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Added function to build kmer table for 2 columns, and fixed bug (with

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line count) when building kmer table of one column
This commit is contained in:
Celine Mercier
2016-12-16 19:10:18 +01:00
parent 490f5fe6b9
commit 303bd6f445
2 changed files with 43 additions and 3 deletions
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42
src/upperband.c
View File

@ -8,8 +8,6 @@
#include "obidmscolumn.h"
#include "obiview.h"
//#include "../libutils/utilities.h"
//#include "../libfasta/sequence.h"
inline static uchar_v hash4m128(uchar_v frag)
@ -242,7 +240,7 @@ Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col, index_t se
fprintf(stderr,"Building kmer tables...");
seq_count = (seq_col->header)->lines_used;
seq_count = (view->infos)->line_count;
// Allocate memory for the table structure
ktable = (Kmer_table_p) malloc(sizeof(Kmer_table_t) * seq_count);
@ -267,6 +265,44 @@ Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col, index_t se
}
Kmer_table_p hash_two_seq_columns(Obiview_p view1, OBIDMS_column_p seq1_col, index_t seq1_idx,
Obiview_p view2, OBIDMS_column_p seq2_col, index_t seq2_idx)
{
size_t seq1_count;
size_t seq2_count;
Kmer_table_p ktable1;
Kmer_table_p ktable2;
Kmer_table_p ktable;
seq1_count = (view1->infos)->line_count;
seq2_count = (view2->infos)->line_count;
// Build the two tables then concatenate them
ktable1 = hash_seq_column(view1, seq1_col, seq1_idx);
if (ktable1 == NULL)
return NULL;
ktable2 = hash_seq_column(view2, seq2_col, seq2_idx);
if (ktable2 == NULL)
return NULL;
// Realloc to hold the 2 tables
ktable = realloc(ktable1, sizeof(Kmer_table_t) * (seq1_count + seq2_count));
if (ktable == NULL)
{
free_kmer_tables(ktable2, seq2_count);
return NULL;
}
// Concatenate
memcpy(ktable+seq1_count, ktable2, sizeof(Kmer_table_t) * seq2_count);
// Free copied table
free(ktable2);
return ktable;
}
void free_kmer_tables(Kmer_table_p ktable, size_t count)
{
size_t i;

4
src/upperband.h
View File

@ -18,7 +18,11 @@ typedef struct {
} Kmer_table_t, *Kmer_table_p;
// TODO doc
Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col, index_t seq_idx);
Kmer_table_p hash_two_seq_columns(Obiview_p view1, OBIDMS_column_p seq1_col, index_t seq1_idx,
Obiview_p view2, OBIDMS_column_p seq2_col, index_t seq2_idx);
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);
void free_kmer_tables(Kmer_table_p ktable, size_t count);