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incorporated edlib
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@sodiumnitrate
sodiumnitrate committed Oct 16, 2023
1 parent b0114ac commit 4cc062f
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4 changes: 3 additions & 1 deletion CMakeLists.txt
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Expand Up @@ -13,10 +13,12 @@ find_package(pybind11 CONFIG REQUIRED)

file (GLOB SOURCE_FILES "src/*.cpp")
file (GLOB HEADER_FILES "src/include/*.hpp")
file (GLOB EDLIB_SRC "src/edlib/src/edlib.cpp")
file (GLOB EDLIB_HEADER "src/edlib/include/edlib.h")

#python_add_library(sequence_analysis_cpp MODULE src/utils.cpp src/genome_map.cpp src/orf.cpp src/pairwise_aligner.cpp src/sam_file.cpp src/seq_set.cpp src/sequence.cpp src/sequence_analysis.cpp WITH_SOABI)

python_add_library(sequence_analysis_cpp MODULE ${SOURCE_FILES} ${HEADER_FILES} WITH_SOABI)
python_add_library(sequence_analysis_cpp MODULE ${SOURCE_FILES} ${HEADER_FILES} ${EDLIB_SRC} ${EDLIB_HEADER} WITH_SOABI)

target_link_libraries(sequence_analysis_cpp PRIVATE pybind11::headers )
target_compile_definitions(sequence_analysis_cpp PRIVATE VERSION_INFO=${PROJECT_VERSION})
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277 changes: 277 additions & 0 deletions src/edlib/include/edlib.h
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#ifndef EDLIB_H
#define EDLIB_H

/**
* @file
* @author Martin Sosic
* @brief Main header file, containing all public functions and structures.
*/

// Define EDLIB_API macro to properly export symbols
#ifdef EDLIB_SHARED
# ifdef _WIN32
# ifdef EDLIB_BUILD
# define EDLIB_API __declspec(dllexport)
# else
# define EDLIB_API __declspec(dllimport)
# endif
# else
# define EDLIB_API __attribute__ ((visibility ("default")))
# endif
#else
# define EDLIB_API
#endif

#ifdef __cplusplus
extern "C" {
#endif

// Status codes
#define EDLIB_STATUS_OK 0
#define EDLIB_STATUS_ERROR 1

/**
* Alignment methods - how should Edlib treat gaps before and after query?
*/
typedef enum {
/**
* Global method. This is the standard method.
* Useful when you want to find out how similar is first sequence to second sequence.
*/
EDLIB_MODE_NW,
/**
* Prefix method. Similar to global method, but with a small twist - gap at query end is not penalized.
* What that means is that deleting elements from the end of second sequence is "free"!
* For example, if we had "AACT" and "AACTGGC", edit distance would be 0, because removing "GGC" from the end
* of second sequence is "free" and does not count into total edit distance. This method is appropriate
* when you want to find out how well first sequence fits at the beginning of second sequence.
*/
EDLIB_MODE_SHW,
/**
* Infix method. Similar as prefix method, but with one more twist - gaps at query end and start are
* not penalized. What that means is that deleting elements from the start and end of second sequence is "free"!
* For example, if we had ACT and CGACTGAC, edit distance would be 0, because removing CG from the start
* and GAC from the end of second sequence is "free" and does not count into total edit distance.
* This method is appropriate when you want to find out how well first sequence fits at any part of
* second sequence.
* For example, if your second sequence was a long text and your first sequence was a sentence from that text,
* but slightly scrambled, you could use this method to discover how scrambled it is and where it fits in
* that text. In bioinformatics, this method is appropriate for aligning read to a sequence.
*/
EDLIB_MODE_HW
} EdlibAlignMode;

/**
* Alignment tasks - what do you want Edlib to do?
*/
typedef enum {
EDLIB_TASK_DISTANCE, //!< Find edit distance and end locations.
EDLIB_TASK_LOC, //!< Find edit distance, end locations and start locations.
EDLIB_TASK_PATH //!< Find edit distance, end locations and start locations and alignment path.
} EdlibAlignTask;

/**
* Describes cigar format.
* @see http://samtools.github.io/hts-specs/SAMv1.pdf
* @see http://drive5.com/usearch/manual/cigar.html
*/
typedef enum {
EDLIB_CIGAR_STANDARD, //!< Match: 'M', Insertion: 'I', Deletion: 'D', Mismatch: 'M'.
EDLIB_CIGAR_EXTENDED //!< Match: '=', Insertion: 'I', Deletion: 'D', Mismatch: 'X'.
} EdlibCigarFormat;

// Edit operations.
#define EDLIB_EDOP_MATCH 0 //!< Match.
#define EDLIB_EDOP_INSERT 1 //!< Insertion to target = deletion from query.
#define EDLIB_EDOP_DELETE 2 //!< Deletion from target = insertion to query.
#define EDLIB_EDOP_MISMATCH 3 //!< Mismatch.

/**
* @brief Defines two given characters as equal.
*/
typedef struct {
char first;
char second;
} EdlibEqualityPair;

/**
* @brief Configuration object for edlibAlign() function.
*/
typedef struct {
/**
* Set k to non-negative value to tell edlib that edit distance is not larger than k.
* Smaller k can significantly improve speed of computation.
* If edit distance is larger than k, edlib will set edit distance to -1.
* Set k to negative value and edlib will internally auto-adjust k until score is found.
*/
int k;

/**
* Alignment method.
* EDLIB_MODE_NW: global (Needleman-Wunsch)
* EDLIB_MODE_SHW: prefix. Gap after query is not penalized.
* EDLIB_MODE_HW: infix. Gaps before and after query are not penalized.
*/
EdlibAlignMode mode;

/**
* Alignment task - tells Edlib what to calculate. Less to calculate, faster it is.
* EDLIB_TASK_DISTANCE - find edit distance and end locations of optimal alignment paths in target.
* EDLIB_TASK_LOC - find edit distance and start and end locations of optimal alignment paths in target.
* EDLIB_TASK_PATH - find edit distance, alignment path (and start and end locations of it in target).
*/
EdlibAlignTask task;

/**
* List of pairs of characters, where each pair defines two characters as equal.
* This way you can extend edlib's definition of equality (which is that each character is equal only
* to itself).
* This can be useful if you have some wildcard characters that should match multiple other characters,
* or e.g. if you want edlib to be case insensitive.
* Can be set to NULL if there are none.
*/
const EdlibEqualityPair* additionalEqualities;

/**
* Number of additional equalities, which is non-negative number.
* 0 if there are none.
*/
int additionalEqualitiesLength;
} EdlibAlignConfig;

/**
* Helper method for easy construction of configuration object.
* @return Configuration object filled with given parameters.
*/
EDLIB_API EdlibAlignConfig edlibNewAlignConfig(
int k, EdlibAlignMode mode, EdlibAlignTask task,
const EdlibEqualityPair* additionalEqualities,
int additionalEqualitiesLength
);

/**
* @return Default configuration object, with following defaults:
* k = -1, mode = EDLIB_MODE_NW, task = EDLIB_TASK_DISTANCE, no additional equalities.
*/
EDLIB_API EdlibAlignConfig edlibDefaultAlignConfig(void);


/**
* Container for results of alignment done by edlibAlign() function.
*/
typedef struct {
/**
* EDLIB_STATUS_OK or EDLIB_STATUS_ERROR. If error, all other fields will have undefined values.
*/
int status;

/**
* -1 if k is non-negative and edit distance is larger than k.
*/
int editDistance;

/**
* Array of zero-based positions in target where optimal alignment paths end.
* If gap after query is penalized, gap counts as part of query (NW), otherwise not.
* Set to NULL if edit distance is larger than k.
* If you do not free whole result object using edlibFreeAlignResult(), do not forget to use free().
*/
int* endLocations;

/**
* Array of zero-based positions in target where optimal alignment paths start,
* they correspond to endLocations.
* If gap before query is penalized, gap counts as part of query (NW), otherwise not.
* Set to NULL if not calculated or if edit distance is larger than k.
* If you do not free whole result object using edlibFreeAlignResult(), do not forget to use free().
*/
int* startLocations;

/**
* Number of end (and start) locations.
*/
int numLocations;

/**
* Alignment is found for first pair of start and end locations.
* Set to NULL if not calculated.
* Alignment is sequence of numbers: 0, 1, 2, 3.
* 0 stands for match.
* 1 stands for insertion to target.
* 2 stands for insertion to query.
* 3 stands for mismatch.
* Alignment aligns query to target from begining of query till end of query.
* If gaps are not penalized, they are not in alignment.
* If you do not free whole result object using edlibFreeAlignResult(), do not forget to use free().
*/
unsigned char* alignment;

/**
* Length of alignment.
*/
int alignmentLength;

/**
* Number of different characters in query and target together.
*/
int alphabetLength;
} EdlibAlignResult;

/**
* Frees memory in EdlibAlignResult that was allocated by edlib.
* If you do not use it, make sure to free needed members manually using free().
*/
EDLIB_API void edlibFreeAlignResult(EdlibAlignResult result);


/**
* Aligns two sequences (query and target) using edit distance (levenshtein distance).
* Through config parameter, this function supports different alignment methods (global, prefix, infix),
* as well as different modes of search (tasks).
* It always returns edit distance and end locations of optimal alignment in target.
* It optionally returns start locations of optimal alignment in target and alignment path,
* if you choose appropriate tasks.
* @param [in] query First sequence.
* @param [in] queryLength Number of characters in first sequence.
* @param [in] target Second sequence.
* @param [in] targetLength Number of characters in second sequence.
* @param [in] config Additional alignment parameters, like alignment method and wanted results.
* @return Result of alignment, which can contain edit distance, start and end locations and alignment path.
* Make sure to clean up the object using edlibFreeAlignResult() or by manually freeing needed members.
*/
EDLIB_API EdlibAlignResult edlibAlign(
const char* query, int queryLength,
const char* target, int targetLength,
const EdlibAlignConfig config
);


/**
* Builds cigar string from given alignment sequence.
* @param [in] alignment Alignment sequence.
* 0 stands for match.
* 1 stands for insertion to target.
* 2 stands for insertion to query.
* 3 stands for mismatch.
* @param [in] alignmentLength
* @param [in] cigarFormat Cigar will be returned in specified format.
* @return Cigar string.
* I stands for insertion.
* D stands for deletion.
* X stands for mismatch. (used only in extended format)
* = stands for match. (used only in extended format)
* M stands for (mis)match. (used only in standard format)
* String is null terminated.
* Needed memory is allocated and given pointer is set to it.
* Do not forget to free it later using free()!
*/
EDLIB_API char* edlibAlignmentToCigar(
const unsigned char* alignment, int alignmentLength,
EdlibCigarFormat cigarFormat
);

#ifdef __cplusplus
}
#endif

#endif // EDLIB_H
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