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* Created by Mengyao Zhao on 6/22/10.
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* Copyright 2010 Boston College. All rights reserved.
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* Last revision by Mengyao Zhao on 07/31/12.
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#include <emmintrin.h>
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/*! @typedef structure of the query profile */
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typedef struct _profile s_profile;
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/*! @typedef structure of the alignment result
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@field score1 the best alignment score
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@field score2 sub-optimal alignment score
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@field ref_begin1 0-based best alignment beginning position on reference; ref_begin1 = -1 when the best alignment beginning
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position is not available
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@field ref_end1 0-based best alignment ending position on reference
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@field read_begin1 0-based best alignment beginning position on read; read_begin1 = -1 when the best alignment beginning
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position is not available
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@field read_end1 0-based best alignment ending position on read
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@field read_end2 0-based sub-optimal alignment ending position on read
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@field cigar best alignment cigar; stored the same as that in BAM format, high 28 bits: length, low 4 bits: M/I/D (0/1/2);
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cigar = 0 when the best alignment path is not available
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@field cigarLen length of the cigar string; cigarLen = 0 when the best alignment path is not available
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/*! @function Create the query profile using the query sequence.
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@param read pointer to the query sequence; the query sequence needs to be numbers
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@param readLen length of the query sequence
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@param mat pointer to the substitution matrix; mat needs to be corresponding to the read sequence
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@param n the square root of the number of elements in mat (mat has n*n elements)
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@param score_size estimated Smith-Waterman score; if your estimated best alignment score is surely < 255 please set 0; if
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your estimated best alignment score >= 255, please set 1; if you don't know, please set 2
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@return pointer to the query profile structure
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@note example for parameter read and mat:
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If the query sequence is: ACGTATC, the sequence that read points to can be: 1234142
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Then if the penalty for match is 2 and for mismatch is -2, the substitution matrix of parameter mat will be:
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mat is the pointer to the array {2, -2, -2, -2, -2, 2, -2, -2, -2, -2, 2, -2, -2, -2, -2, 2}
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s_profile* ssw_init (const int8_t* read, const int32_t readLen, const int8_t* mat, const int32_t n, const int8_t score_size);
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/*! @function Release the memory allocated by function ssw_init.
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@param p pointer to the query profile structure
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void init_destroy (s_profile* p);
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// @function ssw alignment.
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/*! @function Do Striped Smith-Waterman alignment.
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@param prof pointer to the query profile structure
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@param ref pointer to the target sequence; the target sequence needs to be numbers and corresponding to the mat parameter of
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@param refLen length of the target sequence
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@param weight_gapO the absolute value of gap open penalty
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@param weight_gapE the absolute value of gap extension penalty
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@param flag bitwise FLAG; (from high to low) bit 5: when setted as 1, function ssw_align will return the best alignment
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beginning position; bit 6: when setted as 1, if (ref_end1 - ref_begin1 < filterd && read_end1 - read_begin1
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< filterd), (whatever bit 5 is setted) the function will return the best alignment beginning position and
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cigar; bit 7: when setted as 1, if the best alignment score >= filters, (whatever bit 5 is setted) the function
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will return the best alignment beginning position and cigar; bit 8: when setted as 1, (whatever bit 5, 6 or 7 is
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setted) the function will always return the best alignment beginning position and cigar
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@param filters score filter: when bit 7 of flag is setted as 1 and bit 8 is setted as 0, filters will be used (Please check the
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decription of the flag parameter for detailed usage.)
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@param filterd distance filter: when bit 6 of flag is setted as 1 and bit 8 is setted as 0, filterd will be used (Please check
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the decription of the flag parameter for detailed usage.)
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@param maskLen The distance between the optimal and suboptimal alignment ending position >= maskLen. We suggest to use
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readLen/2, if you don't have special concerns. Note: maskLen has to be >= 15, otherwise this function will NOT
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return the suboptimal alignment information. Detailed description of maskLen: After locating the optimal
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alignment ending position, the suboptimal alignment score can be heuristically found by checking the second
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largest score in the array that contains the maximal score of each column of the SW matrix. In order to avoid
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picking the scores that belong to the alignments sharing the partial best alignment, SSW C library masks the
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reference loci nearby (mask length = maskLen) the best alignment ending position and locates the second largest
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score from the unmasked elements.
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@return pointer to the alignment result structure
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@note Whatever the parameter flag is setted, this function will at least return the optimal and sub-optimal alignment score,
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and the optimal alignment ending positions on target and query sequences. If both bit 6 and 7 of the flag are setted
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while bit 8 is not, the function will return cigar only when both criteria are fulfilled. All returned positions are
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s_align* ssw_align (const s_profile* prof,
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const uint8_t weight_gapO,
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const uint8_t weight_gapE,
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const uint16_t filters,
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const int32_t filterd,
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const int32_t maskLen);
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/*! @function Release the memory allocated by function ssw_align.
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@param a pointer to the alignment result structure
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void align_destroy (s_align* a);
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#endif // __cplusplus
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removed
src/ssw.h
