From: barnett <barnett@9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Thu, 23 Apr 2009 20:26:30 +0000 (+0000)
Subject: Removed assertion in GetOffset(), now returns -1 if regionChunks == 0.  Jump() then... 
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=855e80b994faaf1cc12bbb62b314e4b08ef65f3d;p=bamtools.git

Removed assertion in GetOffset(), now returns -1 if regionChunks == 0.  Jump() then returns false if offset = -1, else tries to Jump

git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@17 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
---

diff --git a/BamReader.cpp b/BamReader.cpp
index 4b50d7e..ad584a2 100644
--- a/BamReader.cpp
+++ b/BamReader.cpp
@@ -2,7 +2,7 @@
 
 // Derek Barnett
 // Marth Lab, Boston College
-// Last modified: 6 April 2009
+// Last modified: 23 April 2009
 
 #include "BamReader.h"
 #include <iostream>
@@ -153,7 +153,10 @@ bool BamReader::Jump(int refID, unsigned int left) {
 		m_currentRefID = refID;
 		m_currentLeft  = left;
 		m_isRegionSpecified = true;
-		return ( bam_seek(m_file, GetOffset(m_currentRefID, m_currentLeft), SEEK_SET) == 0 );
+		
+		int64_t offset = GetOffset(m_currentRefID, m_currentLeft);
+		if ( offset == -1 ) { return false; }
+		else { return ( bam_seek(m_file, offset, SEEK_SET) == 0 ); }
 	}
 	return false;
 }
@@ -238,7 +241,7 @@ uint32_t BamReader::CalculateAlignmentEnd(const unsigned int& position, const ve
 	return alignEnd;
 }
 
-uint64_t BamReader::GetOffset(int refID, unsigned int left) {
+int64_t BamReader::GetOffset(int refID, unsigned int left) {
 
 	//  make space for bins
 	uint16_t* bins = (uint16_t*)calloc(MAX_BIN, 2); 		
@@ -298,7 +301,7 @@ uint64_t BamReader::GetOffset(int refID, unsigned int left) {
 	free(bins);
 
 	// there should be at least 1
-	assert(regionChunks.size() > 0);
+	if(regionChunks.size() > 0) { return -1; }
 
 	// sort chunks by start position
 	sort ( regionChunks.begin(), regionChunks.end(), LookupKeyCompare<uint64_t, uint64_t>() );
@@ -323,7 +326,7 @@ uint64_t BamReader::GetOffset(int refID, unsigned int left) {
 	}
 
 	// return beginning file offset of first chunk for region
-	return regionChunks.at(0).first;
+	return (int64_t)regionChunks.at(0).first;
 }
 
 bool BamReader::IsOverlap(BamAlignment& bAlignment) {
diff --git a/BamReader.h b/BamReader.h
index 7748afa..e2b4598 100644
--- a/BamReader.h
+++ b/BamReader.h
@@ -33,7 +33,7 @@
 
 // Derek Barnett
 // Marth Lab, Boston College
-// Last modified: 6 April 2009
+// Last modified: 23 April 2009
 
 #ifndef BAMREADER_H
 #define BAMREADER_H
@@ -205,7 +205,7 @@ class BamReader {
 	private:
 		int      BinsFromRegion(int, unsigned int, uint16_t[MAX_BIN]);
 		uint32_t CalculateAlignmentEnd(const unsigned int&, const vector<CigarOp>&);
-		uint64_t GetOffset(int, unsigned int);
+		int64_t  GetOffset(int, unsigned int);
 		bool     IsOverlap(BamAlignment&);
 		bool     LoadHeader(void);
 		bool     LoadIndex(void);