filterReads.c

#include <zlib.h>
#include <stdio.h>
#include <string.h>
#include "kseq.h"
#include "khash.h"

KSEQ_INIT(gzFile, gzread);
KHASH_SET_INIT_STR(s)
#define BUF_SIZE 2048

char *strstrip(char *s)
{
        size_t size;
        char *end;

        size = strlen(s);

        if (!size)
                return s;

        end = s + size - 1;
        while (end >= s && isspace(*end))
                end--;
        *(end + 1) = '\0';

        while (*s && isspace(*s))
                s++;

        return s;
}


int main(int argc , char *argv[])
{
	//declare variable
	char buf[BUF_SIZE];
	gzFile fp;
	kseq_t *seq;
	int lineno = 0, flag = 0, ret,l;
	char *id, *sequence, *qual, *comment;
	khash_t(s) *h;
	khint_t k;
	

	// print usage if not enough argumnets
	if (argc != 3)
	{
		fprintf(stderr,"Usage: %s <fastq file> <idFile>\n",argv[0]);
		return 1;
	}
	printf("Reading file: %s...\n" ,argv[2] );

	//idFile read
	h = kh_init(s);
	fp = fopen(argv[2], "rb"); // FIXME: check fp
	while (fgets(buf, BUF_SIZE, fp))
	{
		kh_put(s, h, strstrip(strdup(buf)), &ret);	// FIXME: check ret
	}
	fclose(fp);


	//open fastq file
	fp = gzopen(argv[1],"r");
	seq = kseq_init(fp);

	// start reading sequecne
	while ((l = kseq_read(seq)) >= 0)
	{
		id = seq -> name.s;
		comment = seq -> comment.s;
		qual = seq -> qual.s;
		sequence = seq -> seq.s;
		flag = (kh_get(s, h, id) == kh_end(h));
		if (flag==1){
			printf("@%s\t%s\n%s\n+\n%s\n", id,comment,sequence,qual);
		}
	}
	kh_destroy(s,h);
}