi( regionString.substr(foundSecondColon+1).c_str() );
+            }
+        }
+    }
+
+    // -------------------------------
+    // validate reference IDs & genomic positions
+    
+    const RefVector references = reader.GetReferenceData();
+    
+    // if startRefID not found, return false
+    int startRefID = reader.GetReferenceID(startChrom);
+    if ( startRefID == (int)references.size() ) return false;  
+    
+    // if startPos is larger than reference, return false
+    const RefData& startReference = references.at(startRefID);
+    if ( startPos > startReference.RefLength ) return false;
+    
+    // if stopRefID not found, return false
+    int stopRefID = reader.GetReferenceID(stopChrom);
+    if ( stopRefID == (int)references.size() ) return false;
+    
+    // if stopPosition larger than reference, return false
+    const RefData& stopReference = references.at(stopRefID);
+    if ( stopPos > stopReference.RefLength ) return false;
+    
+    // if no stopPosition specified, set to reference end
+    if ( stopPos == -1 ) stopPos = stopReference.RefLength;  
+    
+    // -------------------------------
+    // set up Region struct & return
+    
+    region.StartChromID  = startRefID;
+    region.StopChromID   = stopRefID;
+    region.StartPosition = startPos;
+    region.StopPosition  = stopPos;
+    return true;
+}

diff --git a/bamtools_utilities.h b/bamtools_utilities.h
index 1e280f127e903a2bc5368b32a8e82a667b285656..7d655e69fe2b089bdd97ca90d4a7b92a2273288a 100644 (file)
--- a/bamtools_utilities.h
+++ b/bamtools_utilities.h
@@ -15,7 +15,8 @@
 
 namespace BamTools {
 
-class BamReader;  
+class BamReader;
+class BamMultiReader;
 
 struct Region {
     int StartChromID;
@@ -28,7 +29,10 @@ class Utilities {
   
     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