Major update to BamTools version 1.0

[bamtools.git] / src / utils / bamtools_utilities.cpp

diff --git a/src/utils/bamtools_utilities.cpp b/src/utils/bamtools_utilities.cpp
index b39e60dc913007910e63acf7067ceb405c6ee457..bb65c7b3bbabc23a93235cf8e6c524a316248e69 100644 (file)
--- a/src/utils/bamtools_utilities.cpp
+++ b/src/utils/bamtools_utilities.cpp
@@ -3,30 +3,46 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 3 September 2010
+// Last modified: 26 January 2011
 // ---------------------------------------------------------------------------
 // Provides general utilities used by BamTools sub-tools.
 // ***************************************************************************
 
+#include <api/BamMultiReader.h>
+#include <api/BamReader.h>
+#include <utils/bamtools_utilities.h>
+using namespace BamTools;
+
+#include <algorithm>
 #include <cstdlib>
 #include <fstream>
 #include <iostream>
-#include "bamtools_utilities.h"
-#include "BamReader.h"
-#include "BamMultiReader.h"
 using namespace std;
-using namespace BamTools;
 
+namespace BamTools {
+  
+const char REVCOMP_LOOKUP[] = {'T',  0,  'G', 'H',
+                                0,   0,  'C', 'D',
+                                0,   0,   0,   0,
+                               'K', 'N',  0,   0,
+                                0,  'Y', 'W', 'A',
+                               'A', 'B', 'S', 'X',
+                               'R',  0 };
+  
+} // namespace BamTools 
+  
 // check if a file exists
-bool Utilities::FileExists(const std::string& filename) { 
+bool Utilities::FileExists(const string& filename) {
     ifstream f(filename.c_str(), ifstream::in);
     return !f.fail();
 }
 
 // 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, BamRegion& region) {
-  
+bool Utilities::ParseRegionString(const string& regionString,
+                                  const BamReader& reader,
+                                  BamRegion& region)
+{
     // -------------------------------
     // parse region string
   
@@ -132,8 +148,10 @@ bool Utilities::ParseRegionString(const std::string& regionString, const BamRead
 }
 
 // Same as ParseRegionString() above, but accepts a BamMultiReader
-bool Utilities::ParseRegionString(const std::string& regionString, const BamMultiReader& reader, BamRegion& region) {
-  
+bool Utilities::ParseRegionString(const string& regionString,
+                                  const BamMultiReader& reader,
+                                  BamRegion& region)
+{
     // -------------------------------
     // parse region string
   
@@ -235,6 +253,20 @@ bool Utilities::ParseRegionString(const std::string& regionString, const BamMult
     region.LeftPosition = startPos;
     region.RightRefID = stopRefID;;
     region.RightPosition = stopPos;
-
     return true;
 }
+
+void Utilities::Reverse(string& sequence) {
+    reverse(sequence.begin(), sequence.end());
+}
+
+void Utilities::ReverseComplement(string& sequence) {
+    
+    // do complement, in-place
+    size_t seqLength = sequence.length();
+    for ( size_t i = 0; i < seqLength; ++i )
+        sequence.replace(i, 1, 1, REVCOMP_LOOKUP[(int)sequence.at(i) - 65]);
+    
+    // reverse it
+    Reverse(sequence);
+}