42 lines
1.4 KiB
Common Lisp
42 lines
1.4 KiB
Common Lisp
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inline static int string_index(__global char *s, char c) {
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int i = 0;
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while (1) {
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if (s[i] == c)
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return i;
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++i;
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}
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}
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kernel __attribute__((reqd_work_group_size(1, 1, 1)))
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void fmindex(__global char *bwt,
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__global char *alphabet,
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__global unsigned *ranks,
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__global unsigned *sa,
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__global unsigned *ranges,
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__global char *patterns,
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__global unsigned long *out,
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size_t bwt_sz, size_t alphabet_sz, unsigned pattern_count,
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unsigned pattern_sz, unsigned out_sz) {
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for (unsigned i = 0; i < pattern_count; ++i) {
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int p_idx = pattern_sz - 1;
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char c = patterns[i * pattern_sz + p_idx];
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unsigned start = ranges[2 * string_index(alphabet, c)];
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unsigned end = ranges[2 * string_index(alphabet, c) + 1];
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p_idx -= 1;
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while (p_idx >= 0 && end > 1) {
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c = patterns[i * pattern_sz + p_idx];
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unsigned range_start = ranges[2 * string_index(alphabet, c)];
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int alphabet_idx = string_index(alphabet, c);
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start = range_start + ranks[alphabet_sz * (start - 1) + alphabet_idx];
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end = range_start + ranks[alphabet_sz * (end - 1) + alphabet_idx];
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p_idx -= 1;
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}
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unsigned long match_count = end - start;
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out[i * out_sz] = match_count;
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for (unsigned j = 0; j < match_count; ++j)
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out[i * out_sz + j + 1] = sa[start + j];
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}
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}
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