Added tag support in filter tool.

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

diff --git a/src/utils/bamtools_utilities.cpp b/src/utils/bamtools_utilities.cpp
index 7772587e84c10fe2289535244cd4c723f3986f54..559fc8fd2c1028881fbdd4147384e0be71428eba 100644 (file)
--- a/src/utils/bamtools_utilities.cpp
+++ b/src/utils/bamtools_utilities.cpp
@@ -3,20 +3,33 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 2 June 2010
+// Last modified: 23 September 2010
 // ---------------------------------------------------------------------------
 // Provides general utilities used by BamTools sub-tools.
 // ***************************************************************************
 
+#include <algorithm>
 #include <cstdlib>
-#include <sys/stat.h> 
+#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) { 
+    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) {
@@ -233,9 +246,17 @@ bool Utilities::ParseRegionString(const std::string& regionString, const BamMult
     return true;
 }
 
-bool Utilities::FileExists(const std::string& filename) { 
-
-    struct stat fileInfo; 
-    return stat(filename.c_str(), &fileInfo) == 0;
+void Utilities::Reverse(string& sequence) {
+    reverse(sequence.begin(), sequence.end());
+}
 
+void Utilities::ReverseComplement(std::string& sequence) {
+    
+    // do complement
+    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);
 }