first stuff

configure.ac

+dnl Process this file with autoconf to produce a configure script.
+
+AC_PREREQ(2.59)
+AC_INIT(rock, 1.0)
+
+
+AC_CANONICAL_SYSTEM
+AM_INIT_AUTOMAKE()
+
+AC_PROG_CC
+
+AC_CONFIG_FILES(Makefile src/Makefile)
+AC_OUTPUT
+

src/Makefile.am

+bin_PROGRAMS=rock
+bin_SOURCES=rock.c
+

src/rock.c

+/*
+ ============================================================================
+ Name        : rock.c
+ Author      : Véronique Legrand
+ Version     :
+ Copyright   : Your copyright notice
+ Description : Hello World in C, Ansi-style
+ ============================================================================
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <fcntl.h>
+#include <unistd.h>
+
+int main(void) {
+	/* 1rst step : read a fastq and compute quality score for each record (PE or single) */
+    char * fq_pe1="../data/LM201200065_S106_R1.TM.fq";
+    char * fq_pe2="../data/LM201200065_S106_R2.TM.fq";
+    char * fq_s="../data/LM201200065_S106_RS.TM.fq";
+
+    size_t bufsize=10240;
+    char buf[bufsize];
+    mode_t mode = S_IRUSR | S_IWUSR | S_IRGRP | S_IROTH;
+
+    /* Let's start with the easiest case : single reads. */
+    int f_single=open(fq_s,O_RDONLY,mode);
+
+    /* for each read, we want : offset, filenb, total quality score. */
+    int nread=read(f_single,buf,bufsize);
+    while (nread!=0) {
+
+        nread=read(f_single,buf,bufsize);
+        printf("%s",buf);
+    }
+    close(f_single);
+	return EXIT_SUCCESS;
+}