Removed BamTrimMain.cpp. Missed that one in last commit, removing the old 'toy' examples

diff --git a/BamTrimMain.cpp b/BamTrimMain.cpp
deleted file mode 100644 (file)
index 5b39d76..0000000
--- a/BamTrimMain.cpp
+++ /dev/null
@@ -1,91 +0,0 @@
-// ***************************************************************************\r
-// BamTrimMain.cpp (c) 2009 Derek Barnett\r
-// Marth Lab, Department of Biology, Boston College\r
-// All rights reserved.\r
-// ---------------------------------------------------------------------------\r
-// Last modified: 15 July 2009 (DB)\r
-// ---------------------------------------------------------------------------\r
-// Basic example of reading/writing BAM files. Pulls alignments overlapping \r
-// the range specified by user from one BAM file and writes to a new BAM file.\r
-// ***************************************************************************\r
-\r
-// Std C/C++ includes\r
-#include <cstdlib>\r
-#include <iostream>\r
-#include <string>\r
-using namespace std;\r
-\r
-// BamTools includes\r
-#include "BamReader.h"\r
-#include "BamWriter.h"\r
-using namespace BamTools;\r
-\r
-int main(int argc, char* argv[]) {\r
-\r
-       // validate argument count\r
-       if( argc != 7 ) {\r
-               cerr << "USAGE: " << argv[0] << " <input BAM file> <input BAM index file> <output BAM file> <reference name> <leftBound> <rightBound> " << endl;\r
-               exit(1);\r
-       }\r
-\r
-       // store arguments\r
-       string inBamFilename  = argv[1];\r
-       string indexFilename  = argv[2];\r
-       string outBamFilename = argv[3];\r
-       string referenceName  = argv[4];\r
-       string leftBound_str  = argv[5];\r
-       string rightBound_str = argv[6];\r
-\r
-       // open our BAM reader\r
-       BamReader reader;\r
-       reader.Open(inBamFilename, indexFilename);\r
-\r
-       // get header & reference information\r
-       string header = reader.GetHeaderText();\r
-       RefVector references = reader.GetReferenceData();\r
-       \r
-       // open our BAM writer\r
-       BamWriter writer;\r
-       writer.Open(outBamFilename, header, references);\r
-\r
-       // get reference ID from name\r
-       int refID = 0;\r
-       RefVector::const_iterator refIter = references.begin();\r
-       RefVector::const_iterator refEnd  = references.end();\r
-       for ( ; refIter != refEnd; ++refIter ) {\r
-               if ( (*refIter).RefName == referenceName ) { break; }\r
-               ++refID;\r
-       }\r
-       \r
-       // validate ID\r
-       if ( refIter == refEnd ) {\r
-               cerr << "Reference: " << referenceName << " not found." << endl;\r
-               exit(1);\r
-       }\r
-\r
-       // convert boundary arguments to numeric values\r
-       int leftBound  = (int) atoi( leftBound_str.c_str()  );\r
-       int rightBound = (int) atoi( rightBound_str.c_str() );\r
-       \r
-       // attempt jump to range of interest\r
-       if ( reader.Jump(refID, leftBound) ) {\r
-               \r
-               // while data exists and alignment begin before right bound\r
-               BamAlignment bAlignment;\r
-               while ( reader.GetNextAlignment(bAlignment) && (bAlignment.Position <= rightBound) ) {\r
-                       // save alignment to archive\r
-                       writer.SaveAlignment(bAlignment);\r
-               }\r
-       } \r
-       \r
-       // if jump failed\r
-       else {\r
-               cerr << "Could not jump to ref:pos " << referenceName << ":" << leftBound << endl;\r
-               exit(1);\r
-       }\r
-\r
-       // clean up and exit\r
-       reader.Close();\r
-       writer.Close(); \r
-       return 0;\r
-}
\ No newline at end of file