From: Derek <derekwbarnett@gmail.com>
Date: Tue, 25 May 2010 17:12:27 +0000 (-0400)
Subject: Added templated GetTag() method, compile tested, but not runtime tested
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=8a0328ccbd7db4283b113e1f3480fd5ac334dbbc;p=bamtools.git
Added templated GetTag() method, compile tested, but not runtime tested
---
diff --git a/BamAux.h b/BamAux.h
index 2ce2733..3d14a46 100644
--- a/BamAux.h
+++ b/BamAux.h
@@ -65,12 +65,12 @@ const int BT_SIZEOF_INT = 4;
struct CigarOp;
struct BamAlignment {
-
- // constructors & destructor
- public:
- BamAlignment(void);
- BamAlignment(const BamAlignment& other);
- ~BamAlignment(void);
+
+ // constructors & destructor
+ public:
+ BamAlignment(void);
+ BamAlignment(const BamAlignment& other);
+ ~BamAlignment(void);
// Queries against alignment flags
public:
@@ -99,16 +99,19 @@ struct BamAlignment {
void SetIsSecondaryAlignment(bool ok); // Sets "position is primary alignment" flag
void SetIsSecondMate(bool ok); // Sets "alignment is second mate on read" flag
void SetIsUnmapped(bool ok); // Sets "alignment is mapped" flag
-
- // Tag data access methods
+
+ // Tag data access methods
public:
bool GetEditDistance(uint8_t& editDistance) const; // get "NM" tag data - contributed by Aaron Quinlan
bool GetReadGroup(std::string& readGroup) const; // get "RG" tag data
-
+
+ bool GetTag(const std::string& tag, std::string& destination);
+ template<typename T> bool GetTag(const std::string& tag, T& destination);
+
// Additional data access methods
public:
- int GetEndPosition(bool usePadded = false) const; // calculates alignment end position, based on starting position and CIGAR operations
-
+ int GetEndPosition(bool usePadded = false) const; // calculates alignment end position, based on starting position and CIGAR operations
+
// 'internal' utility methods
private:
static void SkipToNextTag(const char storageType, char* &pTagData, unsigned int& numBytesParsed);
@@ -131,7 +134,7 @@ struct BamAlignment {
int32_t MatePosition; // Position (0-based) where alignment's mate starts
int32_t InsertSize; // Mate-pair insert size
- // Alignment flag query constants
+ // Alignment flag query constants
// Use the get/set methods above instead
private:
enum { PAIRED = 1
@@ -157,14 +160,14 @@ struct CigarOp {
};
struct RefData {
-
+
// data members
std::string RefName; // Name of reference sequence
int32_t RefLength; // Length of reference sequence
bool RefHasAlignments; // True if BAM file contains alignments mapped to reference sequence
-
+
// constructor
- RefData(const int32_t& length = 0,
+ RefData(const int32_t& length = 0,
bool ok = false)
: RefLength(length)
, RefHasAlignments(ok)
@@ -177,14 +180,14 @@ typedef std::vector<BamAlignment> BamAlignmentVector;
// ----------------------------------------------------------------
// Indexing structs & typedefs
-struct Chunk {
+struct Chunk {
// data members
uint64_t Start;
uint64_t Stop;
-
+
// constructor
- Chunk(const uint64_t& start = 0,
+ Chunk(const uint64_t& start = 0,
const uint64_t& stop = 0)
: Start(start)
, Stop(stop)
@@ -213,36 +216,36 @@ struct ReferenceIndex {
};
typedef std::vector<ReferenceIndex> BamIndex;
-
-// ----------------------------------------------------------------
-// BamAlignment member methods
-
-// constructors & destructor
-inline
-BamAlignment::BamAlignment(void) { }
-
-inline
-BamAlignment::BamAlignment(const BamAlignment& other)
- : Name(other.Name)
- , Length(other.Length)
- , QueryBases(other.QueryBases)
- , AlignedBases(other.AlignedBases)
- , Qualities(other.Qualities)
- , TagData(other.TagData)
- , RefID(other.RefID)
- , Position(other.Position)
- , Bin(other.Bin)
- , MapQuality(other.MapQuality)
- , AlignmentFlag(other.AlignmentFlag)
- , CigarData(other.CigarData)
- , MateRefID(other.MateRefID)
- , MatePosition(other.MatePosition)
- , InsertSize(other.InsertSize)
-{ }
-
-inline
-BamAlignment::~BamAlignment(void) { }
-
+
+// ----------------------------------------------------------------
+// BamAlignment member methods
+
+// constructors & destructor
+inline
+BamAlignment::BamAlignment(void) { }
+
+inline
+BamAlignment::BamAlignment(const BamAlignment& other)
+ : Name(other.Name)
+ , Length(other.Length)
+ , QueryBases(other.QueryBases)
+ , AlignedBases(other.AlignedBases)
+ , Qualities(other.Qualities)
+ , TagData(other.TagData)
+ , RefID(other.RefID)
+ , Position(other.Position)
+ , Bin(other.Bin)
+ , MapQuality(other.MapQuality)
+ , AlignmentFlag(other.AlignmentFlag)
+ , CigarData(other.CigarData)
+ , MateRefID(other.MateRefID)
+ , MatePosition(other.MatePosition)
+ , InsertSize(other.InsertSize)
+{ }
+
+inline
+BamAlignment::~BamAlignment(void) { }
+
// Queries against alignment flags
inline bool BamAlignment::IsDuplicate(void) const { return ( (AlignmentFlag & DUPLICATE) != 0 ); }
inline bool BamAlignment::IsFailedQC(void) const { return ( (AlignmentFlag & QC_FAILED) != 0 ); }
@@ -254,8 +257,8 @@ inline bool BamAlignment::IsPaired(void) const { return ( (AlignmentF
inline bool BamAlignment::IsPrimaryAlignment(void) const { return ( (AlignmentFlag & SECONDARY) == 0 ); }
inline bool BamAlignment::IsProperPair(void) const { return ( (AlignmentFlag & PROPER_PAIR) != 0 ); }
inline bool BamAlignment::IsReverseStrand(void) const { return ( (AlignmentFlag & REVERSE) != 0 ); }
-inline bool BamAlignment::IsSecondMate(void) const { return ( (AlignmentFlag & READ_2) != 0 ); }
-
+inline bool BamAlignment::IsSecondMate(void) const { return ( (AlignmentFlag & READ_2) != 0 ); }
+
// Manipulate alignment flags
inline void BamAlignment::SetIsDuplicate(bool ok) { if (ok) AlignmentFlag |= DUPLICATE; else AlignmentFlag &= ~DUPLICATE; }
inline void BamAlignment::SetIsFailedQC(bool ok) { if (ok) AlignmentFlag |= QC_FAILED; else AlignmentFlag &= ~QC_FAILED; }
@@ -267,9 +270,9 @@ inline void BamAlignment::SetIsProperPair(bool ok) { if (ok) AlignmentFl
inline void BamAlignment::SetIsReverseStrand(bool ok) { if (ok) AlignmentFlag |= REVERSE; else AlignmentFlag &= ~REVERSE; }
inline void BamAlignment::SetIsSecondaryAlignment(bool ok) { if (ok) AlignmentFlag |= SECONDARY; else AlignmentFlag &= ~SECONDARY; }
inline void BamAlignment::SetIsSecondMate(bool ok) { if (ok) AlignmentFlag |= READ_2; else AlignmentFlag &= ~READ_2; }
-inline void BamAlignment::SetIsUnmapped(bool ok) { if (ok) AlignmentFlag |= UNMAPPED; else AlignmentFlag &= ~UNMAPPED; }
-
-// calculates alignment end position, based on starting position and CIGAR operations
+inline void BamAlignment::SetIsUnmapped(bool ok) { if (ok) AlignmentFlag |= UNMAPPED; else AlignmentFlag &= ~UNMAPPED; }
+
+// calculates alignment end position, based on starting position and CIGAR operations
inline
int BamAlignment::GetEndPosition(bool usePadded) const {
@@ -283,16 +286,16 @@ int BamAlignment::GetEndPosition(bool usePadded) const {
const char cigarType = (*cigarIter).Type;
if ( cigarType == 'M' || cigarType == 'D' || cigarType == 'N' ) {
alignEnd += (*cigarIter).Length;
- }
- else if ( usePadded && cigarType == 'I' ) {
- alignEnd += (*cigarIter).Length;
+ }
+ else if ( usePadded && cigarType == 'I' ) {
+ alignEnd += (*cigarIter).Length;
}
}
return alignEnd;
}
-// get "NM" tag data - contributed by Aaron Quinlan
-// stores data in 'editDistance', returns success/fail
+// get "NM" tag data - contributed by Aaron Quinlan
+// stores data in 'editDistance', returns success/fail
inline
bool BamAlignment::GetEditDistance(uint8_t& editDistance) const {
@@ -328,10 +331,10 @@ bool BamAlignment::GetEditDistance(uint8_t& editDistance) const {
// assign the editDistance value
std::memcpy(&editDistance, pTagData, 1);
return true;
-}
-
-// get "RG" tag data
-// stores data in 'readGroup', returns success/fail
+}
+
+// get "RG" tag data
+// stores data in 'readGroup', returns success/fail
inline
bool BamAlignment::GetReadGroup(std::string& readGroup) const {
@@ -370,11 +373,88 @@ bool BamAlignment::GetReadGroup(std::string& readGroup) const {
readGroup.resize(readGroupLen);
std::memcpy( (char*)readGroup.data(), pTagData, readGroupLen );
return true;
-}
-
-inline
+}
+
+inline
+bool BamAlignment::GetTag(const std::string& tag, std::string& destination) {
+
+ if ( TagData.empty() ) { return false; }
+
+ // localize the tag data
+ char* pTagData = (char*)TagData.data();
+ const unsigned int tagDataLen = TagData.size();
+ unsigned int numBytesParsed = 0;
+
+ bool foundReadGroupTag = false;
+ while( numBytesParsed < tagDataLen ) {
+
+ const char* pTagType = pTagData;
+ const char* pTagStorageType = pTagData + 2;
+ pTagData += 3;
+ numBytesParsed += 3;
+
+ // check the current tag
+ if ( std::strncmp(pTagType, tag.c_str(), 2) == 0 ) {
+ foundReadGroupTag = true;
+ break;
+ }
+
+ // get the storage class and find the next tag
+ if (*pTagStorageType == '\0') { return false; }
+ SkipToNextTag( *pTagStorageType, pTagData, numBytesParsed );
+ if (*pTagData == '\0') { return false; }
+ }
+
+ // return if the read group tag was not present
+ if ( !foundReadGroupTag ) { return false; }
+
+ // assign the read group
+ const unsigned int dataLen = std::strlen(pTagData);
+ destination.resize(dataLen);
+ std::memcpy( (char*)destination.data(), pTagData, dataLen );
+ return true;
+}
+
+template<typename T>
+bool BamAlignment::GetTag(const std::string& tag, T& destination) {
+
+ if ( TagData.empty() ) { return false; }
+
+ // localize the tag data
+ char* pTagData = (char*)TagData.data();
+ const unsigned int tagDataLen = TagData.size();
+ unsigned int numBytesParsed = 0;
+
+ bool foundDesiredTag = false;
+ while( numBytesParsed < tagDataLen ) {
+
+ const char* pTagType = pTagData;
+ const char* pTagStorageType = pTagData + 2;
+ pTagData += 3;
+ numBytesParsed += 3;
+
+ // check the current tag
+ if ( strncmp(pTagType, tag.c_str(), 2) == 0 ) {
+ foundDesiredTag = true;
+ break;
+ }
+
+ // get the storage class and find the next tag
+ if (*pTagStorageType == '\0') { return false; }
+ SkipToNextTag( *pTagStorageType, pTagData, numBytesParsed );
+ if (*pTagData == '\0') { return false; }
+ }
+ // return if the edit distance tag was not present
+ if ( !foundDesiredTag ) { return false; }
+
+ // assign the editDistance value
+ std::memcpy(&destination, pTagData, sizeof(T));
+ return true;
+}
+
+inline
void BamAlignment::SkipToNextTag(const char storageType, char* &pTagData, unsigned int& numBytesParsed) {
-
+
switch(storageType) {
case 'A':
@@ -415,7 +495,7 @@ void BamAlignment::SkipToNextTag(const char storageType, char* &pTagData, unsign
printf("ERROR: Unknown tag storage class encountered: [%c]\n", *pTagData);
exit(1);
}
-}
+}
// ----------------------------------------------------------------
// Added: 3-35-2010 DWB
@@ -431,7 +511,7 @@ inline bool SystemIsBigEndian(void) {
// swaps endianness of 16-bit value 'in place'
inline void SwapEndian_16(int16_t& x) {
x = ((x >> 8) | (x << 8));
-}
+}
inline void SwapEndian_16(uint16_t& x) {
x = ((x >> 8) | (x << 8));
@@ -444,7 +524,7 @@ inline void SwapEndian_32(int32_t& x) {
((x >> 8) & 0x0000FF00) |
(x << 24)
);
-}
+}
inline void SwapEndian_32(uint32_t& x) {
x = ( (x >> 24) |
@@ -478,19 +558,19 @@ inline void SwapEndian_64(uint64_t& x) {
(x << 56)
);
}
-
+
// swaps endianness of 'next 2 bytes' in a char buffer (in-place)
inline void SwapEndian_16p(char* data) {
uint16_t& value = (uint16_t&)*data;
SwapEndian_16(value);
}
-
+
// swaps endianness of 'next 4 bytes' in a char buffer (in-place)
inline void SwapEndian_32p(char* data) {
uint32_t& value = (uint32_t&)*data;
SwapEndian_32(value);
}
-
+
// swaps endianness of 'next 8 bytes' in a char buffer (in-place)
inline void SwapEndian_64p(char* data) {
uint64_t& value = (uint64_t&)*data;