-/*
- * This file is part of fastq-tools.
- *
- * Copyright (c) 2011 by Daniel C. Jones <dcjones@cs.washington.edu>
- *
- */
+
+#include <stdbool.h>
+#include <stdio.h>
+#include <string.h>
#include "parse.h"
#include "common.h"
-#include <stdlib.h>
-#include <ctype.h>
-
-static const size_t init_str_size = 128;
-static const size_t fastq_buf_size = 4096;
-static void fastq_alloc_str(str_t* s)
+static void str_init(str_t* str)
{
- s->s = malloc_or_die(init_str_size);
- s->s[0] = '\0';
- s->n = 0;
- s->size = init_str_size;
+ str->n = 0;
+ str->size = 128;
+ str->s = malloc_or_die(str->size = 0);
+ str->s[0] = '\0';
}
-static void fastq_expand_str(str_t* s)
+static void str_free(str_t* str)
{
- s->size *= 2;
- realloc_or_die(s->s, s->size);
+ free(str->s);
}
-seq_t* fastq_alloc_seq()
+/* Reserve space for `size` more characters. */
+static void str_reserve_extra(str_t* str, size_t size)
{
- seq_t* seq = malloc_or_die(sizeof(seq_t));
- fastq_alloc_str(&seq->id1);
- fastq_alloc_str(&seq->seq);
- fastq_alloc_str(&seq->id2);
- fastq_alloc_str(&seq->qual);
-
- return seq;
+ if (str->n + size > str->size) {
+ if (str->n + size > 2 * str->size) {
+ str->size = str->n + size;
+ }
+ else str->size *= 2;
+ str->s = realloc_or_die(str->s, str->size * sizeof(char));
+ }
}
-void fastq_free_seq(seq_t* seq)
+/* Copy n characters from c to the end of str. */
+static void str_append(str_t* str, char* c, size_t n)
{
- free(seq->id1.s);
- free(seq->seq.s);
- free(seq->id2.s);
- free(seq->qual.s);
- free(seq);
+ str_reserve_extra(str, n);
+ memcpy(str->s + str->n, c, n);
+ str->n += n;
+ str->s[str->n] = '\0';
}
-typedef enum
+seq_t* seq_create()
{
- STATE_EOF,
- STATE_ERROR,
- STATE_ID1,
- STATE_SEQ,
- STATE_ID2,
- STATE_QUAL
-
-} fastq_state;
-
-
-fastq_t* fastq_open(FILE* f)
-{
- fastq_t* fqf = malloc_or_die(sizeof(fastq_t));
- or_die((int)((fqf->file = gzdopen(fileno(f), "rb")) != NULL),
- "Can not open gzip file.");
-
- fqf->state = STATE_ID1;
- fqf->buf = malloc_or_die(fastq_buf_size);
- fqf->buf[0] = '\0';
- fqf->c = fqf->buf;
-
- return fqf;
+ seq_t* seq = malloc_or_die(sizeof(seq_t));
+ str_init(&seq->id1);
+ str_init(&seq->seq);
+ str_init(&seq->id2);
+ str_init(&seq->qual);
+ return seq;
}
-void fastq_close(fastq_t* fqf)
+void seq_free(seq_t* seq)
{
- gzclose(fqf->file);
- free(fqf->buf);
- free(fqf);
+ str_free(&seq->id1);
+ str_free(&seq->seq);
+ str_free(&seq->id2);
+ str_free(&seq->qual);
+ free(seq);
}
-void fastq_refill(fastq_t* f)
-{
- int errnum;
- const char* errmsg;
+static const size_t parser_buf_size = 1000000;
- int n = gzread(f->file, f->buf, fastq_buf_size - 1);
- if (n <= 0) {
- if (gzeof(f->file)) {
- f->state = STATE_EOF;
- n = 0;
- }
- else {
- errmsg = gzerror(f->file, &errnum);
- fprintf(stderr, "I/O error: %s\n", errmsg);
- exit(1);
- }
- }
+struct fastq_t_
+{
+ FILE* file;
+ size_t readlen;
+ char* buf;
+ char* next;
+ bool linestart;
+};
- f->buf[n] = '\0';
- f->c = f->buf;
-}
-void fastq_get_line(fastq_t* f, str_t* s)
+fastq_t* fastq_create(FILE* file)
{
- size_t i = 0;
-
- if (f->state == STATE_EOF) goto fastq_get_line_done;
-
- while (1) {
- switch (*f->c) {
- case '\0':
- fastq_refill(f);
- if (f->state == STATE_EOF) goto fastq_get_line_done;
- break;
-
- case '\r':
- f->c++;
- break;
-
- case '\n':
- goto fastq_get_line_done;
-
- default:
- while (s->size < i + 2) {
- fastq_expand_str(s);
- }
- if (s) s->s[i++] = *f->c;
- f->c++;
- }
-
- }
-
-fastq_get_line_done:
- if (s) {
- s->s[i] = '\0';
- s->n = i;
- }
+ fastq_t* f = malloc_or_die(sizeof(fastq_t));
+ f->file = file;
+ f->next = f->buf = malloc_or_die(parser_buf_size);
+ f->readlen = 0;
+ f->linestart = true;
+ return f;
}
-
-int fastq_next(fastq_t* f, seq_t* seq)
+void fastq_free(fastq_t* f)
{
- if (f->state == STATE_EOF) return 0;
+ free(f->buf);
+ free(f);
+}
- while (1) {
- /* read more, if needed */
- if (*f->c == '\0' ) {
- fastq_refill(f);
- if (f->state == STATE_EOF) return 0;
- continue;
- }
+typedef enum {
+ FASTQ_STATE_ID1, /* Reading ID1. */
+ FASTQ_STATE_SEQ, /* Reading the sequence. */
+ FASTQ_STATE_ID2, /* Reading ID2. */
+ FASTQ_STATE_QUAL, /* Reading quality scores. */
+} fastq_parser_state_t;
- /* skip over leading whitespace */
- else if (isspace(*f->c)) {
- /* do nothing */
- }
- /* skip comments */
- /*
- else if (*f->c == ';') {
- fastq_get_line(f, NULL);
- if (f->state == STATE_EOF) return 0;
- }
- */
-
- /* read id1 */
- else if (f->state == STATE_ID1) {
- if (*f->c == '@' || *f->c == '>') {
- f->c++;
- fastq_get_line(f, &seq->id1);
- if (f->state == STATE_EOF) return 0;
-
- f->state = STATE_SEQ;
- }
- else {
- fprintf(stderr,
- "Malformed FASTQ file: expecting an '@' or '>', saw a '%c'\n",
- *f->c);
- exit(1);
+bool fastq_read(fastq_t* f, seq_t* seq)
+{
+ seq->id1.n = seq->seq.n = seq->id2.n = seq->qual.n = 0;
+ fastq_parser_state_t state = FASTQ_STATE_ID1;
+ char* end = f->buf + f->readlen;
+ do {
+ while (f->next < end) {
+ /* Consume pointless special characters prefixing IDs */
+ if ((state == FASTQ_STATE_ID1 && f->linestart && f->next[0] == '@') ||
+ (state == FASTQ_STATE_ID2 && f->linestart && f->next[0] == '+')) {
+ f->linestart = false;
+ ++f->next;
+ continue;
}
- }
-
- /* read sequence */
- else if (f->state == STATE_SEQ) {
- fastq_get_line(f, &seq->seq);
- if (f->state == STATE_EOF) return 0;
-
- f->state = STATE_ID2;
- }
-
- /* read id2 */
- else if (f->state == STATE_ID2) {
- if (*f->c == '+') {
- f->c++;
- fastq_get_line(f, &seq->id2);
- if (f->state == STATE_EOF) return 0;
- f->state = STATE_QUAL;
+ char* u = memchr(f->next, '\n', end - f->next);
+ if (u == NULL) {
+ f->linestart = false;
+ u = end;
}
- else {
- /* fasta style entry */
- seq->id2.s[0] = '\0';
- seq->qual.s[0] = '\0';
-
- f->state = STATE_ID1;
- break;
+ else f->linestart = true;
+
+ switch (state) {
+ case FASTQ_STATE_ID1:
+ str_append(&seq->id1, f->next, u - f->next);
+ if (f->linestart) state = FASTQ_STATE_SEQ;
+ break;
+
+ case FASTQ_STATE_SEQ:
+ str_append(&seq->seq, f->next, u - f->next);
+ if (f->linestart) state = FASTQ_STATE_ID2;
+ break;
+
+ case FASTQ_STATE_ID2:
+ str_append(&seq->id2, f->next, u - f->next);
+ if (f->linestart) state = FASTQ_STATE_QUAL;
+ break;
+
+ case FASTQ_STATE_QUAL:
+ str_append(&seq->qual, f->next, u - f->next);
+ if (f->linestart) {
+ f->next = u + 1;
+ return true;
+ }
+ break;
}
- }
- /* read quality string */
- else if (f->state == STATE_QUAL) {
- fastq_get_line(f, &seq->qual);
- if (f->state == STATE_EOF) return 1;
-
- f->state = STATE_ID1;
- break;
+ f->next = u + 1;
}
- else {
- fputs("Inexplicable error in fastq parser.\n", stderr);
- exit(1);
- }
+ /* Try to read more. */
+ f->readlen = fread(f->buf, 1, parser_buf_size, f->file);
+ f->next = f->buf;
+ end = f->buf + f->readlen;
+ } while (f->readlen);
- f->c++;
- }
-
- return 1;
+ return false;
}
-void fastq_rewind(fastq_t* fqf)
+void fastq_print(FILE* fout, const seq_t* seq)
{
- gzrewind(fqf->file);
- fqf->state = STATE_ID1;
- fqf->buf[0] = '\0';
- fqf->c = fqf->buf;
-}
-
-
-void fastq_print(FILE* fout, seq_t* seq)
-{
- /* FASTQ */
- if (seq->qual.n > 0) {
- fprintf(fout, "@%s\n%s\n+%s\n%s\n",
- seq->id1.s,
- seq->seq.s,
- seq->id2.s,
- seq->qual.s );
- }
-
- /* FASTA */
- else {
- fprintf(fout, ">%s\n%s\n",
- seq->id1.s,
- seq->seq.s );
- }
+ fprintf(fout, "@%s\n%s\n+%s\n%s\n",
+ seq->id1.s,
+ seq->seq.s,
+ seq->id2.s,
+ seq->qual.s );
}
projects / fastq-tools.git / blobdiff