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

line count) when building kmer table of one column

src/upperband.c

@@ -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;

src/upperband.h

@@ -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);