From 07b1eefa80db51e39bea1735b3ff4da0ae79179c Mon Sep 17 00:00:00 2001
From: Calvin <calvin@EESI>
Date: Wed, 15 May 2013 13:43:39 -0400
Subject: use zlib natively for sanity, and remove some crap, update makefile
with -lz
---
src/c/Makefile | 2 +-
src/c/quikr_functions.c | 26 ++++++++------------------
2 files changed, 9 insertions(+), 19 deletions(-)
(limited to 'src/c')
diff --git a/src/c/Makefile b/src/c/Makefile
index ba0c799..152121a 100644
--- a/src/c/Makefile
+++ b/src/c/Makefile
@@ -1,7 +1,7 @@
UNAME := $(shell uname)
CC = gcc
QUIKR_TRAIN_CFLAGS = -O3 -s -mtune=native -Wall -lm -lz -D$(UNAME)
-QUIKR_CFLAGS = -O3 -s -mtune=native -Wextra -Wall -lm -pthread -L../ -I../ -std=gnu99 -fopenmp -D$(UNAME)
+QUIKR_CFLAGS = -O3 -s -mtune=native -Wextra -Wall -lm -pthread -L../ -I../ -std=gnu99 -fopenmp -D$(UNAME) -lz
all: quikr_train_ quikr_ multifasta_to_otu_
multifasta_to_otu_:
diff --git a/src/c/quikr_functions.c b/src/c/quikr_functions.c
index 7e18e64..31afb3b 100644
--- a/src/c/quikr_functions.c
+++ b/src/c/quikr_functions.c
@@ -6,6 +6,7 @@
#include <unistd.h>
#include <string.h>
#include <math.h>
+#include <zlib.h>
int count_sequences(char *filename) {
char command[512];
@@ -86,19 +87,14 @@ double *load_sensing_matrix(char *filename, int height, int width) {
int x = 0;
int y = 0;
- char *line = NULL;
- char *val;
- char command[512];
- size_t len = 0;
- FILE *sensing_matrix_fh = NULL;
+ gzFile sensing_matrix_fh = NULL;
double *sensing_matrix = malloc(height * width * sizeof(double));
if(sensing_matrix == NULL) {
fprintf(stderr, "Could not allocate memory for the sensing matrix\n");
}
- sprintf(command, "gzip -cd %s", filename);
- sensing_matrix_fh = popen(command, "r");
+ sensing_matrix_fh = gzopen(filename, "r");
if(sensing_matrix_fh == NULL) {
fprintf(stderr, "could not open %s", filename);
exit(EXIT_FAILURE);
@@ -106,20 +102,14 @@ double *load_sensing_matrix(char *filename, int height, int width) {
// read our sensing matrix in
for(x = 0; x < height; x++) {
- getline(&line, &len, sensing_matrix_fh);
- char *ptr;
-
- // Read our first element in outside of the loop
- val = strtok_r(line,"\t", &ptr);
- sensing_matrix[width*x + 1] = atof(val);
- // iterate through and load the array
- for (y = 2; y < width; y++) {
- val = strtok_r(NULL, "\t", &ptr);
- sensing_matrix[width*x + y] = atof(val);
+ for (y = 1; y < width; y++) {
+ char buffer[14];
+ gzgets(sensing_matrix_fh, buffer, 14);
+ sensing_matrix[width*x + y] = atof(buffer);
}
}
- pclose(sensing_matrix_fh);
+ gzclose(sensing_matrix_fh);
return sensing_matrix;
}
--
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