seperate function for getting a rare value

4 files changed, 66 insertions, 54 deletions

diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c
index 9a9ee88..1ae1802 100644
--- a/src/c/multifasta_to_otu.c
+++ b/src/c/multifasta_to_otu.c
@@ -21,10 +21,6 @@
 
 #define USAGE "Usage:\n\tmultifasta_to_otu [OPTION...] - create a QIIME OTU table based on Quikr results. \n\nOptions:\n\n-i, --input-directory\n\tthe directory containing the samples' fasta files of reads (note each file should correspond to a separate sample)\n\n-f, --input-filelist\n\ta file containing list of fasta files to process seperated by newline (same rules apply as input-directory)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (sensing from quikr_train)\n\n-k, --kmer\n\tspecify what size of kmer to use. (default value is 6)\n\n-l, --lambda\n\tlambda value to use. (default value is 10000)\n\n-j, --jobs\n\t specifies how many jobs to run at once. (default value is the number of CPUs)\n\n-o, --output\n\tthe OTU table, with NUM_READS_PRESENT for each sample which is compatible with QIIME's convert_biom.py (or a sequence table if not OTU's)\n\n-v, --verbose\n\tverbose mode.\n\n-V, --version\n\tprint version."
 
-static int cmp (const void * a, const void * b) {
-	return ( *(double*)a - *(double*)b );
-}
-
 char **get_fasta_files_from_file(char *fn) {
 	char **files;
 	int files_count = 0;
@@ -336,7 +332,7 @@ int main(int argc, char **argv) {
 
 		printf("Beginning to process samples\n");
 
-	#pragma omp parallel for shared(solutions, sensing_matrix_ptr, width, done, sequences)
+	#pragma omp parallel for shared(solutions, sensing_matrix_ptr, done)
 	for(size_t i = 0; i < dir_count; i++ ) {
 
 		size_t x = 0;
@@ -356,8 +352,6 @@ int main(int argc, char **argv) {
 		// load counts matrix
 		double *count_matrix = malloc(width * sizeof(double));
 		check_malloc(count_matrix, NULL);
-		double *sorted_count_matrix = malloc(width * sizeof(double));
-		check_malloc(sorted_count_matrix, NULL);
 
 		// convert our matrix into  doubles
 		{
@@ -365,33 +359,13 @@ int main(int argc, char **argv) {
 
 			for(x = 0; x < width; x++) {
 				count_matrix[x] = (double)integer_counts[x];
-				sorted_count_matrix[x] = count_matrix[x];
 			}
 
 			free(integer_counts);
 		}
 
-		// sort our array
-		qsort(sorted_count_matrix, width, sizeof(double), cmp);
-
-		// get our "rare" counts
-		for(y = 0; y < width; y++) {
-			double percentage = 0;
-
-			rare_value = sorted_count_matrix[y];
-			rare_width = 0;
-			for(x = 0; x < width; x++) {
-				if(count_matrix[x] <= rare_value) {
-					rare_width++;
-				}
-			}
-			percentage = (double)rare_width / (double)width;
-
-			if(percentage >= rare_percent)
-				break;
-		}
-		
-		free(sorted_count_matrix);
+		// get_rare_value
+		get_rare_value(count_matrix, width, rare_percent, &rare_value, &rare_width);
 
 		if(verbose)
 			printf("there are %llu values less than %llu\n", rare_width, rare_value);
diff --git a/src/c/quikr.c b/src/c/quikr.c
index 0e15c5b..fd1fbe5 100644
--- a/src/c/quikr.c
+++ b/src/c/quikr.c
@@ -11,7 +11,6 @@
 #include "quikr_functions.h"
 #include "quikr.h"
 
-#define sensing_matrix(i,j) (sensing_matrix[width*i + j])
 #define USAGE "Usage:\n\tquikr [OPTION...] - Calculate estimated frequencies of bacteria in a sample.\n\nOptions:\n\n-i, --input\n\tthe sample's fasta file of NGS READS (fasta format)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (trained from quikr_train)\n\n-k, --kmer\n\tspecify what size of kmer to use. (default value is 6)\n\n-l, --lambda\n\tlambda value to use. (default value is 10000)\n\n-o, --output\n\tOTU_FRACTION_PRESENT a vector representing the percentage of database sequence's presence in sample. (csv output)\n\n-v, --verbose\n\tverbose mode.\n\n-V, --version\n\tprint version."
 
 int main(int argc, char **argv) {
@@ -29,7 +28,6 @@ int main(int argc, char **argv) {
 	unsigned long long rare_value = 0;
 	unsigned long long rare_width = 0;
 
-	double percentage = 1.0;
 	double rare_percent = 1.0;
 
 	unsigned long long width = 0;
@@ -116,7 +114,6 @@ int main(int argc, char **argv) {
 	}
 
 	if(verbose) {
-		printf("rare width:%llu\n", rare_width);
 		printf("kmer: %u\n", kmer);
 		printf("lambda: %llu\n", lambda);
 		printf("fasta: %s\n", input_fasta_filename);
@@ -142,53 +139,51 @@ int main(int argc, char **argv) {
 	// 4 "ACGT" ^ Kmer gives us the size of output rows
 	width = pow_four(kmer);
 
+	// load sensing matrix
+	struct matrix *sensing_matrix = load_sensing_matrix(sensing_matrix_filename, kmer);
+
+	if(verbose) {
+		printf("width: %llu\n", width);
+		printf("sequences: %llu\n", sensing_matrix->sequences);
+	}
+
+
+
 	// load counts matrix
 	double *count_matrix = malloc(width * sizeof(double));
 	check_malloc(count_matrix, NULL);
 
+	// convert our matrix into doubles
 	{
 		unsigned long long *integer_counts = get_kmer_counts_from_file(input_fasta_filename, kmer);
 
-		for(x = 0; x < width; x++)
+		for(x = 0; x < width; x++) {
 			count_matrix[x] = (double)integer_counts[x];
+		}
 
 		free(integer_counts);
 	}
 
-	// load sensing matrix
-	struct matrix *sensing_matrix = load_sensing_matrix(sensing_matrix_filename, kmer);
-
-	// get our "rare" counts
-	while(1) {
-		rare_width = 0;
-		for(x = 0; x < width; x++) {
-			if(count_matrix[x] < rare_value) {
-				rare_width++;
-			}
-		}
-		percentage = (float)rare_width / (float)width;
-
-		if(percentage >= rare_percent)
-			break;
-
-		rare_value++;
-	}
+	// get_rare_value
+	get_rare_value(count_matrix, width, rare_percent, &rare_value, &rare_width);
 
 	if(verbose)
 		printf("there are %llu values less than %llu\n", rare_width, rare_value);
 
-	// add a extra space for our zero's array
+	// add a extra space for our zero's array, so we can set the first column to 1's
 	rare_width++;
 
 	// store our count matrix
 	double *count_matrix_rare = calloc(rare_width, sizeof(double));
 	check_malloc(count_matrix_rare, NULL);
 
-	double *sensing_matrix_rare = malloc((rare_width) * sensing_matrix->sequences * sizeof(double));
+	double *sensing_matrix_rare = calloc(rare_width * sensing_matrix->sequences, sizeof(double));
 	check_malloc(sensing_matrix_rare, NULL);
 
 	// copy only kmers from our original counts that match our rareness percentage
 	// in both our count matrix and our sensing matrix
+	//
+	// y = 1 because we are offsetting the arrah by 1, so we can set the first row to all 1's
 	for(x = 0, y = 1;  x < width; x++) {
 		if(count_matrix[x] <= rare_value) {
 			count_matrix_rare[y] = count_matrix[x];
@@ -200,6 +195,7 @@ int main(int argc, char **argv) {
 		}
 	}
 
+
 	// normalize our kmer counts and our sensing_matrix
 	normalize_matrix(count_matrix_rare, 1, rare_width);
 	normalize_matrix(sensing_matrix_rare, sensing_matrix->sequences, rare_width);
@@ -208,6 +204,7 @@ int main(int argc, char **argv) {
 	for(x = 1; x < rare_width; x++)
 		count_matrix_rare[x] *= lambda;
 
+	//TODO use one loop
 	for(x = 0; x < sensing_matrix->sequences; x++) {
 		for(y = 1; y < rare_width; y++) {
 			sensing_matrix_rare[rare_width*x + y] *= lambda;
@@ -221,7 +218,6 @@ int main(int argc, char **argv) {
 		sensing_matrix_rare[x*rare_width] = 1.0;
 	}
 
-	// run NNLS
 	double *solution = nnls(sensing_matrix_rare, count_matrix_rare, sensing_matrix->sequences, rare_width);
 
 	// normalize our solution vector
diff --git a/src/c/quikr_functions.c b/src/c/quikr_functions.c
index 061d3b8..5bbe913 100644
--- a/src/c/quikr_functions.c
+++ b/src/c/quikr_functions.c
@@ -10,6 +10,7 @@
 #include "kmer_utils.h"
 #include "quikr.h"
 
+
 void check_malloc(void *ptr, char *error) {
 	if (ptr == NULL) {
 		if(error != NULL)  {
@@ -20,6 +21,44 @@ void check_malloc(void *ptr, char *error) {
 		exit(EXIT_FAILURE);
 	}
 }
+static int double_cmp (const void * a, const void * b) {
+	return ( *(double*)a - *(double*)b );
+}
+
+void get_rare_value(double *count_matrix, unsigned long long width, double rare_percent, unsigned long long *ret_rare_value, unsigned long long  *ret_rare_width) { 
+	size_t y, x;
+	unsigned long long rare_width = 0;
+	double rare_value = 0;
+
+	// allocate * sort a temporary matrix
+	double *sorted_count_matrix = malloc(width * sizeof(double));
+	check_malloc(sorted_count_matrix, NULL);
+
+	memcpy(sorted_count_matrix, count_matrix, width * sizeof(double));
+
+	qsort(sorted_count_matrix, width, sizeof(double), double_cmp);
+
+	// get our "rare" counts
+	for(y = 0; y < width; y++) {
+		double percentage = 0;
+
+		rare_value = sorted_count_matrix[y];
+		rare_width = 0;
+		for(x = 0; x < width; x++) {
+			if(count_matrix[x] <= rare_value) {
+				rare_width++;
+			}
+		}
+		percentage = (double)rare_width / (double)width;
+
+		if(percentage >= rare_percent)
+			break;
+	}
+
+	free(sorted_count_matrix);
+	*ret_rare_width = rare_width;
+	*ret_rare_value = rare_value;
+}
 
 void debug_arrays(double *count_matrix, struct matrix *sensing_matrix) {
 	FILE *count_fh = fopen("count.mat", "w");
diff --git a/src/c/quikr_functions.h b/src/c/quikr_functions.h
index 369d68c..978f614 100644
--- a/src/c/quikr_functions.h
+++ b/src/c/quikr_functions.h
@@ -9,3 +9,6 @@ void normalize_matrix(double *matrix, int height, int width);
 
 // load a sensing matrix  
 struct matrix *load_sensing_matrix(const char *filename, unsigned int target_kmer);
+
+// get_rare_value 
+void get_rare_value(double *count_matrix, unsigned long long width, double rare_percent, unsigned long long *ret_rare_value, unsigned long long  *ret_rare_width);