kseq.h

/* The MIT License 
 
   Copyright (c) 2008 Genome Research Ltd (GRL). 
 
   Permission is hereby granted, free of charge, to any person obtaining 
   a copy of this software and associated documentation files (the 
   "Software"), to deal in the Software without restriction, including 
   without limitation the rights to use, copy, modify, merge, publish, 
   distribute, sublicense, and/or sell copies of the Software, and to 
   permit persons to whom the Software is furnished to do so, subject to 
   the following conditions: 
 
   The above copyright notice and this permission notice shall be 
   included in all copies or substantial portions of the Software. 
 
   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND 
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS 
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN 
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN 
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 
   SOFTWARE. 
*/  
  
/* Contact: Heng Li <lh3@sanger.ac.uk> */  
  
/* Last Modified: 12APR2009 */  

#ifndef KSEQ_H
#define KSEQ_H

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


typedef struct __kstring_t {
	size_t l, m;
	char *s;
} kstring_t;


typedef struct __kstream_t {
  char *buf; 
  int begin, end, is_eof; 
  gzFile f; 
} kstream_t; 

static inline kstream_t *ks_init(gzFile f) { 
  kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t));
  ks->f = f;
  ks->buf = (char*)malloc(4096); 
  return ks; 
} 

static inline void ks_destroy(kstream_t *ks) { 
  if (ks) { free(ks->buf); free(ks); } 
} 

static inline int ks_getc(kstream_t *ks) {
  if (ks->is_eof && ks->begin >= ks->end) return -1; 
  if (ks->begin >= ks->end) { 
    ks->begin = 0; ks->end = gzread(ks->f, ks->buf, 4096); 
    if (ks->end < 4096) ks->is_eof = 1; 
    if (ks->end == 0) return -1; 
  } 
  return (int)ks->buf[ks->begin++]; 
} 



static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) 
{ 
  if (dret) 
    *dret = 0;
  str->l = 0;
  if (ks->begin >= ks->end && ks->is_eof) 
    return -1; 
  for (;;) 
    { 
      int i; 
      if (ks->begin >= ks->end) { 
	if (!ks->is_eof) {
	  ks->begin = 0; 
	  ks->end = gzread(ks->f, ks->buf, 4096); 
	  if (ks->end < 4096) 
	    ks->is_eof = 1; 
	  if (ks->end == 0) 
	    break; 
	} 
	else 
	  break; 
      }
    
      if (delimiter > 1) { 
	for (i = ks->begin; i < ks->end; ++i) 
	  if (ks->buf[i] == delimiter) 
	    break; 
      } else if (delimiter == 0) { 
	for (i = ks->begin; i < ks->end; ++i) 
	  if (isspace(ks->buf[i])) 
	    break;
      } else if (delimiter == 1) { 
	for (i = ks->begin; i < ks->end; ++i) 
	  if (isspace(ks->buf[i]) && ks->buf[i] != ' ')
	    break;
      } else 
	i = 0; 
    
      if (str->m - str->l < i - ks->begin + 1) {
	str->m = str->l + (i - ks->begin) + 1;
	(--(str->m), (str->m)|=(str->m)>>1, (str->m)|=(str->m)>>2, (str->m)|=(str->m)>>4, (str->m)|=(str->m)>>8, (str->m)|=(str->m)>>16, ++(str->m));
	str->s = (char*)realloc(str->s, str->m); 
      } 
    
      memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); 
      str->l = str->l + (i - ks->begin); 
      ks->begin = i + 1;
      if (i < ks->end) { 
	if (dret) 
	  *dret = ks->buf[i];
	break; 
      } 
    } 
  
  if (str->l == 0) { 
    str->m = 1; 
    str->s = (char*)calloc(1, 1); 
  } 
  str->s[str->l] = '\0';
  return str->l; 
} 



typedef struct 
{ kstring_t name, comment, seq, qual; int last_char; kstream_t *f; } 
kseq_t; 

static inline kseq_t *kseq_init(gzFile fd) { 
  kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); s->f = ks_init(fd); return s; 
} 

static inline void kseq_rewind(kseq_t *ks) { 
  ks->last_char = 0; ks->f->is_eof = ks->f->begin = ks->f->end = 0; 
} 

static inline void kseq_destroy(kseq_t *ks) { 
  if (!ks) return; free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); ks_destroy(ks->f); free(ks); 
} 

static int kseq_read(kseq_t *seq) { 
  int c; kstream_t *ks = seq->f; 
  if (seq->last_char == 0) { 
    while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@');
    if (c == -1) 
      return -1; 
    seq->last_char = c; 
  } 
  seq->comment.l = seq->seq.l = seq->qual.l = 0;
  if (ks_getuntil(ks, 0, &seq->name, &c) < 0) 
    return -1; 

  if (c != '\n') 
    ks_getuntil(ks, '\n', &seq->comment, 0); 
  while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') {
    if (isgraph(c)) { 
      if (seq->seq.l + 1 >= seq->seq.m) { 
        seq->seq.m = seq->seq.l + 2;
	(--(seq->seq.m), (seq->seq.m)|=(seq->seq.m)>>1, (seq->seq.m)|=(seq->seq.m)>>2, (seq->seq.m)|=(seq->seq.m)>>4, (seq->seq.m)|=(seq->seq.m)>>8, (seq->seq.m)|=(seq->seq.m)>>16, ++(seq->seq.m)); 
	seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); 
      }
    
      seq->seq.s[seq->seq.l++] = (char)c; 
    } 
  } 

  if (c == '>' || c == '@') 
    seq->last_char = c; 

  seq->seq.s[seq->seq.l] = 0; 

  if (c != '+') return seq->seq.l; 

  if (seq->qual.m < seq->seq.m) { 
    seq->qual.m = seq->seq.m; 
    seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); 
  } 

  while ((c = ks_getc(ks)) != -1 && c != '\n');

  if (c == -1) 
    return -2;

  while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l) 
    if (c >= 33 && c <= 127) 
      seq->qual.s[seq->qual.l++] = (unsigned char)c;
  
  seq->qual.s[seq->qual.l] = 0; 
  seq->last_char = 0; 
  if (seq->seq.l != seq->qual.l) return -2; 

  return seq->seq.l; 
};



#endif