From: barnett <barnett@9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Fri, 25 Sep 2009 17:59:46 +0000 (+0000)
Subject: Changed BamAlignment::InsertSize to signed int... need to test
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=5255969ee7c62eb6f08365ff5ddd5dc90498c3ce;p=bamtools.git

Changed BamAlignment::InsertSize to signed int... need to test

git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@26 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
---

diff --git a/BamAux.h b/BamAux.h
index 701f35a..7f47afe 100644
--- a/BamAux.h
+++ b/BamAux.h
@@ -280,7 +280,8 @@ namespace BamTools {
 			std::vector<CigarOp> CigarData; //!< CIGAR operations for this alignment
 			unsigned int MateRefID;         //!< ID number for reference sequence where alignment's mate was aligned
 			unsigned int MatePosition;      //!< Position (0-based) where alignment's mate starts
-			unsigned int InsertSize;        //!< Mate-pair insert size
+			//unsigned int InsertSize;        //!< Mate-pair insert size
+			signed int   InsertSize;		//!< Mate-pair insert size
 		
 		// Alignment flag query constants
 		private:
diff --git a/BamDumpMain.cpp b/BamDumpMain.cpp
index f76852a..2c31015 100644
--- a/BamDumpMain.cpp
+++ b/BamDumpMain.cpp
@@ -50,6 +50,7 @@ int main(int argc, char* argv[]) {
 // Spit out basic BamAlignment data 
 void PrintAlignment(const BamAlignment& alignment) {
 	cout << "---------------------------------" << endl;
-	cout << "Name: " << alignment.Name << endl;
-	cout << "Aligned to: " << alignment.RefID << ":" << alignment.Position << endl;
+	cout << "Name: "       << alignment.Name << endl;
+	cout << "Aligned to: " << alignment.RefID;
+	cout << ":"            << alignment.Position << endl;
 }
diff --git a/BamReader.cpp b/BamReader.cpp
index 4f0f361..f9df5cf 100644
--- a/BamReader.cpp
+++ b/BamReader.cpp
@@ -572,7 +572,8 @@ bool BamReader::LoadNextAlignment(BamAlignment& bAlignment) {
 	querySequenceLength     = BgzfUnpackUnsignedInt(&x[16]);
 	bAlignment.MateRefID    = BgzfUnpackUnsignedInt(&x[20]);
 	bAlignment.MatePosition = BgzfUnpackUnsignedInt(&x[24]);
-	bAlignment.InsertSize   = BgzfUnpackUnsignedInt(&x[28]);
+	//bAlignment.InsertSize   = BgzfUnpackUnsignedInt(&x[28]);
+	bAlignment.InsertSize   = BgzfUnpackSignedInt(&x[28]);
 
 	// calculate lengths/offsets
 	const unsigned int dataLength      = blockLength - BAM_CORE_SIZE;
diff --git a/BamReader.h b/BamReader.h
index a4a82e4..ed8397d 100644
--- a/BamReader.h
+++ b/BamReader.h
@@ -181,6 +181,8 @@ namespace BamTools {
 			static inline unsigned int BgzfUnpackUnsignedInt(char* buffer);
 			// unpacks a buffer into an unsigned short
 			static inline unsigned short BgzfUnpackUnsignedShort(char* buffer);
+			// unpacks a buffer into a signed int
+			static inline signed int BgzfUnpackSignedInt(char* buffer);
 			// calculate bins that overlap region ( left to reference end for now )
 			int BinsFromRegion(int, unsigned int, uint16_t[MAX_BIN]);
 			// calculates alignment end position based on starting position and provided CIGAR operations
@@ -244,6 +246,16 @@ namespace BamTools {
 		un.valueBuffer[1] = buffer[1];
 		return un.value;
 	}
+	
+	// unpacks a buffer into a signed int
+	inline signed int BamReader::BgzfUnpackSignedInt(char* buffer) {
+		union { signed int value; unsigned char valueBuffer[sizeof(signed int)]; } un;
+		un.valueBuffer[0] = buffer[0];
+		un.valueBuffer[1] = buffer[1];
+		un.valueBuffer[2] = buffer[2];
+		un.valueBuffer[3] = buffer[3];
+		return un.value;
+	}
 
 	// --------------------------------------------------------------------------------------
 	// template classes/methods (internal - can exclude from main documentation)