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// Copyright © 2016 by Justin Bedő
//
// Permission to use, copy, modify, and/or distribute this software for
// any purpose with or without fee is hereby granted, provided that the
// above copyright notice and this permission notice appear in all copies.
//
// THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL
// WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED
// WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR
// BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES
// OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS,
// WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION,
// ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS
// SOFTWARE.
//
#include<fcntl.h>
#include<stdint.h>
#include<stdio.h>
#include<stdlib.h>
#include<string.h>
#include<sys/mman.h>
#include<sys/stat.h>
#include<sys/types.h>
#include<unistd.h>
#include<zlib.h>
#include"dict.h"
//#define BITMIX
typedef enum {
TINSEQ,
TOUTSEQ
} TState;
typedef struct {
gzFile f;
TState s;
} tokeniser;
tokeniser*
new_tokeniser(char *path)
{
tokeniser *tok = malloc(sizeof(tokeniser));
if(tok == NULL)
error("new_tokeniser");
tok->f = gzopen(path, "rb");
if(tok->f == NULL)
error("gzopen");
tok->s = TOUTSEQ;
return tok;
}
int
getTok(tokeniser *tok)
{
int c;
switch(tok->s){
case TOUTSEQ:
c = gzgetc(tok->f);
while(c != -1 && c != '@') c = gzgetc(tok->f);
while(c != -1 && c != '\n') c = gzgetc(tok->f);
tok->s = TINSEQ;
case TINSEQ:
c = gzgetc(tok->f);
while(c != -1 && c == '\n') c = gzgetc(tok->f);
switch(c){
case -1:
return -1;
case 'A':
case 'a':
return 0;
case 'C':
case 'c':
return 1;
case 'G':
case 'g':
return 2;
case 'T':
case 't':
return 3;
case '+':
tok->s = TOUTSEQ;
default:
return -2;
}
}
}
void
usage(char *name)
{
fprintf(stderr, "usage: %s <input fastq> <bloom output>\n", name);
exit(-1);
}
inline
uint64_t bitmix(uint64_t x)
{
x ^= x >> 31;
x *= 0x7fb5d329728ea185;
x ^= x >> 27;
x *= 0x81dadef4bc2dd44d;
x ^= x >> 33;
return x;
}
int
main(int argc, char **argv)
{
if(argc != 3)
usage(argv[0]);
tokeniser *t = new_tokeniser(argv[1]);
// map bloom filter
uint64_t *bloom;
if(access(argv[2], F_OK) == -1){
int bfd = open(argv[2], O_RDWR | O_CREAT, S_IRUSR | S_IWUSR);
if(bfd == -1)
error("open");
if(ftruncate(bfd, BLOOMSIZE * sizeof(uint64_t)) == -1)
error("ftruncate");
bloom = (uint64_t *)mmap(NULL, BLOOMSIZE * sizeof(uint64_t), PROT_WRITE, MAP_SHARED, bfd, 0);
if(bloom == MAP_FAILED)
error("mmap");
bzero(bloom, BLOOMSIZE * sizeof(uint64_t));
}else{
struct stat sb;
int bfd = open(argv[2], O_RDWR);
if(bfd == -1)
error("open");
if(fstat(bfd, &sb) == -1)
error("fstat");
if(sb.st_size != BLOOMSIZE * sizeof(uint64_t)){
fprintf(stderr, "incompatible bloom table\n");
return -1;
}
bloom = (uint64_t *)mmap(NULL, BLOOMSIZE * sizeof(uint64_t), PROT_WRITE, MAP_SHARED, bfd, 0);
if(bloom == MAP_FAILED)
error("mmap");
}
int tok;
uint64_t term = 0;
int bits;
while((tok = getTok(t)) != -1){
if(tok < 0){
term = 0;
continue;
}
term ^= term << 3;
term += tok;
//term = (term * 16777619) ^ tok;
#ifdef BITMIX
bits = bitmix(term);
#else
bits = term;
#endif
if(!bit(bloom,bits)){
term = 0;
set(bloom,bits);
}
}
int cnt = 0;
for(int i = 0; i < BLOOMSIZE; i++)
cnt += __builtin_popcountll(bloom[i]);
printf("%d bits out of %d set\n", cnt, BLOOMSIZE * 64);
}
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