From 0d00f380644c78a321e8891562bf165317af10b4 Mon Sep 17 00:00:00 2001
From: barnett <barnett@9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Tue, 8 Dec 2009 18:57:41 +0000
Subject: [PATCH] Fixed some signed/unsigned int issues
git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@32 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
---
BamAux.h | 6 +++---
BamReader.cpp | 39 +++++++++++++++++++++------------------
BamReader.h | 2 +-
BamTrimMain.cpp | 4 ++--
4 files changed, 27 insertions(+), 24 deletions(-)
diff --git a/BamAux.h b/BamAux.h
index d5510d1..eec5556 100644
--- a/BamAux.h
+++ b/BamAux.h
@@ -230,9 +230,9 @@ struct CigarOp {
struct RefData {
// data members
- std::string RefName; // Name of reference sequence
- unsigned int RefLength; // Length of reference sequence
- bool RefHasAlignments; // True if BAM file contains alignments mapped to reference sequence
+ std::string RefName; // Name of reference sequence
+ int RefLength; // Length of reference sequence
+ bool RefHasAlignments; // True if BAM file contains alignments mapped to reference sequence
// constructor
RefData(void)
: RefLength(0)
diff --git a/BamReader.cpp b/BamReader.cpp
index 386a485..8dc2eb0 100644
--- a/BamReader.cpp
+++ b/BamReader.cpp
@@ -40,9 +40,9 @@ struct BamReader::BamReaderPrivate {
string IndexFilename;
// user-specified region values
- bool IsRegionSpecified;
- int CurrentRefID;
- unsigned int CurrentLeft;
+ bool IsRegionSpecified;
+ int CurrentRefID;
+ int CurrentLeft;
// BAM character constants
const char* DNA_LOOKUP;
@@ -60,7 +60,7 @@ struct BamReader::BamReaderPrivate {
// flie operations
void Close(void);
- bool Jump(int refID, unsigned int position = 0);
+ bool Jump(int refID, int position = 0);
void Open(const string& filename, const string& indexFilename = "");
bool Rewind(void);
@@ -83,11 +83,11 @@ struct BamReader::BamReaderPrivate {
// *** reading alignments and auxiliary data *** //
// calculate bins that overlap region ( left to reference end for now )
- int BinsFromRegion(int, unsigned int, uint16_t[MAX_BIN]);
+ int BinsFromRegion(int refID, int left, uint16_t[MAX_BIN]);
// calculates alignment end position based on starting position and provided CIGAR operations
- unsigned int CalculateAlignmentEnd(const unsigned int& position, const std::vector<CigarOp>& cigarData);
+ int CalculateAlignmentEnd(const int& position, const std::vector<CigarOp>& cigarData);
// calculate file offset for first alignment chunk overlapping 'left'
- int64_t GetOffset(int refID, unsigned int left);
+ int64_t GetOffset(int refID, int left);
// checks to see if alignment overlaps current region
bool IsOverlap(BamAlignment& bAlignment);
// retrieves header text from BAM file
@@ -134,7 +134,7 @@ BamReader::~BamReader(void) {
// file operations
void BamReader::Close(void) { d->Close(); }
-bool BamReader::Jump(int refID, unsigned int position) { return d->Jump(refID, position); }
+bool BamReader::Jump(int refID, int position) { return d->Jump(refID, position); }
void BamReader::Open(const string& filename, const string& indexFilename) { d->Open(filename, indexFilename); }
bool BamReader::Rewind(void) { return d->Rewind(); }
@@ -171,11 +171,11 @@ BamReader::BamReaderPrivate::~BamReaderPrivate(void) {
}
// calculate bins that overlap region ( left to reference end for now )
-int BamReader::BamReaderPrivate::BinsFromRegion(int refID, unsigned int left, uint16_t list[MAX_BIN]) {
+int BamReader::BamReaderPrivate::BinsFromRegion(int refID, int left, uint16_t list[MAX_BIN]) {
// get region boundaries
- uint32_t begin = left;
- uint32_t end = References.at(refID).RefLength - 1;
+ int32_t begin = left;
+ int32_t end = References.at(refID).RefLength - 1;
// initialize list, bin '0' always a valid bin
int i = 0;
@@ -238,7 +238,7 @@ bool BamReader::BamReaderPrivate::BuildIndex(void) {
// if lastCoordinate greater than BAM position - file not sorted properly
else if ( lastCoordinate > bAlignment.Position ) {
printf("BAM file not properly sorted:\n");
- printf("Alignment %s : %u > %u on reference (id = %d)", bAlignment.Name.c_str(), lastCoordinate, bAlignment.Position, bAlignment.RefID);
+ printf("Alignment %s : %d > %d on reference (id = %d)", bAlignment.Name.c_str(), lastCoordinate, bAlignment.Position, bAlignment.RefID);
exit(1);
}
@@ -324,10 +324,10 @@ bool BamReader::BamReaderPrivate::BuildIndex(void) {
}
// calculates alignment end position based on starting position and provided CIGAR operations
-unsigned int BamReader::BamReaderPrivate::CalculateAlignmentEnd(const unsigned int& position, const vector<CigarOp>& cigarData) {
+int BamReader::BamReaderPrivate::CalculateAlignmentEnd(const int& position, const vector<CigarOp>& cigarData) {
// initialize alignment end to starting position
- unsigned int alignEnd = position;
+ int alignEnd = position;
// iterate over cigar operations
vector<CigarOp>::const_iterator cigarIter = cigarData.begin();
@@ -361,9 +361,12 @@ bool BamReader::BamReaderPrivate::CreateIndex(void) {
// clear out index
ClearIndex();
+ // build (& save) index from BAM file
bool ok = true;
ok &= BuildIndex();
ok &= WriteIndex();
+
+ // return success/fail
return ok;
}
@@ -406,7 +409,7 @@ bool BamReader::BamReaderPrivate::GetNextAlignment(BamAlignment& bAlignment) {
}
// calculate closest indexed file offset for region specified
-int64_t BamReader::BamReaderPrivate::GetOffset(int refID, unsigned int left) {
+int64_t BamReader::BamReaderPrivate::GetOffset(int refID, int left) {
// calculate which bins overlap this region
uint16_t* bins = (uint16_t*)calloc(MAX_BIN, 2);
@@ -508,14 +511,14 @@ bool BamReader::BamReaderPrivate::IsOverlap(BamAlignment& bAlignment) {
if ( bAlignment.RefID != CurrentRefID ) { return false; }
// read starts after left boundary
- if ( bAlignment.Position >= (int32_t)CurrentLeft) { return true; }
+ if ( bAlignment.Position >= CurrentLeft) { return true; }
// return whether alignment end overlaps left boundary
return ( CalculateAlignmentEnd(bAlignment.Position, bAlignment.CigarData) >= CurrentLeft );
}
// jumps to specified region(refID, leftBound) in BAM file, returns success/fail
-bool BamReader::BamReaderPrivate::Jump(int refID, unsigned int position) {
+bool BamReader::BamReaderPrivate::Jump(int refID, int position) {
// if data exists for this reference and position is valid
if ( References.at(refID).RefHasAlignments && (position <= References.at(refID).RefLength) ) {
@@ -833,7 +836,7 @@ void BamReader::BamReaderPrivate::LoadReferenceData(void) {
// get reference name and reference sequence length
mBGZF.Read(refName, refNameLength);
mBGZF.Read(buffer, 4);
- const unsigned int refLength = BgzfData::UnpackUnsignedInt(buffer);
+ const int refLength = BgzfData::UnpackSignedInt(buffer);
// store data for reference
RefData aReference;
diff --git a/BamReader.h b/BamReader.h
index 2587b00..6332cde 100644
--- a/BamReader.h
+++ b/BamReader.h
@@ -39,7 +39,7 @@ class BamReader {
// close BAM file
void Close(void);
// performs random-access jump to reference, position
- bool Jump(int refID, unsigned int position = 0);
+ bool Jump(int refID, int position = 0);
// opens BAM file (and optional BAM index file, if provided)
void Open(const std::string& filename, const std::string& indexFilename = "");
// returns file pointer to beginning of alignments
diff --git a/BamTrimMain.cpp b/BamTrimMain.cpp
index 7349115..5b39d76 100644
--- a/BamTrimMain.cpp
+++ b/BamTrimMain.cpp
@@ -64,8 +64,8 @@ int main(int argc, char* argv[]) {
}
// convert boundary arguments to numeric values
- unsigned int leftBound = (unsigned int) atoi( leftBound_str.c_str() );
- unsigned int rightBound = (unsigned int) atoi( rightBound_str.c_str() );
+ 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) ) {
--
2.39.5