From 31708e4a1ebc33e1171d027094e80440ae58e7fc Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 29 Jun 2011 10:22:54 -0400
Subject: [PATCH] Don't track BamTools/include
---
src/utils/BamTools/include/api/BamAlignment.h | 207 --------
src/utils/BamTools/include/api/BamAux.h | 457 ------------------
src/utils/BamTools/include/api/BamConstants.h | 128 -----
src/utils/BamTools/include/api/BamIndex.h | 80 ---
.../BamTools/include/api/BamMultiReader.h | 127 -----
src/utils/BamTools/include/api/BamReader.h | 118 -----
src/utils/BamTools/include/api/BamWriter.h | 64 ---
src/utils/BamTools/include/api/SamConstants.h | 96 ----
src/utils/BamTools/include/api/SamHeader.h | 69 ---
src/utils/BamTools/include/api/SamProgram.h | 62 ---
.../BamTools/include/api/SamProgramChain.h | 86 ----
src/utils/BamTools/include/api/SamReadGroup.h | 69 ---
.../include/api/SamReadGroupDictionary.h | 87 ----
src/utils/BamTools/include/api/SamSequence.h | 61 ---
.../include/api/SamSequenceDictionary.h | 89 ----
src/utils/BamTools/include/api/api_global.h | 22 -
.../BamTools/include/shared/bamtools_global.h | 79 ---
17 files changed, 1901 deletions(-)
delete mode 100644 src/utils/BamTools/include/api/BamAlignment.h
delete mode 100644 src/utils/BamTools/include/api/BamAux.h
delete mode 100644 src/utils/BamTools/include/api/BamConstants.h
delete mode 100644 src/utils/BamTools/include/api/BamIndex.h
delete mode 100644 src/utils/BamTools/include/api/BamMultiReader.h
delete mode 100644 src/utils/BamTools/include/api/BamReader.h
delete mode 100644 src/utils/BamTools/include/api/BamWriter.h
delete mode 100644 src/utils/BamTools/include/api/SamConstants.h
delete mode 100644 src/utils/BamTools/include/api/SamHeader.h
delete mode 100644 src/utils/BamTools/include/api/SamProgram.h
delete mode 100644 src/utils/BamTools/include/api/SamProgramChain.h
delete mode 100644 src/utils/BamTools/include/api/SamReadGroup.h
delete mode 100644 src/utils/BamTools/include/api/SamReadGroupDictionary.h
delete mode 100644 src/utils/BamTools/include/api/SamSequence.h
delete mode 100644 src/utils/BamTools/include/api/SamSequenceDictionary.h
delete mode 100644 src/utils/BamTools/include/api/api_global.h
delete mode 100644 src/utils/BamTools/include/shared/bamtools_global.h
diff --git a/src/utils/BamTools/include/api/BamAlignment.h b/src/utils/BamTools/include/api/BamAlignment.h
deleted file mode 100644
index 7535d93f..00000000
--- a/src/utils/BamTools/include/api/BamAlignment.h
+++ /dev/null
@@ -1,207 +0,0 @@
-// ***************************************************************************
-// BamAlignment.h (c) 2009 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 22 April 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides the BamAlignment data structure
-// ***************************************************************************
-
-#ifndef BAMALIGNMENT_H
-#define BAMALIGNMENT_H
-
-#include <api/api_global.h>
-#include <api/BamAux.h>
-#include <string>
-#include <vector>
-
-namespace BamTools {
-
-// forward declaration of BamAlignment's friend classes
-namespace Internal {
- class BamReaderPrivate;
- class BamWriterPrivate;
-} // namespace Internal
-
-// BamAlignment data structure
-struct API_EXPORT BamAlignment {
-
- // constructors & destructor
- public:
- BamAlignment(void);
- BamAlignment(const BamAlignment& other);
- ~BamAlignment(void);
-
- // queries against alignment flags
- public:
- bool IsDuplicate(void) const; // returns true if this read is a PCR duplicate
- bool IsFailedQC(void) const; // returns true if this read failed quality control
- bool IsFirstMate(void) const; // returns true if alignment is first mate on read
- bool IsMapped(void) const; // returns true if alignment is mapped
- bool IsMateMapped(void) const; // returns true if alignment's mate is mapped
- bool IsMateReverseStrand(void) const; // returns true if alignment's mate mapped to reverse strand
- bool IsPaired(void) const; // returns true if alignment part of paired-end read
- bool IsPrimaryAlignment(void) const; // returns true if reported position is primary alignment
- bool IsProperPair(void) const; // returns true if alignment is part of read that satisfied paired-end resolution
- bool IsReverseStrand(void) const; // returns true if alignment mapped to reverse strand
- bool IsSecondMate(void) const; // returns true if alignment is second mate on read
-
- // manipulate alignment flags
- public:
- void SetIsDuplicate(bool ok); // sets value of "PCR duplicate" flag
- void SetIsFailedQC(bool ok); // sets value of "failed quality control" flag
- void SetIsFirstMate(bool ok); // sets value of "alignment is first mate" flag
- void SetIsMapped(bool ok); // sets value of "alignment is mapped" flag
- void SetIsMateMapped(bool ok); // sets value of "alignment's mate is mapped" flag
- void SetIsMateReverseStrand(bool ok); // sets value of "alignment's mate mapped to reverse strand" flag
- void SetIsPaired(bool ok); // sets value of "alignment part of paired-end read" flag
- void SetIsPrimaryAlignment(bool ok); // sets value of "position is primary alignment" flag
- void SetIsProperPair(bool ok); // sets value of "alignment is part of read that satisfied paired-end resolution" flag
- void SetIsReverseStrand(bool ok); // sets value of "alignment mapped to reverse strand" flag
- void SetIsSecondMate(bool ok); // sets value of "alignment is second mate on read" flag
-
- // legacy methods (consider deprecated, but still available)
- void SetIsMateUnmapped(bool ok); // complement of using SetIsMateMapped()
- void SetIsSecondaryAlignment(bool ok); // complement of using SetIsPrimaryAlignment()
- void SetIsUnmapped(bool ok); // complement of using SetIsMapped()
-
- // tag data access methods
- public:
-
- // -------------------------------------------------------------------------------------
- // N.B. - The following tag access methods may not be used on BamAlignments fetched
- // using BamReader::GetNextAlignmentCore(). Attempting to use them will not result in
- // error message (to keep output clean) but will ALWAYS return false. Only user-created
- // BamAlignments or those retrieved using BamReader::GetNextAlignment() are valid here.
- //
- // You can call BuildCharData() on such an alignment retrieved by GetNextAlignmentCore().
- // This populates all the character data, and will enable subsequent queries on tag data.
- // -------------------------------------------------------------------------------------
-
- // adds a tag
- bool AddTag(const std::string& tag, const std::string& type, const std::string& value);
- bool AddTag(const std::string& tag, const std::string& type, const uint32_t& value);
- bool AddTag(const std::string& tag, const std::string& type, const int32_t& value);
- bool AddTag(const std::string& tag, const std::string& type, const float& value);
-
- // adds a "binary array" tag
- bool AddTag(const std::string& tag, const std::vector<uint8_t>& values);
- bool AddTag(const std::string& tag, const std::vector<int8_t>& values);
- bool AddTag(const std::string& tag, const std::vector<uint16_t>& values);
- bool AddTag(const std::string& tag, const std::vector<int16_t>& values);
- bool AddTag(const std::string& tag, const std::vector<uint32_t>& values);
- bool AddTag(const std::string& tag, const std::vector<int32_t>& values);
- bool AddTag(const std::string& tag, const std::vector<float>& values);
-
- // edits a tag
- bool EditTag(const std::string& tag, const std::string& type, const std::string& value);
- bool EditTag(const std::string& tag, const std::string& type, const uint32_t& value);
- bool EditTag(const std::string& tag, const std::string& type, const int32_t& value);
- bool EditTag(const std::string& tag, const std::string& type, const float& value);
-
- // edits a "binary array" tag
- bool EditTag(const std::string& tag, const std::vector<uint8_t>& values);
- bool EditTag(const std::string& tag, const std::vector<int8_t>& values);
- bool EditTag(const std::string& tag, const std::vector<uint16_t>& values);
- bool EditTag(const std::string& tag, const std::vector<int16_t>& values);
- bool EditTag(const std::string& tag, const std::vector<uint32_t>& values);
- bool EditTag(const std::string& tag, const std::vector<int32_t>& values);
- bool EditTag(const std::string& tag, const std::vector<float>& values);
-
- // retrieves data for a tag
- bool GetTag(const std::string& tag, std::string& destination) const;
- bool GetTag(const std::string& tag, uint32_t& destination) const;
- bool GetTag(const std::string& tag, int32_t& destination) const;
- bool GetTag(const std::string& tag, float& destination) const;
-
- // retrieves data for a "binary array" tag
- bool GetTag(const std::string& tag, std::vector<uint32_t>& destination) const;
- bool GetTag(const std::string& tag, std::vector<int32_t>& destination) const;
- bool GetTag(const std::string& tag, std::vector<float>& destination) const;
-
- // retrieves the BAM tag-type character for a tag
- bool GetTagType(const std::string& tag, char& type) const;
-
- // legacy methods (consider deprecated, but still available)
- bool GetEditDistance(uint32_t& editDistance) const; // retrieves value of "NM" tag
- bool GetReadGroup(std::string& readGroup) const; // retrieves value of "RG" tag
-
- // returns true if alignment has a record for this tag name
- bool HasTag(const std::string& tag) const;
-
- // removes a tag
- bool RemoveTag(const std::string& tag);
-
- // additional methods
- public:
- // populates alignment string fields
- bool BuildCharData(void);
- // calculates alignment end position
- int GetEndPosition(bool usePadded = false, bool zeroBased = true) const;
-
- // public data fields
- public:
- std::string Name; // read name
- int32_t Length; // length of query sequence
- std::string QueryBases; // 'original' sequence (as reported from sequencing machine)
- std::string AlignedBases; // 'aligned' sequence (includes any indels, padding, clipping)
- std::string Qualities; // FASTQ qualities (ASCII characters, not numeric values)
- std::string TagData; // tag data (use provided methods to query/modify)
- int32_t RefID; // ID number for reference sequence
- int32_t Position; // position (0-based) where alignment starts
- uint16_t Bin; // BAM (standard) index bin number for this alignment
- uint16_t MapQuality; // mapping quality score
- uint32_t AlignmentFlag; // alignment bit-flag (use provided methods to query/modify)
- std::vector<CigarOp> CigarData; // CIGAR operations for this alignment
- int32_t MateRefID; // ID number for reference sequence where alignment's mate was aligned
- int32_t MatePosition; // position (0-based) where alignment's mate starts
- int32_t InsertSize; // mate-pair insert size
- std::string Filename; // name of BAM file which this alignment comes from
-
- //! \cond
- // internal utility methods
- private:
- bool FindTag(const std::string& tag,
- char*& pTagData,
- const unsigned int& tagDataLength,
- unsigned int& numBytesParsed) const;
- bool IsValidSize(const std::string& tag,
- const std::string& type) const;
- bool SkipToNextTag(const char storageType,
- char*& pTagData,
- unsigned int& numBytesParsed) const;
-
- // internal data
- private:
-
- struct BamAlignmentSupportData {
-
- // data members
- std::string AllCharData;
- uint32_t BlockLength;
- uint32_t NumCigarOperations;
- uint32_t QueryNameLength;
- uint32_t QuerySequenceLength;
- bool HasCoreOnly;
-
- // constructor
- BamAlignmentSupportData(void)
- : BlockLength(0)
- , NumCigarOperations(0)
- , QueryNameLength(0)
- , QuerySequenceLength(0)
- , HasCoreOnly(false)
- { }
- };
- BamAlignmentSupportData SupportData;
- friend class Internal::BamReaderPrivate;
- friend class Internal::BamWriterPrivate;
- //! \endcond
-};
-
-typedef std::vector<BamAlignment> BamAlignmentVector;
-
-} // namespace BamTools
-
-#endif // BAMALIGNMENT_H
diff --git a/src/utils/BamTools/include/api/BamAux.h b/src/utils/BamTools/include/api/BamAux.h
deleted file mode 100644
index d171e706..00000000
--- a/src/utils/BamTools/include/api/BamAux.h
+++ /dev/null
@@ -1,457 +0,0 @@
-// ***************************************************************************
-// BamAux.h (c) 2009 Derek Barnett, Michael Str�mberg
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 4 March 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides data structures & utility methods that are used throughout the API.
-// ***************************************************************************
-
-#ifndef BAMAUX_H
-#define BAMAUX_H
-
-#include <api/api_global.h>
-#include <fstream>
-#include <iostream>
-#include <string>
-#include <vector>
-
-/*! \file BamAux.h
-
- Provides data structures & utility methods that are used throughout the API.
-*/
-/*! \namespace BamTools
- \brief Contains all BamTools classes & methods.
-
- The BamTools API contained in this namespace contains classes and methods
- for reading, writing, and manipulating BAM alignment files.
-*/
-namespace BamTools {
-
-// ----------------------------------------------------------------
-// CigarOp
-
-/*! \struct BamTools::CigarOp
- \brief Represents a CIGAR alignment operation.
-
- \sa http://samtools.sourceforge.net/SAM-1.3.pdf for more details on using CIGAR operations.
-*/
-struct API_EXPORT CigarOp {
-
- char Type; //!< CIGAR operation type (MIDNSHP)
- uint32_t Length; //!< CIGAR operation length (number of bases)
-
- //! constructor
- CigarOp(const char type = '\0',
- const uint32_t& length = 0)
- : Type(type)
- , Length(length)
- { }
-};
-
-// ----------------------------------------------------------------
-// RefData
-
-/*! \struct BamTools::RefData
- \brief Represents a reference sequence entry
-*/
-struct API_EXPORT RefData {
-
- std::string RefName; //!< name of reference sequence
- int32_t RefLength; //!< length of reference sequence
-
- //! constructor
- RefData(const std::string& name = "",
- const int32_t& length = 0)
- : RefName(name)
- , RefLength(length)
- { }
-};
-
-//! convenience typedef for vector of RefData entries
-typedef std::vector<RefData> RefVector;
-
-// ----------------------------------------------------------------
-// BamRegion
-
-/*! \struct BamTools::BamRegion
- \brief Represents a sequential genomic region
-
- Allowed to span multiple (sequential) references.
-*/
-struct API_EXPORT BamRegion {
-
- int LeftRefID; //!< reference ID for region's left boundary
- int LeftPosition; //!< position for region's left boundary
- int RightRefID; //!< reference ID for region's right boundary
- int RightPosition; //!< position for region's right boundary
-
- //! constructor
- BamRegion(const int& leftID = -1,
- const int& leftPos = -1,
- const int& rightID = -1,
- const int& rightPos = -1)
- : LeftRefID(leftID)
- , LeftPosition(leftPos)
- , RightRefID(rightID)
- , RightPosition(rightPos)
- { }
-
- //! copy constructor
- BamRegion(const BamRegion& other)
- : LeftRefID(other.LeftRefID)
- , LeftPosition(other.LeftPosition)
- , RightRefID(other.RightRefID)
- , RightPosition(other.RightPosition)
- { }
-
- //! Clears region boundaries
- void clear(void) {
- LeftRefID = -1; LeftPosition = -1;
- RightRefID = -1; RightPosition = -1;
- }
-
- //! Returns true if region has a left boundary
- bool isLeftBoundSpecified(void) const {
- return ( LeftRefID >= 0 && LeftPosition >= 0 );
- }
-
- //! Returns true if region boundaries are not defined
- bool isNull(void) const {
- return ( !isLeftBoundSpecified() && !isRightBoundSpecified() );
- }
-
- //! Returns true if region has a right boundary
- bool isRightBoundSpecified(void) const {
- return ( RightRefID >= 0 && RightPosition >= 0 );
- }
-};
-
-// ----------------------------------------------------------------
-// General utility methods
-
-/*! \fn bool FileExists(const std::string& filename)
- \brief checks if file exists
-
- Attempts to open file in a read-only mode.
-
- \return \c true if file can be opened successfully
-*/
-API_EXPORT inline bool FileExists(const std::string& filename) {
- std::ifstream f(filename.c_str(), std::ifstream::in);
- return !f.fail();
-}
-
-/*! \fn void SwapEndian_16(int16_t& x)
- \brief swaps endianness of signed 16-bit integer, in place
-
- Swaps endian representation of value in \a x.
-*/
-API_EXPORT inline void SwapEndian_16(int16_t& x) {
- x = ((x >> 8) | (x << 8));
-}
-
-/*! \fn void SwapEndian_16(uint16_t& x)
- \brief swaps endianness of unsigned 16-bit integer, in place
-
- Swaps endian representation of value in \a x.
-*/
-API_EXPORT inline void SwapEndian_16(uint16_t& x) {
- x = ((x >> 8) | (x << 8));
-}
-
-/*! \fn void SwapEndian_32(int32_t& x)
- \brief swaps endianness of signed 32-bit integer, in place
-
- Swaps endian representation of value in \a x.
-*/
-API_EXPORT inline void SwapEndian_32(int32_t& x) {
- x = ( (x >> 24) |
- ((x << 8) & 0x00FF0000) |
- ((x >> 8) & 0x0000FF00) |
- (x << 24)
- );
-}
-
-/*! \fn void SwapEndian_32(uint32_t& x)
- \brief swaps endianness of unsigned 32-bit integer, in place
-
- Swaps endian representation of value in \a x.
-*/
-API_EXPORT inline void SwapEndian_32(uint32_t& x) {
- x = ( (x >> 24) |
- ((x << 8) & 0x00FF0000) |
- ((x >> 8) & 0x0000FF00) |
- (x << 24)
- );
-}
-
-/*! \fn void SwapEndian_64(int64_t& x)
- \brief swaps endianness of signed 64-bit integer, in place
-
- Swaps endian representation of value in \a x.
-*/
-API_EXPORT inline void SwapEndian_64(int64_t& x) {
- x = ( (x >> 56) |
- ((x << 40) & 0x00FF000000000000ll) |
- ((x << 24) & 0x0000FF0000000000ll) |
- ((x << 8) & 0x000000FF00000000ll) |
- ((x >> 8) & 0x00000000FF000000ll) |
- ((x >> 24) & 0x0000000000FF0000ll) |
- ((x >> 40) & 0x000000000000FF00ll) |
- (x << 56)
- );
-}
-
-/*! \fn void SwapEndian_64(uint64_t& x)
- \brief swaps endianness of unsigned 64-bit integer, in place
-
- Swaps endian representation of value in \a x.
-*/
-API_EXPORT inline void SwapEndian_64(uint64_t& x) {
- x = ( (x >> 56) |
- ((x << 40) & 0x00FF000000000000ll) |
- ((x << 24) & 0x0000FF0000000000ll) |
- ((x << 8) & 0x000000FF00000000ll) |
- ((x >> 8) & 0x00000000FF000000ll) |
- ((x >> 24) & 0x0000000000FF0000ll) |
- ((x >> 40) & 0x000000000000FF00ll) |
- (x << 56)
- );
-}
-
-/*! \fn void SwapEndian_16p(char* data)
- \brief swaps endianness of the next 2 bytes in a buffer, in place
-
- Swaps endian representation the next 2 bytes in \a data.
-*/
-API_EXPORT inline void SwapEndian_16p(char* data) {
- uint16_t& value = (uint16_t&)*data;
- SwapEndian_16(value);
-}
-
-/*! \fn void SwapEndian_32p(char* data)
- \brief swaps endianness of the next 4 bytes in a buffer, in place
-
- Swaps endian representation the next 4 bytes in \a data.
-*/
-API_EXPORT inline void SwapEndian_32p(char* data) {
- uint32_t& value = (uint32_t&)*data;
- SwapEndian_32(value);
-}
-
-/*! \fn void SwapEndian_64p(char* data)
- \brief swaps endianness of the next 8 bytes in a buffer, in place
-
- Swaps endian representation the next 8 bytes in \a data.
-*/
-API_EXPORT inline void SwapEndian_64p(char* data) {
- uint64_t& value = (uint64_t&)*data;
- SwapEndian_64(value);
-}
-
-/*! \fn bool SystemIsBigEndian(void)
- \brief checks host architecture's byte order
- \return \c true if system uses big-endian ordering
-*/
-API_EXPORT inline bool SystemIsBigEndian(void) {
- const uint16_t one = 0x0001;
- return ((*(char*) &one) == 0 );
-}
-
-/*! \fn void PackUnsignedInt(char* buffer, unsigned int value)
- \brief stores unsigned integer value in a byte buffer
-
- \param buffer destination buffer
- \param value unsigned integer to 'pack' in buffer
-*/
-API_EXPORT inline void PackUnsignedInt(char* buffer, unsigned int value) {
- buffer[0] = (char)value;
- buffer[1] = (char)(value >> 8);
- buffer[2] = (char)(value >> 16);
- buffer[3] = (char)(value >> 24);
-}
-
-/*! \fn void PackUnsignedShort(char* buffer, unsigned short value)
- \brief stores unsigned short integer value in a byte buffer
-
- \param buffer destination buffer
- \param value unsigned short integer to 'pack' in buffer
-*/
-API_EXPORT inline void PackUnsignedShort(char* buffer, unsigned short value) {
- buffer[0] = (char)value;
- buffer[1] = (char)(value >> 8);
-}
-
-/*! \fn double UnpackDouble(const char* buffer)
- \brief reads a double value from byte buffer
-
- \param buffer source byte buffer
- \return the (double) value read from the buffer
-*/
-API_EXPORT inline double UnpackDouble(const char* buffer) {
- union { double value; unsigned char valueBuffer[sizeof(double)]; } un;
- un.value = 0;
- un.valueBuffer[0] = buffer[0];
- un.valueBuffer[1] = buffer[1];
- un.valueBuffer[2] = buffer[2];
- un.valueBuffer[3] = buffer[3];
- un.valueBuffer[4] = buffer[4];
- un.valueBuffer[5] = buffer[5];
- un.valueBuffer[6] = buffer[6];
- un.valueBuffer[7] = buffer[7];
- return un.value;
-}
-
-/*! \fn double UnpackDouble(char* buffer)
- \brief reads a double value from byte buffer
-
- This is an overloaded function.
-
- \param buffer source byte buffer
- \return the (double) value read from the buffer
-*/
-API_EXPORT inline double UnpackDouble(char* buffer) {
- return UnpackDouble( (const char*)buffer );
-}
-
-/*! \fn double UnpackFloat(const char* buffer)
- \brief reads a float value from byte buffer
-
- \param buffer source byte buffer
- \return the (float) value read from the buffer
-*/
-API_EXPORT inline float UnpackFloat(const char* buffer) {
- union { float value; unsigned char valueBuffer[sizeof(float)]; } un;
- un.value = 0;
- un.valueBuffer[0] = buffer[0];
- un.valueBuffer[1] = buffer[1];
- un.valueBuffer[2] = buffer[2];
- un.valueBuffer[3] = buffer[3];
- return un.value;
-}
-
-/*! \fn double UnpackFloat(char* buffer)
- \brief reads a float value from byte buffer
-
- This is an overloaded function.
-
- \param buffer source byte buffer
- \return the (float) value read from the buffer
-*/
-API_EXPORT inline float UnpackFloat(char* buffer) {
- return UnpackFloat( (const char*)buffer );
-}
-
-/*! \fn signed int UnpackSignedInt(const char* buffer)
- \brief reads a signed integer value from byte buffer
-
- \param buffer source byte buffer
- \return the (signed int) value read from the buffer
-*/
-API_EXPORT inline signed int UnpackSignedInt(const char* buffer) {
- union { signed int value; unsigned char valueBuffer[sizeof(signed int)]; } un;
- un.value = 0;
- un.valueBuffer[0] = buffer[0];
- un.valueBuffer[1] = buffer[1];
- un.valueBuffer[2] = buffer[2];
- un.valueBuffer[3] = buffer[3];
- return un.value;
-}
-
-/*! \fn signed int UnpackSignedInt(char* buffer)
- \brief reads a signed integer value from byte buffer
-
- This is an overloaded function.
-
- \param buffer source byte buffer
- \return the (signed int) value read from the buffer
-*/
-API_EXPORT inline signed int UnpackSignedInt(char* buffer) {
- return UnpackSignedInt( (const char*) buffer );
-}
-
-/*! \fn signed short UnpackSignedShort(const char* buffer)
- \brief reads a signed short integer value from byte buffer
-
- \param buffer source byte buffer
- \return the (signed short) value read from the buffer
-*/
-API_EXPORT inline signed short UnpackSignedShort(const char* buffer) {
- union { signed short value; unsigned char valueBuffer[sizeof(signed short)]; } un;
- un.value = 0;
- un.valueBuffer[0] = buffer[0];
- un.valueBuffer[1] = buffer[1];
- return un.value;
-}
-
-/*! \fn signed short UnpackSignedShort(char* buffer)
- \brief reads a signed short integer value from byte buffer
-
- This is an overloaded function.
-
- \param buffer source byte buffer
- \return the (signed short) value read from the buffer
-*/
-API_EXPORT inline signed short UnpackSignedShort(char* buffer) {
- return UnpackSignedShort( (const char*)buffer );
-}
-
-/*! \fn unsigned int UnpackUnsignedInt(const char* buffer)
- \brief reads an unsigned integer value from byte buffer
-
- \param buffer source byte buffer
- \return the (unsigned int) value read from the buffer
-*/
-API_EXPORT inline unsigned int UnpackUnsignedInt(const char* buffer) {
- union { unsigned int value; unsigned char valueBuffer[sizeof(unsigned int)]; } un;
- un.value = 0;
- un.valueBuffer[0] = buffer[0];
- un.valueBuffer[1] = buffer[1];
- un.valueBuffer[2] = buffer[2];
- un.valueBuffer[3] = buffer[3];
- return un.value;
-}
-
-/*! \fn unsigned int UnpackUnsignedInt(char* buffer)
- \brief reads an unsigned integer value from byte buffer
-
- This is an overloaded function.
-
- \param buffer source byte buffer
- \return the (unsigned int) value read from the buffer
-*/
-API_EXPORT inline unsigned int UnpackUnsignedInt(char* buffer) {
- return UnpackUnsignedInt( (const char*)buffer );
-}
-
-/*! \fn unsigned short UnpackUnsignedShort(const char* buffer)
- \brief reads an unsigned short integer value from byte buffer
-
- \param buffer source byte buffer
- \return the (unsigned short) value read from the buffer
-*/
-API_EXPORT inline unsigned short UnpackUnsignedShort(const char* buffer) {
- union { unsigned short value; unsigned char valueBuffer[sizeof(unsigned short)]; } un;
- un.value = 0;
- un.valueBuffer[0] = buffer[0];
- un.valueBuffer[1] = buffer[1];
- return un.value;
-}
-
-/*! \fn unsigned short UnpackUnsignedShort(char* buffer)
- \brief reads an unsigned short integer value from byte buffer
-
- This is an overloaded function.
-
- \param buffer source byte buffer
- \return the (unsigned short) value read from the buffer
-*/
-API_EXPORT inline unsigned short UnpackUnsignedShort(char* buffer) {
- return UnpackUnsignedShort( (const char*)buffer );
-}
-
-} // namespace BamTools
-
-#endif // BAMAUX_H
diff --git a/src/utils/BamTools/include/api/BamConstants.h b/src/utils/BamTools/include/api/BamConstants.h
deleted file mode 100644
index e433c8e7..00000000
--- a/src/utils/BamTools/include/api/BamConstants.h
+++ /dev/null
@@ -1,128 +0,0 @@
-// ***************************************************************************
-// BamConstants.h (c) 2011 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 19 April 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides basic constants for handling BAM files.
-// ***************************************************************************
-
-#ifndef BAM_CONSTANTS_H
-#define BAM_CONSTANTS_H
-
-#include <string>
-
-/*! \namespace BamTools::Constants
- \brief Provides basic constants for handling BAM files.
-*/
-
-namespace BamTools {
-namespace Constants {
-
-const int BAM_SIZEOF_INT = 4;
-
-// header magic number
-const char* const BAM_HEADER_MAGIC = "BAM\1";
-const unsigned int BAM_HEADER_MAGIC_LENGTH = 4;
-
-// BAM alignment core size
-const int BAM_CORE_SIZE = 32;
-const int BAM_CORE_BUFFER_SIZE = 8;
-
-// BAM alignment flags
-const int BAM_ALIGNMENT_PAIRED = 0x0001;
-const int BAM_ALIGNMENT_PROPER_PAIR = 0x0002;
-const int BAM_ALIGNMENT_UNMAPPED = 0x0004;
-const int BAM_ALIGNMENT_MATE_UNMAPPED = 0x0008;
-const int BAM_ALIGNMENT_REVERSE_STRAND = 0x0010;
-const int BAM_ALIGNMENT_MATE_REVERSE_STRAND = 0x0020;
-const int BAM_ALIGNMENT_READ_1 = 0x0040;
-const int BAM_ALIGNMENT_READ_2 = 0x0080;
-const int BAM_ALIGNMENT_SECONDARY = 0x0100;
-const int BAM_ALIGNMENT_QC_FAILED = 0x0200;
-const int BAM_ALIGNMENT_DUPLICATE = 0x0400;
-
-// CIGAR constants
-const char* const BAM_CIGAR_LOOKUP = "MIDNSHP=X";
-const int BAM_CIGAR_MATCH = 0;
-const int BAM_CIGAR_INS = 1;
-const int BAM_CIGAR_DEL = 2;
-const int BAM_CIGAR_REFSKIP = 3;
-const int BAM_CIGAR_SOFTCLIP = 4;
-const int BAM_CIGAR_HARDCLIP = 5;
-const int BAM_CIGAR_PAD = 6;
-const int BAM_CIGAR_SEQMATCH = 7;
-const int BAM_CIGAR_MISMATCH = 8;
-
-const char BAM_CIGAR_MATCH_CHAR = 'M';
-const char BAM_CIGAR_INS_CHAR = 'I';
-const char BAM_CIGAR_DEL_CHAR = 'D';
-const char BAM_CIGAR_REFSKIP_CHAR = 'N';
-const char BAM_CIGAR_SOFTCLIP_CHAR = 'S';
-const char BAM_CIGAR_HARDCLIP_CHAR = 'H';
-const char BAM_CIGAR_PAD_CHAR = 'P';
-const char BAM_CIGAR_SEQMATCH_CHAR = '=';
-const char BAM_CIGAR_MISMATCH_CHAR = 'X';
-
-const int BAM_CIGAR_SHIFT = 4;
-const int BAM_CIGAR_MASK = ((1 << BAM_CIGAR_SHIFT) - 1);
-
-// BAM tag types
-const char BAM_TAG_TYPE_ASCII = 'A';
-const char BAM_TAG_TYPE_UINT8 = 'c';
-const char BAM_TAG_TYPE_INT8 = 'C';
-const char BAM_TAG_TYPE_UINT16 = 's';
-const char BAM_TAG_TYPE_INT16 = 'S';
-const char BAM_TAG_TYPE_UINT32 = 'i';
-const char BAM_TAG_TYPE_INT32 = 'I';
-const char BAM_TAG_TYPE_FLOAT = 'f';
-const char BAM_TAG_TYPE_STRING = 'Z';
-const char BAM_TAG_TYPE_HEX = 'H';
-const char BAM_TAG_TYPE_ARRAY = 'B';
-
-const size_t BAM_TAG_TAGSIZE = 2;
-const size_t BAM_TAG_TYPESIZE = 1;
-const int BAM_TAG_ARRAYBASE_SIZE = 8;
-
-// DNA bases
-const char* const BAM_DNA_LOOKUP = "=ACMGRSVTWYHKDBN";
-const unsigned char BAM_BASECODE_EQUAL = 0;
-const unsigned char BAM_BASECODE_A = 1;
-const unsigned char BAM_BASECODE_C = 2;
-const unsigned char BAM_BASECODE_G = 4;
-const unsigned char BAM_BASECODE_T = 8;
-const unsigned char BAM_BASECODE_N = 15;
-
-const char BAM_DNA_EQUAL = '=';
-const char BAM_DNA_A = 'A';
-const char BAM_DNA_C = 'C';
-const char BAM_DNA_G = 'G';
-const char BAM_DNA_T = 'T';
-const char BAM_DNA_N = 'N';
-const char BAM_DNA_DEL = '-';
-const char BAM_DNA_PAD = '*';
-
-// zlib constants
-const int GZIP_ID1 = 31;
-const int GZIP_ID2 = 139;
-const int CM_DEFLATE = 8;
-const int FLG_FEXTRA = 4;
-const int OS_UNKNOWN = 255;
-const int BGZF_XLEN = 6;
-const int BGZF_ID1 = 66;
-const int BGZF_ID2 = 67;
-const int BGZF_LEN = 2;
-const int GZIP_WINDOW_BITS = -15;
-const int Z_DEFAULT_MEM_LEVEL = 8;
-
-// BZGF constants
-const int BGZF_BLOCK_HEADER_LENGTH = 18;
-const int BGZF_BLOCK_FOOTER_LENGTH = 8;
-const int BGZF_MAX_BLOCK_SIZE = 65536;
-const int BGZF_DEFAULT_BLOCK_SIZE = 65536;
-
-} // namespace Constants
-} // namespace BamTools
-
-#endif // BAM_CONSTANTS_H
diff --git a/src/utils/BamTools/include/api/BamIndex.h b/src/utils/BamTools/include/api/BamIndex.h
deleted file mode 100644
index 00a8f017..00000000
--- a/src/utils/BamTools/include/api/BamIndex.h
+++ /dev/null
@@ -1,80 +0,0 @@
-// ***************************************************************************
-// BamIndex.h (c) 2009 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 5 April 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides basic BAM index interface
-// ***************************************************************************
-
-#ifndef BAM_INDEX_H
-#define BAM_INDEX_H
-
-#include <api/api_global.h>
-#include <api/BamAux.h>
-#include <string>
-
-namespace BamTools {
-
-namespace Internal {
- class BamReaderPrivate;
-} // namespace Internal
-
-/*! \class BamTools::BamIndex
- \brief Provides methods for generating & loading BAM index files.
-
- This class straddles the line between public API and internal
- implementation detail. Most client code should never have to use this
- class directly.
-
- It is exposed to the public API to allow advanced users to implement
- their own custom indexing schemes.
-
- More documentation on methods & enums coming soon.
-*/
-
-class API_EXPORT BamIndex {
-
- // enums
- public:
- // specify index-caching behavior
- enum IndexCacheMode { FullIndexCaching = 0 // store entire index file contents in memory
- , LimitedIndexCaching // store only index data for current reference
- , NoIndexCaching // do not store any index data between jumps
- };
-
- // list of supported BamIndex types
- enum IndexType { BAMTOOLS = 0
- , STANDARD
- };
-
- // ctor & dtor
- public:
- BamIndex(Internal::BamReaderPrivate* reader) : m_reader(reader) { }
- virtual ~BamIndex(void) { }
-
- // index interface
- public:
- // builds index from associated BAM file & writes out to index file
- virtual bool Create(void) =0; // creates index file from BAM file
- // returns whether reference has alignments or no
- virtual bool HasAlignments(const int& referenceID) const =0;
- // attempts to use index data to jump to @region, returns success/fail
- // a "successful" jump indicates no error, but not whether this region has data
- // * thus, the method sets a flag to indicate whether there are alignments
- // available after the jump position
- virtual bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion) =0;
- // loads existing data from file into memory
- virtual bool Load(const std::string& filename) =0;
- // change the index caching behavior
- virtual void SetCacheMode(const BamIndex::IndexCacheMode& mode) =0;
-
- // data members
- protected:
- Internal::BamReaderPrivate* m_reader; // copy, not ownedprivate:
-};
-
-} // namespace BamTools
-
-#endif // BAM_INDEX_H
diff --git a/src/utils/BamTools/include/api/BamMultiReader.h b/src/utils/BamTools/include/api/BamMultiReader.h
deleted file mode 100644
index cc49ec8e..00000000
--- a/src/utils/BamTools/include/api/BamMultiReader.h
+++ /dev/null
@@ -1,127 +0,0 @@
-// ***************************************************************************
-// BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 15 March 2011 (DB)
-// ---------------------------------------------------------------------------
-// Convenience class for reading multiple BAM files.
-// ***************************************************************************
-
-#ifndef BAMMULTIREADER_H
-#define BAMMULTIREADER_H
-
-#include <api/api_global.h>
-#include <api/BamReader.h>
-#include <map>
-#include <sstream>
-#include <string>
-#include <utility>
-
-namespace BamTools {
-
-namespace Internal {
- class BamMultiReaderPrivate;
-} // namespace Internal
-
-class API_EXPORT BamMultiReader {
-
- public:
- enum SortOrder { SortedByPosition = 0
- , SortedByReadName
- , Unsorted
- };
-
- // constructor / destructor
- public:
- BamMultiReader(void);
- ~BamMultiReader(void);
-
- // public interface
- public:
-
- // ----------------------
- // BAM file operations
- // ----------------------
-
- // closes all open BAM files
- void Close(void);
- // close only the requested BAM file
- void CloseFile(const std::string& filename);
- // returns list of filenames for all open BAM files
- const std::vector<std::string> Filenames(void) const;
- // returns true if multireader has any open BAM files
- bool HasOpenReaders(void) const;
- // performs random-access jump within current BAM files
- bool Jump(int refID, int position = 0);
- // opens BAM files
- bool Open(const std::vector<std::string>& filenames);
- // opens a single BAM file, adding to any other current BAM files
- bool OpenFile(const std::string& filename);
- // returns file pointers to beginning of alignments
- bool Rewind(void);
- // sets the target region of interest
- bool SetRegion(const BamRegion& region);
- // sets the target region of interest
- bool SetRegion(const int& leftRefID,
- const int& leftPosition,
- const int& rightRefID,
- const int& rightPosition);
-
- // ----------------------
- // access alignment data
- // ----------------------
-
- // retrieves next available alignment
- bool GetNextAlignment(BamAlignment& alignment);
- // retrieves next available alignmnet (without populating the alignment's string data fields)
- bool GetNextAlignmentCore(BamAlignment& alignment);
-
- // sets the expected sorting order for reading across multiple BAM files
- void SetSortOrder(const SortOrder& order);
-
- // ----------------------
- // access auxiliary data
- // ----------------------
-
- // returns unified SAM header for all files
- SamHeader GetHeader(void) const;
- // returns unified SAM header text for all files
- std::string GetHeaderText(void) const;
- // returns number of reference sequences
- int GetReferenceCount(void) const;
- // returns all reference sequence entries.
- const BamTools::RefVector GetReferenceData(void) const;
- // returns the ID of the reference with this name.
- int GetReferenceID(const std::string& refName) const;
-
- // ----------------------
- // BAM index operations
- // ----------------------
-
- // creates index files for current BAM files
- bool CreateIndexes(const BamIndex::IndexType& type = BamIndex::STANDARD);
- // returns true if all BAM files have index data available
- bool HasIndexes(void) const;
- // looks for index files that match current BAM files
- bool LocateIndexes(const BamIndex::IndexType& preferredType = BamIndex::STANDARD);
- // opens index files for current BAM files.
- bool OpenIndexes(const std::vector<std::string>& indexFilenames);
- // changes the caching behavior of the index data
- void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);
-
- // deprecated methods
- public:
- // returns \c true if all BAM files have index data available.
- bool IsIndexLoaded(void) const;
- // convenience method for printing filenames to stdout
- void PrintFilenames(void) const;
-
- // private implementation
- private:
- Internal::BamMultiReaderPrivate* d;
-};
-
-} // namespace BamTools
-
-#endif // BAMMULTIREADER_H
diff --git a/src/utils/BamTools/include/api/BamReader.h b/src/utils/BamTools/include/api/BamReader.h
deleted file mode 100644
index 85b0c0d5..00000000
--- a/src/utils/BamTools/include/api/BamReader.h
+++ /dev/null
@@ -1,118 +0,0 @@
-// ***************************************************************************
-// BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 4 March 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides read access to BAM files.
-// ***************************************************************************
-
-#ifndef BAMREADER_H
-#define BAMREADER_H
-
-#include <api/api_global.h>
-#include <api/BamAlignment.h>
-#include <api/BamIndex.h>
-#include <api/SamHeader.h>
-#include <string>
-
-namespace BamTools {
-
-namespace Internal {
- class BamReaderPrivate;
-} // namespace Internal
-
-class API_EXPORT BamReader {
-
- // constructor / destructor
- public:
- BamReader(void);
- ~BamReader(void);
-
- // public interface
- public:
-
- // ----------------------
- // BAM file operations
- // ----------------------
-
- // closes the current BAM file
- void Close(void);
- // returns filename of current BAM file
- const std::string GetFilename(void) const;
- // returns true if a BAM file is open for reading
- bool IsOpen(void) const;
- // performs random-access jump within BAM file
- bool Jump(int refID, int position = 0);
- // opens a BAM file
- bool Open(const std::string& filename);
- // returns internal file pointer to beginning of alignment data
- bool Rewind(void);
- // sets the target region of interest
- bool SetRegion(const BamRegion& region);
- // sets the target region of interest
- bool SetRegion(const int& leftRefID,
- const int& leftPosition,
- const int& rightRefID,
- const int& rightPosition);
-
- // ----------------------
- // access alignment data
- // ----------------------
-
- // retrieves next available alignment
- bool GetNextAlignment(BamAlignment& alignment);
- // retrieves next available alignmnet (without populating the alignment's string data fields)
- bool GetNextAlignmentCore(BamAlignment& alignment);
-
- // ----------------------
- // access header data
- // ----------------------
-
- // returns SAM header data
- SamHeader GetHeader(void) const;
- // returns SAM header data, as SAM-formatted text
- std::string GetHeaderText(void) const;
-
- // ----------------------
- // access reference data
- // ----------------------
-
- // returns the number of reference sequences
- int GetReferenceCount(void) const;
- // returns all reference sequence entries
- const RefVector& GetReferenceData(void) const;
- // returns the ID of the reference with this name
- int GetReferenceID(const std::string& refName) const;
-
- // ----------------------
- // BAM index operations
- // ----------------------
-
- // creates an index file for current BAM file, using the requested index type
- bool CreateIndex(const BamIndex::IndexType& type = BamIndex::STANDARD);
- // returns true if index data is available
- bool HasIndex(void) const;
- // looks in BAM file's directory for a matching index file
- bool LocateIndex(const BamIndex::IndexType& preferredType = BamIndex::STANDARD);
- // opens a BAM index file
- bool OpenIndex(const std::string& indexFilename);
- // sets a custom BamIndex on this reader
- void SetIndex(BamIndex* index);
- // changes the caching behavior of the index data
- void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);
-
- // deprecated methods
- public:
- // returns true if index data is available
- bool IsIndexLoaded(void) const;
-
- // private implementation
- private:
- Internal::BamReaderPrivate* d;
-};
-
-} // namespace BamTools
-
-#endif // BAMREADER_H
diff --git a/src/utils/BamTools/include/api/BamWriter.h b/src/utils/BamTools/include/api/BamWriter.h
deleted file mode 100644
index 476dbecf..00000000
--- a/src/utils/BamTools/include/api/BamWriter.h
+++ /dev/null
@@ -1,64 +0,0 @@
-// ***************************************************************************
-// BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 4 March 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides the basic functionality for producing BAM files
-// ***************************************************************************
-
-#ifndef BAMWRITER_H
-#define BAMWRITER_H
-
-#include <api/api_global.h>
-#include <api/BamAux.h>
-#include <string>
-
-namespace BamTools {
-
-class BamAlignment;
-class SamHeader;
-
-namespace Internal {
- class BamWriterPrivate;
-} // namespace Internal
-
-class API_EXPORT BamWriter {
-
- public: enum CompressionMode { Compressed = 0
- , Uncompressed
- };
-
- // ctor & dtor
- public:
- BamWriter(void);
- ~BamWriter(void);
-
- // public interface
- public:
- // closes the current BAM file
- void Close(void);
- // returns true if BAM file is open for writing
- bool IsOpen(void) const;
- // opens a BAM file for writing
- bool Open(const std::string& filename,
- const std::string& samHeaderText,
- const RefVector& referenceSequences);
- // opens a BAM file for writing
- bool Open(const std::string& filename,
- const SamHeader& samHeader,
- const RefVector& referenceSequences);
- // saves the alignment to the alignment archive
- void SaveAlignment(const BamAlignment& alignment);
- // sets the output compression mode
- void SetCompressionMode(const CompressionMode& compressionMode);
-
- // private implementation
- private:
- Internal::BamWriterPrivate* d;
-};
-
-} // namespace BamTools
-
-#endif // BAMWRITER_H
diff --git a/src/utils/BamTools/include/api/SamConstants.h b/src/utils/BamTools/include/api/SamConstants.h
deleted file mode 100644
index d3459202..00000000
--- a/src/utils/BamTools/include/api/SamConstants.h
+++ /dev/null
@@ -1,96 +0,0 @@
-// ***************************************************************************
-// SamConstants.h (c) 2010 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 19 April 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides constants for SAM header
-// ***************************************************************************
-
-#ifndef SAM_CONSTANTS_H
-#define SAM_CONSTANTS_H
-
-#include <api/api_global.h>
-#include <string>
-
-namespace BamTools {
-namespace Constants {
-
-// basic char constants used in SAM format
-const char SAM_COLON = ':';
-const char SAM_EQUAL = '=';
-const char SAM_PERIOD = '.';
-const char SAM_STAR = '*';
-const char SAM_TAB = '\t';
-const std::string SAM_DIGITS = "0123456789";
-
-// HD entries
-const std::string SAM_HD_BEGIN_TOKEN = "@HD";
-const std::string SAM_HD_VERSION_TAG = "VN";
-const std::string SAM_HD_SORTORDER_TAG = "SO";
-const std::string SAM_HD_GROUPORDER_TAG = "GO";
-
-// SQ entries
-const std::string SAM_SQ_BEGIN_TOKEN = "@SQ";
-const std::string SAM_SQ_ASSEMBLYID_TAG = "AS";
-const std::string SAM_SQ_CHECKSUM_TAG = "M5";
-const std::string SAM_SQ_LENGTH_TAG = "LN";
-const std::string SAM_SQ_NAME_TAG = "SN";
-const std::string SAM_SQ_SPECIES_TAG = "SP";
-const std::string SAM_SQ_URI_TAG = "UR";
-
-// RG entries
-const std::string SAM_RG_BEGIN_TOKEN = "@RG";
-const std::string SAM_RG_DESCRIPTION_TAG = "DS";
-const std::string SAM_RG_FLOWORDER_TAG = "FO";
-const std::string SAM_RG_ID_TAG = "ID";
-const std::string SAM_RG_KEYSEQUENCE_TAG = "KS";
-const std::string SAM_RG_LIBRARY_TAG = "LB";
-const std::string SAM_RG_PLATFORMUNIT_TAG = "PU";
-const std::string SAM_RG_PREDICTEDINSERTSIZE_TAG = "PI";
-const std::string SAM_RG_PRODUCTIONDATE_TAG = "DT";
-const std::string SAM_RG_PROGRAM_TAG = "PG";
-const std::string SAM_RG_SAMPLE_TAG = "SM";
-const std::string SAM_RG_SEQCENTER_TAG = "CN";
-const std::string SAM_RG_SEQTECHNOLOGY_TAG = "PL";
-
-// PG entries
-const std::string SAM_PG_BEGIN_TOKEN = "@PG";
-const std::string SAM_PG_COMMANDLINE_TAG = "CL";
-const std::string SAM_PG_ID_TAG = "ID";
-const std::string SAM_PG_NAME_TAG = "PN";
-const std::string SAM_PG_PREVIOUSPROGRAM_TAG = "PP";
-const std::string SAM_PG_VERSION_TAG = "VN";
-
-// CO entries
-const std::string SAM_CO_BEGIN_TOKEN = "@CO";
-
-// HD:SO values
-const std::string SAM_HD_SORTORDER_COORDINATE = "coordinate";
-const std::string SAM_HD_SORTORDER_QUERYNAME = "queryname";
-const std::string SAM_HD_SORTORDER_UNKNOWN = "unknown";
-const std::string SAM_HD_SORTORDER_UNSORTED = "unsorted";
-
-// HD:GO values
-const std::string SAM_HD_GROUPORDER_NONE = "none";
-const std::string SAM_HD_GROUPORDER_QUERY = "query";
-const std::string SAM_HD_GROUPORDER_REFERENCE = "reference";
-
-// SQ:LN values
-const unsigned int SAM_SQ_LENGTH_MIN = 1;
-const unsigned int SAM_SQ_LENGTH_MAX = 536870911; // 2^29 - 1
-
-// RG:PL values
-const std::string SAM_RG_SEQTECHNOLOGY_CAPILLARY = "CAPILLARY";
-const std::string SAM_RG_SEQTECHNOLOGY_HELICOS = "HELICOS";
-const std::string SAM_RG_SEQTECHNOLOGY_ILLUMINA = "ILLUMINA";
-const std::string SAM_RG_SEQTECHNOLOGY_IONTORRENT = "IONTORRENT";
-const std::string SAM_RG_SEQTECHNOLOGY_LS454 = "LS454";
-const std::string SAM_RG_SEQTECHNOLOGY_PACBIO = "PACBIO";
-const std::string SAM_RG_SEQTECHNOLOGY_SOLID = "SOLID";
-
-} // namespace Constants
-} // namespace BamTools
-
-#endif // SAM_CONSTANTS_H
diff --git a/src/utils/BamTools/include/api/SamHeader.h b/src/utils/BamTools/include/api/SamHeader.h
deleted file mode 100644
index 5c7a1019..00000000
--- a/src/utils/BamTools/include/api/SamHeader.h
+++ /dev/null
@@ -1,69 +0,0 @@
-// ***************************************************************************
-// SamHeader.h (c) 2010 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 18 April 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides direct read/write access to the SAM header data fields.
-// ***************************************************************************
-
-#ifndef SAM_HEADER_H
-#define SAM_HEADER_H
-
-#include <api/api_global.h>
-#include <api/SamProgramChain.h>
-#include <api/SamReadGroupDictionary.h>
-#include <api/SamSequenceDictionary.h>
-#include <string>
-#include <vector>
-
-namespace BamTools {
-
-struct API_EXPORT SamHeader {
-
- // ctor & dtor
- SamHeader(const std::string& headerText = "");
- SamHeader(const SamHeader& other);
- ~SamHeader(void);
-
- // query/modify entire SamHeader
- void Clear(void); // clears all header contents
- bool IsValid(bool verbose = false) const; // returns true if SAM header is well-formed
- void SetHeaderText(const std::string& headerText); // replaces data fields with contents of SAM-formatted text
- std::string ToString(void) const; // returns the printable, SAM-formatted header text
-
- // convenience query methods
- bool HasVersion(void) const; // returns true if header contains format version entry
- bool HasSortOrder(void) const; // returns true if header contains sort order entry
- bool HasGroupOrder(void) const; // returns true if header contains group order entry
- bool HasSequences(void) const; // returns true if header contains any sequence entries
- bool HasReadGroups(void) const; // returns true if header contains any read group entries
- bool HasPrograms(void) const; // returns true if header contains any program record entries
- bool HasComments(void) const; // returns true if header contains comments
-
- // --------------
- // data members
- // --------------
-
- // header metadata (@HD line)
- std::string Version; // VN:<Version> *Required for valid SAM header, if @HD record is present*
- std::string SortOrder; // SO:<SortOrder>
- std::string GroupOrder; // GO:<GroupOrder>
-
- // header sequences (@SQ entries)
- SamSequenceDictionary Sequences;
-
- // header read groups (@RG entries)
- SamReadGroupDictionary ReadGroups;
-
- // header program data (@PG entries)
- SamProgramChain Programs;
-
- // header comments (@CO entries)
- std::vector<std::string> Comments;
-};
-
-} // namespace BamTools
-
-#endif // SAM_HEADER_H
diff --git a/src/utils/BamTools/include/api/SamProgram.h b/src/utils/BamTools/include/api/SamProgram.h
deleted file mode 100644
index 3c89059b..00000000
--- a/src/utils/BamTools/include/api/SamProgram.h
+++ /dev/null
@@ -1,62 +0,0 @@
-// ***************************************************************************
-// SamProgram.h (c) 2011 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 19 April 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides direct read/write access to the SAM header program records.
-// ***************************************************************************
-
-#ifndef SAM_PROGRAM_H
-#define SAM_PROGRAM_H
-
-#include "api/api_global.h"
-#include <string>
-
-namespace BamTools {
-
-class SamProgramChain;
-
-struct API_EXPORT SamProgram {
-
- // ctor & dtor
- SamProgram(void);
- SamProgram(const std::string& id);
- SamProgram(const SamProgram& other);
- ~SamProgram(void);
-
- // query/modify entire program record
- void Clear(void); // clears all data fields
-
- // convenience query methods
- bool HasCommandLine(void) const; // returns true if program record has a command line entry
- bool HasID(void) const; // returns true if program record has an ID
- bool HasName(void) const; // returns true if program record has a name
- bool HasPreviousProgramID(void) const; // returns true if program record has a 'previous program ID'
- bool HasVersion(void) const; // returns true if program record has a version
-
- // data members
- std::string CommandLine; // CL:<CommandLine>
- std::string ID; // ID:<ID> *Required for valid SAM header*
- std::string Name; // PN:<Name>
- std::string PreviousProgramID; // PP:<PreviousProgramID>
- std::string Version; // VN:<Version>
-
- // internal (non-standard) methods & fields
- private:
- bool HasNextProgramID(void) const;
- std::string NextProgramID;
- friend class BamTools::SamProgramChain;
-};
-
-/*! \fn bool operator==(const SamProgram& lhs, const SamProgram& rhs)
- \brief tests equality by comparing program IDs
-*/
-API_EXPORT inline bool operator==(const SamProgram& lhs, const SamProgram& rhs) {
- return lhs.ID == rhs.ID;
-}
-
-} // namespace BamTools
-
-#endif // SAM_PROGRAM_H
diff --git a/src/utils/BamTools/include/api/SamProgramChain.h b/src/utils/BamTools/include/api/SamProgramChain.h
deleted file mode 100644
index 4cb16fc3..00000000
--- a/src/utils/BamTools/include/api/SamProgramChain.h
+++ /dev/null
@@ -1,86 +0,0 @@
-// ***************************************************************************
-// SamProgramChain.h (c) 2011 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 19 April 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides methods for operating on a SamProgram record "chain"
-// ***************************************************************************
-
-#ifndef SAM_PROGRAMCHAIN_H
-#define SAM_PROGRAMCHAIN_H
-
-#include <api/api_global.h>
-#include <api/SamProgram.h>
-#include <string>
-#include <vector>
-
-namespace BamTools {
-
-// chain is *NOT* sorted in any order
-// use First()/Last() to retrieve oldest/newest programs, respectively
-typedef std::vector<SamProgram> SamProgramContainer;
-typedef SamProgramContainer::iterator SamProgramIterator;
-typedef SamProgramContainer::const_iterator SamProgramConstIterator;
-
-class API_EXPORT SamProgramChain {
-
- // ctor & dtor
- public:
- SamProgramChain(void);
- SamProgramChain(const SamProgramChain& other);
- ~SamProgramChain(void);
-
- // query/modify program data
- public:
- // appends a program record to the chain
- void Add(SamProgram& program);
- void Add(std::vector<SamProgram>& programs);
-
- // clears all read group entries
- void Clear(void);
-
- // returns true if chain contains this program record (matches on ID)
- bool Contains(const SamProgram& program) const;
- bool Contains(const std::string& programId) const;
-
- // returns the first (oldest) program in the chain
- SamProgram& First(void);
- const SamProgram& First(void) const;
-
- // returns true if chain is empty
- bool IsEmpty(void) const;
-
- // returns last (most recent) program in the chain
- SamProgram& Last(void);
- const SamProgram& Last(void) const;
-
- // returns number of program records in the chain
- int Size(void) const;
-
- // retrieves a modifiable reference to the SamProgram object associated with this ID
- SamProgram& operator[](const std::string& programId);
-
- // retrieve STL-compatible iterators
- public:
- SamProgramIterator Begin(void); // returns iterator to begin()
- SamProgramConstIterator Begin(void) const; // returns const_iterator to begin()
- SamProgramConstIterator ConstBegin(void) const; // returns const_iterator to begin()
- SamProgramIterator End(void); // returns iterator to end()
- SamProgramConstIterator End(void) const; // returns const_iterator to end()
- SamProgramConstIterator ConstEnd(void) const; // returns const_iterator to end()
-
- // internal methods
- private:
- int IndexOf(const std::string& programId) const;
- const std::string NextIdFor(const std::string& programId) const;
-
- // data members
- private:
- SamProgramContainer m_data;
-};
-
-} // namespace BamTools
-
-#endif // SAM_PROGRAMCHAIN_H
diff --git a/src/utils/BamTools/include/api/SamReadGroup.h b/src/utils/BamTools/include/api/SamReadGroup.h
deleted file mode 100644
index b203d3cd..00000000
--- a/src/utils/BamTools/include/api/SamReadGroup.h
+++ /dev/null
@@ -1,69 +0,0 @@
-// ***************************************************************************
-// SamReadGroup.h (c) 2010 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 18 April 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides direct read/write access to the SAM read group data fields.
-// ***************************************************************************
-
-#ifndef SAM_READGROUP_H
-#define SAM_READGROUP_H
-
-#include "api/api_global.h"
-#include <string>
-
-namespace BamTools {
-
-struct API_EXPORT SamReadGroup {
-
- // ctor & dtor
- SamReadGroup(void);
- SamReadGroup(const std::string& id);
- SamReadGroup(const SamReadGroup& other);
- ~SamReadGroup(void);
-
- // query/modify entire read group
- void Clear(void); // clears all data fields
-
- // convenience query methods
- bool HasDescription(void) const; // returns true if read group has a description
- bool HasFlowOrder(void) const; // returns true if read group has a flow order entry
- bool HasID(void) const; // returns true if read group has a group ID
- bool HasKeySequence(void) const; // returns true if read group has a key sequence
- bool HasLibrary(void) const; // returns true if read group has a library name
- bool HasPlatformUnit(void) const; // returns true if read group has a platform unit ID
- bool HasPredictedInsertSize(void) const; // returns true if read group has a predicted insert size
- bool HasProductionDate(void) const; // returns true if read group has a production date
- bool HasProgram(void) const; // returns true if read group has a program entry
- bool HasSample(void) const; // returns true if read group has a sample name
- bool HasSequencingCenter(void) const; // returns true if read group has a sequencing center ID
- bool HasSequencingTechnology(void) const; // returns true if read group has a sequencing technology ID
-
-
- // data fields
- std::string Description; // DS:<Description>
- std::string FlowOrder; // FO:<FlowOrder>
- std::string ID; // ID:<ID> *Required for valid SAM header*
- std::string KeySequence; // KS:<KeySequence>
- std::string Library; // LB:<Library>
- std::string PlatformUnit; // PU:<PlatformUnit>
- std::string PredictedInsertSize; // PI:<PredictedInsertSize>
- std::string ProductionDate; // DT:<ProductionDate>
- std::string Program; // PG:<Program>
- std::string Sample; // SM:<Sample>
- std::string SequencingCenter; // CN:<SequencingCenter>
- std::string SequencingTechnology; // PL:<SequencingTechnology>
-};
-
-/*! \fn bool operator==(const SamReadGroup& lhs, const SamReadGroup& rhs)
- \brief tests equality by comparing read group IDs
-*/
-API_EXPORT inline bool operator==(const SamReadGroup& lhs, const SamReadGroup& rhs) {
- return lhs.ID == rhs.ID;
-}
-
-} // namespace BamTools
-
-#endif // SAM_READGROUP_H
diff --git a/src/utils/BamTools/include/api/SamReadGroupDictionary.h b/src/utils/BamTools/include/api/SamReadGroupDictionary.h
deleted file mode 100644
index 8ec40e22..00000000
--- a/src/utils/BamTools/include/api/SamReadGroupDictionary.h
+++ /dev/null
@@ -1,87 +0,0 @@
-// ***************************************************************************
-// SamReadGroupDictionary.h (c) 2010 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 18 April 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides methods for operating on a collection of SamReadGroup entries.
-// ***************************************************************************
-
-#ifndef SAM_READGROUP_DICTIONARY_H
-#define SAM_READGROUP_DICTIONARY_H
-
-#include <api/api_global.h>
-#include <api/SamReadGroup.h>
-#include <string>
-#include <vector>
-
-namespace BamTools {
-
-typedef std::vector<SamReadGroup> SamReadGroupContainer;
-typedef SamReadGroupContainer::iterator SamReadGroupIterator;
-typedef SamReadGroupContainer::const_iterator SamReadGroupConstIterator;
-
-class API_EXPORT SamReadGroupDictionary {
-
- // ctor & dtor
- public:
- SamReadGroupDictionary(void);
- SamReadGroupDictionary(const SamReadGroupDictionary& other);
- ~SamReadGroupDictionary(void);
-
- // query/modify read group data
- public:
- // adds a read group
- void Add(const SamReadGroup& readGroup);
- void Add(const std::string& readGroupId);
-
- // adds multiple read groups
- void Add(const std::vector<SamReadGroup>& readGroups);
- void Add(const std::vector<std::string>& readGroupIds);
-
- // clears all read group entries
- void Clear(void);
-
- // returns true if dictionary contains this read group
- bool Contains(const SamReadGroup& readGroup) const;
- bool Contains(const std::string& readGroupId) const;
-
- // returns true if dictionary is empty
- bool IsEmpty(void) const;
-
- // removes read group, if found
- void Remove(const SamReadGroup& readGroup);
- void Remove(const std::string& readGroupId);
-
- // removes multiple read groups
- void Remove(const std::vector<SamReadGroup>& readGroups);
- void Remove(const std::vector<std::string>& readGroupIds);
-
- // returns number of read groups in dictionary
- int Size(void) const;
-
- // retrieves a modifiable reference to the SamReadGroup object associated with this ID
- SamReadGroup& operator[](const std::string& readGroupId);
-
- // retrieve STL-compatible iterators
- public:
- SamReadGroupIterator Begin(void); // returns iterator to begin()
- SamReadGroupConstIterator Begin(void) const; // returns const_iterator to begin()
- SamReadGroupConstIterator ConstBegin(void) const; // returns const_iterator to begin()
- SamReadGroupIterator End(void); // returns iterator to end()
- SamReadGroupConstIterator End(void) const; // returns const_iterator to end()
- SamReadGroupConstIterator ConstEnd(void) const; // returns const_iterator to end()
-
- // internal methods
- private:
- int IndexOf(const std::string& readGroupId) const;
-
- // data members
- private:
- SamReadGroupContainer m_data;
-};
-
-} // namespace BamTools
-
-#endif // SAM_READGROUP_DICTIONARY_H
diff --git a/src/utils/BamTools/include/api/SamSequence.h b/src/utils/BamTools/include/api/SamSequence.h
deleted file mode 100644
index 054e58f9..00000000
--- a/src/utils/BamTools/include/api/SamSequence.h
+++ /dev/null
@@ -1,61 +0,0 @@
-// ***************************************************************************
-// SamSequence.h (c) 2010 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 18 April 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides direct read/write access to the SAM sequence data fields.
-// ***************************************************************************
-
-#ifndef SAM_SEQUENCE_H
-#define SAM_SEQUENCE_H
-
-#include <api/api_global.h>
-#include <string>
-
-namespace BamTools {
-
-struct API_EXPORT SamSequence {
-
- // ctor & dtor
- SamSequence(void);
- SamSequence(const std::string& name, const int& length);
- SamSequence(const std::string& name, const std::string& length);
- SamSequence(const SamSequence& other);
- ~SamSequence(void);
-
- // query/modify entire sequence
- void Clear(void); // clears all contents
-
- // convenience query methods
- bool HasAssemblyID(void) const; // returns true if sequence has an assembly ID
- bool HasChecksum(void) const; // returns true if sequence has an MD5 checksum
- bool HasLength(void) const; // returns true if sequence has a length
- bool HasName(void) const; // returns true if sequence has a name
- bool HasSpecies(void) const; // returns true if sequence has a species ID
- bool HasURI(void) const; // returns true if sequence has a URI
-
- // data members
- std::string AssemblyID; // AS:<AssemblyID>
- std::string Checksum; // M5:<Checksum>
- std::string Length; // LN:<Length> *Required for valid SAM header*
- std::string Name; // SN:<Name> *Required for valid SAM header*
- std::string Species; // SP:<Species>
- std::string URI; // UR:<URI>
-};
-
-/*! \fn bool operator==(const SamSequence& lhs, const SamSequence& rhs)
- \brief tests equality by comparing sequence names, lengths, & checksums (if available)
-*/
-API_EXPORT inline bool operator==(const SamSequence& lhs, const SamSequence& rhs) {
- if ( lhs.Name != rhs.Name ) return false;
- if ( lhs.Length != rhs.Length ) return false;
- if ( lhs.HasChecksum() && rhs.HasChecksum() )
- return (lhs.Checksum == rhs.Checksum);
- else return true;
-}
-
-} // namespace BamTools
-
-#endif // SAM_SEQUENCE_H
diff --git a/src/utils/BamTools/include/api/SamSequenceDictionary.h b/src/utils/BamTools/include/api/SamSequenceDictionary.h
deleted file mode 100644
index 1ac73261..00000000
--- a/src/utils/BamTools/include/api/SamSequenceDictionary.h
+++ /dev/null
@@ -1,89 +0,0 @@
-// ***************************************************************************
-// SamSequenceDictionary.h (c) 2010 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 18 April 2011
-// ---------------------------------------------------------------------------
-// Provides methods for operating on a collection of SamSequence entries.
-// ***************************************************************************
-
-#ifndef SAM_SEQUENCE_DICTIONARY_H
-#define SAM_SEQUENCE_DICTIONARY_H
-
-#include <api/api_global.h>
-#include <api/SamSequence.h>
-#include <string>
-#include <map>
-#include <vector>
-
-namespace BamTools {
-
-typedef std::vector<SamSequence> SamSequenceContainer;
-typedef SamSequenceContainer::iterator SamSequenceIterator;
-typedef SamSequenceContainer::const_iterator SamSequenceConstIterator;
-
-class API_EXPORT SamSequenceDictionary {
-
- // ctor & dtor
- public:
- SamSequenceDictionary(void);
- SamSequenceDictionary(const SamSequenceDictionary& other);
- ~SamSequenceDictionary(void);
-
- // query/modify sequence data
- public:
- // adds a sequence
- void Add(const SamSequence& sequence);
- void Add(const std::string& name, const int& length);
-
- // adds multiple sequences
- void Add(const std::vector<SamSequence>& sequences);
- void Add(const std::map<std::string, int>& sequenceMap);
-
- // clears all sequence entries
- void Clear(void);
-
- // returns true if dictionary contains this sequence
- bool Contains(const SamSequence& sequence) const;
- bool Contains(const std::string& sequenceName) const;
-
- // returns true if dictionary is empty
- bool IsEmpty(void) const;
-
- // removes sequence, if found
- void Remove(const SamSequence& sequence);
- void Remove(const std::string& sequenceName);
-
- // removes multiple sequences
- void Remove(const std::vector<SamSequence>& sequences);
- void Remove(const std::vector<std::string>& sequenceNames);
-
- // returns number of sequences in dictionary
- int Size(void) const;
-
- // retrieves a modifiable reference to the SamSequence object associated with this name
- SamSequence& operator[](const std::string& sequenceName);
-
- // retrieve STL-compatible iterators
- public:
- SamSequenceIterator Begin(void); // returns iterator to begin()
- SamSequenceConstIterator Begin(void) const; // returns const_iterator to begin()
- SamSequenceConstIterator ConstBegin(void) const; // returns const_iterator to begin()
- SamSequenceIterator End(void); // returns iterator to end()
- SamSequenceConstIterator End(void) const; // returns const_iterator to end()
- SamSequenceConstIterator ConstEnd(void) const; // returns const_iterator to end()
-
- // internal methods
- private:
- int IndexOf(const std::string& name) const;
-
- // data members
- private:
- SamSequenceContainer m_data;
-};
-
-} // namespace BamTools
-
-#endif // SAM_SEQUENCE_DICTIONARY_H
-
diff --git a/src/utils/BamTools/include/api/api_global.h b/src/utils/BamTools/include/api/api_global.h
deleted file mode 100644
index 84fcad21..00000000
--- a/src/utils/BamTools/include/api/api_global.h
+++ /dev/null
@@ -1,22 +0,0 @@
-// ***************************************************************************
-// api_global.h (c) 2010 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 19 November 2010 (DB)
-// ---------------------------------------------------------------------------
-// Provides macros for exporting & importing BamTools API library symbols
-// ***************************************************************************
-
-#ifndef API_GLOBAL_H
-#define API_GLOBAL_H
-
-#include "shared/bamtools_global.h"
-
-#ifdef BAMTOOLS_API_LIBRARY
-# define API_EXPORT BAMTOOLS_LIBRARY_EXPORT
-#else
-# define API_EXPORT BAMTOOLS_LIBRARY_IMPORT
-#endif
-
-#endif // API_GLOBAL_H
diff --git a/src/utils/BamTools/include/shared/bamtools_global.h b/src/utils/BamTools/include/shared/bamtools_global.h
deleted file mode 100644
index 6e3cb39e..00000000
--- a/src/utils/BamTools/include/shared/bamtools_global.h
+++ /dev/null
@@ -1,79 +0,0 @@
-// ***************************************************************************
-// bamtools_global.h (c) 2010 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 3 March 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides the basic definitions for exporting & importing library symbols.
-// Also provides some platform-specific rules for definitions.
-// ***************************************************************************
-
-#ifndef BAMTOOLS_GLOBAL_H
-#define BAMTOOLS_GLOBAL_H
-
-/*! \brief Library export macro
- \internal
-*/
-#ifndef BAMTOOLS_LIBRARY_EXPORT
-# if defined(WIN32)
-# define BAMTOOLS_LIBRARY_EXPORT __declspec(dllexport)
-# else
-# define BAMTOOLS_LIBRARY_EXPORT __attribute__((visibility("default")))
-# endif
-#endif // BAMTOOLS_LIBRARY_EXPORT
-
-/*! \brief Library import macro
- \internal
-*/
-#ifndef BAMTOOLS_LIBRARY_IMPORT
-# if defined(WIN32)
-# define BAMTOOLS_LIBRARY_IMPORT __declspec(dllimport)
-# else
-# define BAMTOOLS_LIBRARY_IMPORT
-# endif
-#endif // BAMTOOLS_LIBRARY_IMPORT
-
-/*! \brief Platform-specific type definitions
- \internal
-*/
-#ifndef BAMTOOLS_LFS
-#define BAMTOOLS_LFS
- #ifdef WIN32
- #define ftell64(a) _ftelli64(a)
- #define fseek64(a,b,c) _fseeki64(a,b,c)
- #else
- #define ftell64(a) ftello(a)
- #define fseek64(a,b,c) fseeko(a,b,c)
- #endif
-#endif // BAMTOOLS_LFS
-
-/*! \def ftell64(a)
- \brief Platform-independent tell() operation.
- \internal
-*/
-/*! \def fseek64(a,b,c)
- \brief Platform-independent seek() operation.
- \internal
-*/
-
-/*! \brief Platform-specific type definitions
- \internal
-*/
-#ifndef BAMTOOLS_TYPES
-#define BAMTOOLS_TYPES
- #ifdef _MSC_VER
- typedef char int8_t;
- typedef unsigned char uint8_t;
- typedef short int16_t;
- typedef unsigned short uint16_t;
- typedef int int32_t;
- typedef unsigned int uint32_t;
- typedef long long int64_t;
- typedef unsigned long long uint64_t;
- #else
- #include <stdint.h>
- #endif
-#endif // BAMTOOLS_TYPES
-
-#endif // BAMTOOLS_GLOBAL_H
--
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