27 lines
783 B
C
27 lines
783 B
C
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#ifndef UPPERBAND_H_
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#define UPPERBAND_H_
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// TODO doc
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#include <stdbool.h>
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#include <stdio.h>
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#include "obiblob.h"
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#include "obiview.h"
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#include "obidmscolumn.h"
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typedef struct {
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unsigned char* table; // 4mer occurrence table built using the build_table function
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int32_t over; // count of 4mers with an occurrence greater than 255 (overflow)
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} Kmer_table_t, *Kmer_table_p;
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Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col, index_t seq_idx);
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void align_filters(Kmer_table_p ktable, Obi_blob_p seq1, Obi_blob_p seq2, index_t idx1, index_t idx2, double threshold, bool normalize, int reference, bool similarity_mode, double* score, int* LCSmin, bool can_be_identical);
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void free_kmer_tables(Kmer_table_p ktable, size_t count);
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#endif
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