From: Derek <derekwbarnett@gmail.com>
Date: Wed, 26 May 2010 20:17:14 +0000 (-0400)
Subject: Removed BamTrimMain.cpp. Missed that one in last commit, removing the old 'toy' examples
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=aa45b408b8ce3f760f4bb5b79a9fad648c245437;p=bamtools.git

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