finding the fastest way to extract from a fastq

fqextract.c

#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include "khash.h" // khash.h from samtools/bwa/seqtk/klib
KHASH_SET_INIT_STR(s)

#define BUF_SIZE 4096

int main(int argc, char *argv[])
{
    char buf[BUF_SIZE];
    FILE *fp;
    int lineno = 0, flag = 0, ret;
    khash_t(s) *h;
    if (argc == 1) {
        fprintf(stderr, "Usage: cat in.fq | fqextract <name.lst>\n");
        return 1;
    }
    h = kh_init(s);
    fp = fopen(argv[1], "rb"); // FIXME: check fp
    while (fgets(buf, BUF_SIZE, fp))
        kh_put(s, h, strdup(buf), &ret); // FIXME: check ret
    fclose(fp);
    while (fgets(buf, BUF_SIZE, stdin)) {
        if (++lineno%4 == 1)
            flag = (kh_get(s, h, buf + 1) != kh_end(h));
        if (flag) fputs(buf, stdout);
    }
    kh_destroy(s, h); // FIXME: free keys before destroy
    return 0;
}

Makefile

CC=gcc
FLAGS=-O3 -Wall
FQ=input.fastq
LIST=list.txt
TMP=/stornext/snfs0/next-gen/Illumina/Instruments/700733/110803_SN733_0151_BD07UMACXX/Results/Project_110803_SN733_0151_BD07UMACXX/Sample_D07UMACXX-8-ID12/D07UMACXX-8-ID12_1_sequence.txt
uname_S := $(shell sh -c 'uname -s 2>/dev/null || echo not')

ifeq ($(uname_S),Linux)
	O_FQ=$(TMP)
	SED=sed
else
	O_FQ=/Users/drio/sshfs/ardmore$(TMP)
	SED=gsed
endif

ifndef N_READS
	N_READS=1000000
endif

BIN=fqextract
BIN_MM=mmap_fqextract
LINE=@printf '_________________________________________________ ';

all: clean run

run: $(FQ) $(LIST) $(BIN) $(BIN_MM) out.txt out_mmap.txt diff

diff: out.txt out_mmap.txt
	$(LINE) echo "DIFF"
	diff $+ | wc -l

out.txt: $(FQ) $(BIN) $(LIST)
	$(LINE) echo "BM: $(BIN)"
	time cat $(FQ) | ./$(BIN) $(LIST) > out.txt

out_mmap.txt: $(FQ) $(BIN_MM) $(LIST)
	$(LINE) echo "BM: $(BIN_MM)"
	time ./$(BIN_MM) $(LIST) $(FQ) > out_mmap.txt

khash.h:
	curl https://raw.github.com/attractivechaos/klib/master/khash.h > $@

$(FQ): $(O_FQ)
	time head -$(N_READS) $< | awk '{print $$1}' > $@
	@echo "Number of reads: `cat $@ | egrep -e "^@HWI" | wc -l`"

$(LIST): $(FQ)
	egrep -e "^@HWI" $< | awk '{print $$1}' | $(SED) -s 's/@//' |\
	ruby -ne 'puts $$_ if rand(1000) % 5 == 0' > $@
	wc -l $@

$(BIN): $(BIN).c khash.h
	$(CC) $(FLAGS) $< -o $@

$(BIN_MM): $(BIN_MM).c khash.h
	$(CC) $(FLAGS) $< -o $@

clean:
	rm -f out* $(LIST) $(FQ) $(BIN) $(BIN_MM)

.PHONY: clean

mmap_fqextract.c

#include <stdio.h>
#include <string.h>
#include <stdlib.h>

#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <unistd.h>
#include <sys/mman.h>

#include "khash.h" // khash.h from samtools/bwa/seqtk/klib
KHASH_SET_INIT_STR(s)

#define BUF_SIZE 4096

int main(int argc, char *argv[])
{
  char buf[BUF_SIZE];
  int fd;
  int lineno = 0, flag = 0, ret, bp = 0;
  struct stat sb;
  char *p, *mp; // start of mmap data, pointer within the mmap data
  off_t len;

  khash_t(s) *h;
  if (argc == 2) {
    fprintf(stderr, "Usage: fqextract <name.lst> <in.fq>\n");
    return 1;
  }

  h = kh_init(s);

  fd = open(argv[1], O_RDONLY); // FIXME: check fp
  fstat(fd, &sb);
  p = mmap(0, sb.st_size, PROT_READ, MAP_SHARED, fd, 0);
  close(fd);

  for (len=0; len < sb.st_size; len++) {
    if (p[len] == '\n') {
      buf[bp] = '\0';
      bp = 0;
      kh_put(s, h, strdup(buf), &ret); // FIXME: check ret
    }
    else
      buf[bp++] = p[len];
  }
  munmap(p, sb.st_size);

  fd = open(argv[2], O_RDWR); // FIXME: check fp
  fstat(fd, &sb);
  p = mmap(0, sb.st_size, PROT_WRITE, MAP_SHARED, fd, 0);
  close(fd);

  for (len=0, mp=p, lineno=0; len < sb.st_size; len++) {
    if (p[len] == '\n') {
      if (lineno == 0) {
        p[len] = '\0';
        flag = (kh_get(s, h, mp+1) != kh_end(h));
        p[len] = '\n';
        lineno = 1;
      }
      else if (lineno == 3)  {
        p[len+1] = '\0';
        if (flag) fputs(mp, stdout);
        p[len+1] = '@';
        mp = p + len + 1;
        lineno = 0;
      }
      else {
        lineno++;
      }
    }
  }
  munmap(p, sb.st_size);

  kh_destroy(s, h); // FIXME: free keys before destroy
  return 0;
}

I do not understand how to use this program...

I downloaded it and tried 'make all' but it failed with this error :
make: *** No rule to make target /stornext/snfs0/next-gen/Illumina/Instruments/700733/110803_SN733_0151_BD07UMACXX/Results/Project_110803_SN733_0151_BD07UMACXX/Sample_D07UMACXX-8-ID12/D07UMACXX-8-ID12_1_sequence.txt', needed by input.fastq'. Stop.

Am I not supposed to build it ?

Any help would be very much appreciated.

Thanks !