xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-24 06:18:13 +08:00
Code Issues Packages Projects Releases Wiki Activity

Using klib

Browse Source
This commit is contained in:
Haoyu Cheng
2019-05-10 16:14:01 -04:00
parent 0b209dd1e9
commit eee68408be
7 changed files with 438 additions and 251 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Assembly.cpp
+14 -11
View File
@@ -1,28 +1,31 @@
#include "Assembly.h"
#include <stdio.h>
#include <stdlib.h>
#include <zlib.h>
#include "Process_Read.h"
void Counting()
{
Read r;
init_Read(&r);
kseq_t *seq = (kseq_t*)calloc(1, sizeof(kseq_t));
long long read_number = 0;
while (inputRead(&r))
while (get_read(seq))
{
fprintf(stderr,"%s\n",r.name);
fprintf(stderr,"%s\n",r.seq);
fprintf(stderr,"@%s\n",seq->name.s);
fprintf(stderr,"%s\n",seq->seq.s);
fprintf(stderr,"+\n");
fprintf(stderr,"%s\n",r.qual);
fprintf(stderr,"%s\n",seq->qual.s);
read_number++;
clear_read(&r);
}
fprintf(stdout, "read_number: %lld\n",read_number);
CommandLines.cpp
+17 -30
View File
@@ -1,7 +1,7 @@
#include "CommandLines.h"
#include <stdlib.h>
#include <getopt.h>
#include <stdio.h>
#include "ketopt.h"
char* read_file_name = NULL;
char* output_file_name = NULL;
@@ -17,41 +17,28 @@ void Print_H()
int CommandLine_process (int argc, char *argv[])
{
int o;
int index;
static struct option longOptions[] =
{
{"seq", required_argument, 0, 'q'},
{"threads", required_argument, 0, 't'},
{"threads", required_argument, 0, 'o'},
{0, 0, 0, 0},
static ko_longopt_t longopts[] = {
{ "help", ko_no_argument, 100},
{ "seq", ko_required_argument, 101},
{ "output", ko_required_argument, 102},
{ "thread", ko_required_argument, 103},
{ NULL, 0, 0 }
};
ketopt_t opt = KETOPT_INIT;
while ( (o = getopt_long ( argc, argv, "q:t:o:", longOptions, &index)) != -1 )
{
switch (o)
{
case 'q':
read_file_name = optarg;
break;
case 'o':
output_file_name = optarg;
break;
case 't':
thread_num = atoi(optarg);
break;
case '?':
fprintf(stderr, "Unrecognized option!\n" );
return 0;
break;
default:
Print_H();
return 0;
}
int i, c;
while ((c = ketopt(&opt, argc, argv, 1, "ht:o:q:", longopts)) >= 0) {
if (c == 100 || c == 'h') Print_H();
else if (c == 103 || c == 't') thread_num = atoi(opt.arg);
else if (c == 102 || c == 'o') output_file_name = opt.arg;
else if (c == 101 || c == 'q') read_file_name = opt.arg;
else if (c == '?') printf("unknown opt: -%c\n", opt.opt? opt.opt : ':');
else if (c == ':') printf("missing arg: -%c\n", opt.opt? opt.opt : ':');
}
if (argc == 1)
{
Print_H();
Process_Read.cpp
+35 -140
View File
@@ -2,163 +2,58 @@
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <zlib.h>
#include <fcntl.h>
int format = -1;
FILE *_r_fp = NULL;
gzFile g_r_fp;
gzFile fp;
kseq_t *seq;
int check_file_format(char *fileName)
void init_kseq(char* file)
{
int i = 0;
fp = gzopen(file, "r");
seq = kseq_init(fp);
}
char* file_extention;
i = strlen(fileName) - 1;
while (i >= 0 && fileName[i] != '.')
{
i--;
}
if (i < 0)
{
fprintf(stderr,
"ERROR: the input read files must be FASTQ format (file extension: .fq or .fastq) or compressed FASTQ format (file extension: .fq.gz or .fastq.gz)!\n");
exit(0);
}
if ((strcmp(".fq", fileName+i) == 0)
||
strcmp(".fastq", fileName + i) == 0)
{
return FASTQ;
}
else if (strcmp(".gz", fileName + i) == 0)
{
i--;
while (i >= 0 && fileName[i] != '.')
{
i--;
}
if (i < 0)
{
fprintf(stderr,
"ERROR: the input read files must be FASTQ format (file extension: .fq or .fastq) or compressed FASTQ format (file extension: .fq.gz or .fastq.gz)!\n");
exit(0);
}
if ((strcmp(".fq.gz", fileName + i) == 0)
||
strcmp(".fastq.gz", fileName + i) == 0)
{
return FASTQGZ;
}
else
{
fprintf(stderr,
"ERROR: the input read files must be FASTQ format (file extension: .fq or .fastq) or compressed FASTQ format (file extension: .fq.gz or .fastq.gz)!\n");
exit(0);
}
}
fprintf(stderr,
"ERROR: the input read files must be FASTQ format (file extension: .fq or .fastq) or compressed FASTQ format (file extension: .fq.gz or .fastq.gz)!\n");
exit(0);
void destory_kseq()
{
kseq_destroy(seq);
gzclose(fp);
}
int initiReadAllReads(char *fileName)
inline void exchage_kstring_t(kstring_t* a, kstring_t* b)
{
format = check_file_format(fileName);
if (format == FASTQ)
{
_r_fp = fopen(fileName, "r");
if (_r_fp == NULL)
{
return 0;
}
fprintf(stdout,
" Read files are in FASTQ format...\n");
}
else if (format == FASTQGZ)
{
int fd = open(fileName, O_CREAT | O_RDONLY, 0666);
g_r_fp = gzdopen(fd, "rb");
fprintf(stdout,
" Read files are in compressed FASTQ format...\n");
}
else
{
fprintf(stderr,
"ERROR: the input read files must be FASTQ format (file extension: .fq or .fastq) or compressed FASTQ format (file extension: .fq.gz or .fastq.gz)!\n");
exit(0);
}
kstring_t tmp;
tmp = *a;
*a = *b;
*b = tmp;
}
#define BUFFER_SIZE 20000
char Read_Buffer[BUFFER_SIZE];
char true_flag[2];
inline char *Input_line_from_file(char *seq)
int get_read(kseq_t *s)
{
if (format == FASTQ)
int l;
if ((l = kseq_read(seq)) >= 0)
{
return fgets(Read_Buffer, BUFFER_SIZE, _r_fp);
exchage_kstring_t(&seq->comment, &s->comment);
exchage_kstring_t(&seq->name, &s->name);
exchage_kstring_t(&seq->qual, &s->qual);
exchage_kstring_t(&seq->seq, &s->seq);
return 1;
}
else
{
seq = gzgets(g_r_fp, seq, BUFFER_SIZE);
return (!gzeof(g_r_fp)) ? true_flag : NULL;
}
}
inline int get_whole_line(str_v* line)
{
while(Input_line_from_file(Read_Buffer))
{
append_str(line, Read_Buffer);
if (line->centext[line->length - 1] == '\n')
{
line->length--;
line->centext[line->length] = '\0';
return 1;
}
}
return 0;
}
int inputRead(Read *read)
{
int buffer_length;
if (get_whole_line(&read->name))
{
get_whole_line(&read->seq);
Input_line_from_file(Read_Buffer);
get_whole_line(&read->qual);
return 1;
return 0;
}
return 0;
}
}
Process_Read.h
+6 -64
View File
@@ -4,73 +4,15 @@
#include<stdint.h>
#include <string.h>
#include <stdlib.h>
#include <zlib.h>
#include "kseq.h"
#define FASTQ 1
#define FASTQGZ 2
KSEQ_INIT(gzFile, gzread)
#define NAME_SZIE 25
#define SEQ_SZIE 20000
void init_kseq(char* file);
void destory_kseq();
int get_read(kseq_t *s);
typedef struct
{
char* centext;
uint32_t length;
uint32_t size;
}str_v;
inline void init_str_v(str_v* buf, uint32_t length)
{
buf->size = length + 1;
buf->length = 0;
buf->centext = (char*)malloc(sizeof(char)*buf->size);
}
inline void append_str(str_v* buf, char* input)
{
int length = strlen(input);
buf->length = buf->length + length;
if (buf->length > buf->size)
{
buf->centext = (char*)realloc(buf->centext, buf->length + 1);
}
memcpy(buf->centext + buf->length - length, input, length);
buf->centext[buf->length] = '\0';
}
inline void clear_str(str_v* buf)
{
buf->length = 0;
}
typedef struct
{
str_v name;
str_v seq;
str_v qual;
} Read;
inline void init_Read(Read* r)
{
init_str_v(&r->name, NAME_SZIE);
init_str_v(&r->seq, SEQ_SZIE);
init_str_v(&r->qual, SEQ_SZIE);
}
inline void clear_read(Read* r)
{
clear_str(&r->name);
clear_str(&r->seq);
clear_str(&r->qual);
}
int initiReadAllReads(char *fileName);
int inputRead(Read *read);
#endif
ketopt.h
+120
View File
@@ -0,0 +1,120 @@
#ifndef KETOPT_H
#define KETOPT_H
#include <string.h> /* for strchr() and strncmp() */
#define ko_no_argument 0
#define ko_required_argument 1
#define ko_optional_argument 2
typedef struct {
int ind; /* equivalent to optind */
int opt; /* equivalent to optopt */
char *arg; /* equivalent to optarg */
int longidx; /* index of a long option; or -1 if short */
/* private variables not intended for external uses */
int i, pos, n_args;
} ketopt_t;
typedef struct {
char *name;
int has_arg;
int val;
} ko_longopt_t;
static ketopt_t KETOPT_INIT = { 1, 0, 0, -1, 1, 0, 0 };
static void ketopt_permute(char *argv[], int j, int n) /* move argv[j] over n elements to the left */
{
int k;
char *p = argv[j];
for (k = 0; k < n; ++k)
argv[j - k] = argv[j - k - 1];
argv[j - k] = p;
}
/**
* Parse command-line options and arguments
*
* This fuction has a similar interface to GNU's getopt_long(). Each call
* parses one option and returns the option name. s->arg points to the option
* argument if present. The function returns -1 when all command-line arguments
* are parsed. In this case, s->ind is the index of the first non-option
* argument.
*
* @param s status; shall be initialized to KETOPT_INIT on the first call
* @param argc length of argv[]
* @param argv list of command-line arguments; argv[0] is ignored
* @param permute non-zero to move options ahead of non-option arguments
* @param ostr option string
* @param longopts long options
*
* @return ASCII for a short option; ko_longopt_t::val for a long option; -1 if
* argv[] is fully processed; '?' for an unknown option or an ambiguous
* long option; ':' if an option argument is missing
*/
static int ketopt(ketopt_t *s, int argc, char *argv[], int permute, const char *ostr, const ko_longopt_t *longopts)
{
int opt = -1, i0, j;
if (permute) {
while (s->i < argc && (argv[s->i][0] != '-' || argv[s->i][1] == '\0'))
++s->i, ++s->n_args;
}
s->arg = 0, s->longidx = -1, i0 = s->i;
if (s->i >= argc || argv[s->i][0] != '-' || argv[s->i][1] == '\0') {
s->ind = s->i - s->n_args;
return -1;
}
if (argv[s->i][0] == '-' && argv[s->i][1] == '-') { /* "--" or a long option */
if (argv[s->i][2] == '\0') { /* a bare "--" */
ketopt_permute(argv, s->i, s->n_args);
++s->i, s->ind = s->i - s->n_args;
return -1;
}
s->opt = 0, opt = '?', s->pos = -1;
if (longopts) { /* parse long options */
int k, n_exact = 0, n_partial = 0;
const ko_longopt_t *o = 0, *o_exact = 0, *o_partial = 0;
for (j = 2; argv[s->i][j] != '\0' && argv[s->i][j] != '='; ++j) {} /* find the end of the option name */
for (k = 0; longopts[k].name != 0; ++k)
if (strncmp(&argv[s->i][2], longopts[k].name, j - 2) == 0) {
if (longopts[k].name[j - 2] == 0) ++n_exact, o_exact = &longopts[k];
else ++n_partial, o_partial = &longopts[k];
}
if (n_exact > 1 || (n_exact == 0 && n_partial > 1)) return '?';
o = n_exact == 1? o_exact : n_partial == 1? o_partial : 0;
if (o) {
s->opt = opt = o->val, s->longidx = o - longopts;
if (argv[s->i][j] == '=') s->arg = &argv[s->i][j + 1];
if (o->has_arg == 1 && argv[s->i][j] == '\0') {
if (s->i < argc - 1) s->arg = argv[++s->i];
else opt = ':'; /* missing option argument */
}
}
}
} else { /* a short option */
const char *p;
if (s->pos == 0) s->pos = 1;
opt = s->opt = argv[s->i][s->pos++];
p = strchr((char*)ostr, opt);
if (p == 0) {
opt = '?'; /* unknown option */
} else if (p[1] == ':') {
if (argv[s->i][s->pos] == 0) {
if (s->i < argc - 1) s->arg = argv[++s->i];
else opt = ':'; /* missing option argument */
} else s->arg = &argv[s->i][s->pos];
s->pos = -1;
}
}
if (s->pos < 0 || argv[s->i][s->pos] == 0) {
++s->i, s->pos = 0;
if (s->n_args > 0) /* permute */
for (j = i0; j < s->i; ++j)
ketopt_permute(argv, j, s->n_args);
}
s->ind = s->i - s->n_args;
return opt;
}
#endif
kseq.h
+242
View File
@@ -0,0 +1,242 @@
/* The MIT License
Copyright (c) 2008, 2009, 2011 Attractive Chaos <attractor@live.co.uk>
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.
*/
/* Last Modified: 05MAR2012 */
#ifndef AC_KSEQ_H
#define AC_KSEQ_H
#include <ctype.h>
#include <string.h>
#include <stdlib.h>
#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
#define KS_SEP_TAB 1 // isspace() && !' '
#define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows)
#define KS_SEP_MAX 2
#define __KS_TYPE(type_t) \
typedef struct __kstream_t { \
unsigned char *buf; \
int begin, end, is_eof; \
type_t f; \
} kstream_t;
#define ks_err(ks) ((ks)->end == -1)
#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
#define __KS_BASIC(type_t, __bufsize) \
static inline kstream_t *ks_init(type_t f) \
{ \
kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
ks->f = f; \
ks->buf = (unsigned char*)malloc(__bufsize); \
return ks; \
} \
static inline void ks_destroy(kstream_t *ks) \
{ \
if (ks) { \
free(ks->buf); \
free(ks); \
} \
}
#define __KS_GETC(__read, __bufsize) \
static inline int ks_getc(kstream_t *ks) \
{ \
if (ks_err(ks)) return -3; \
if (ks->is_eof && ks->begin >= ks->end) return -1; \
if (ks->begin >= ks->end) { \
ks->begin = 0; \
ks->end = __read(ks->f, ks->buf, __bufsize); \
if (ks->end == 0) { ks->is_eof = 1; return -1;} \
if (ks->end == -1) { ks->is_eof = 1; return -3;}\
} \
return (int)ks->buf[ks->begin++]; \
}
#ifndef KSTRING_T
#define KSTRING_T kstring_t
typedef struct __kstring_t {
size_t l, m;
char *s;
} kstring_t;
#endif
#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif
#define __KS_GETUNTIL(__read, __bufsize) \
static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
{ \
int gotany = 0; \
if (dret) *dret = 0; \
str->l = append? str->l : 0; \
for (;;) { \
int i; \
if (ks_err(ks)) return -3; \
if (ks->begin >= ks->end) { \
if (!ks->is_eof) { \
ks->begin = 0; \
ks->end = __read(ks->f, ks->buf, __bufsize); \
if (ks->end == 0) { ks->is_eof = 1; break; } \
if (ks->end == -1) { ks->is_eof = 1; return -3; } \
} else break; \
} \
if (delimiter == KS_SEP_LINE) { \
for (i = ks->begin; i < ks->end; ++i) \
if (ks->buf[i] == '\n') break; \
} else if (delimiter > KS_SEP_MAX) { \
for (i = ks->begin; i < ks->end; ++i) \
if (ks->buf[i] == delimiter) break; \
} else if (delimiter == KS_SEP_SPACE) { \
for (i = ks->begin; i < ks->end; ++i) \
if (isspace(ks->buf[i])) break; \
} else if (delimiter == KS_SEP_TAB) { \
for (i = ks->begin; i < ks->end; ++i) \
if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
} else i = 0; /* never come to here! */ \
if (str->m - str->l < (size_t)(i - ks->begin + 1)) { \
str->m = str->l + (i - ks->begin) + 1; \
kroundup32(str->m); \
str->s = (char*)realloc(str->s, str->m); \
} \
gotany = 1; \
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 (!gotany && ks_eof(ks)) return -1; \
if (str->s == 0) { \
str->m = 1; \
str->s = (char*)calloc(1, 1); \
} else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \
str->s[str->l] = '\0'; \
return str->l; \
} \
static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
{ return ks_getuntil2(ks, delimiter, str, dret, 0); }
#define KSTREAM_INIT(type_t, __read, __bufsize) \
__KS_TYPE(type_t) \
__KS_BASIC(type_t, __bufsize) \
__KS_GETC(__read, __bufsize) \
__KS_GETUNTIL(__read, __bufsize)
#define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)
#define __KSEQ_BASIC(SCOPE, type_t) \
SCOPE kseq_t *kseq_init(type_t fd) \
{ \
kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
s->f = ks_init(fd); \
return s; \
} \
SCOPE 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); \
}
/* Return value:
>=0 length of the sequence (normal)
-1 end-of-file
-2 truncated quality string
-3 error reading stream
*/
#define __KSEQ_READ(SCOPE) \
SCOPE int kseq_read(kseq_t *seq) \
{ \
int c,r; \
kstream_t *ks = seq->f; \
if (seq->last_char == 0) { /* then jump to the next header line */ \
while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '@'); \
if (c < 0) return c; /* end of file or error*/ \
seq->last_char = c; \
} /* else: the first header char has been read in the previous call */ \
seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
if ((r=ks_getuntil(ks, 0, &seq->name, &c)) < 0) return r; /* normal exit: EOF or error */ \
if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \
if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
seq->seq.m = 256; \
seq->seq.s = (char*)malloc(seq->seq.m); \
} \
while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '+' && c != '@') { \
if (c == '\n') continue; /* skip empty lines */ \
seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
} \
if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
seq->seq.m = seq->seq.l + 2; \
kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \
seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
} \
seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
if (c != '+') return seq->seq.l; /* FASTA */ \
if (seq->qual.m < seq->seq.m) { /* allocate memory for qual in case insufficient */ \
seq->qual.m = seq->seq.m; \
seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
} \
while ((c = ks_getc(ks)) >= 0 && c != '\n'); /* skip the rest of '+' line */ \
if (c == -1) return -2; /* error: no quality string */ \
while ((c = ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l)); \
if (c == -3) return -3; /* stream error */ \
seq->last_char = 0; /* we have not come to the next header line */ \
if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
return seq->seq.l; \
}
#define __KSEQ_TYPE(type_t) \
typedef struct { \
kstring_t name, comment, seq, qual; \
int last_char; \
kstream_t *f; \
} kseq_t;
#define KSEQ_INIT2(SCOPE, type_t, __read) \
KSTREAM_INIT(type_t, __read, 16384) \
__KSEQ_TYPE(type_t) \
__KSEQ_BASIC(SCOPE, type_t) \
__KSEQ_READ(SCOPE)
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
#define KSEQ_DECLARE(type_t) \
__KS_TYPE(type_t) \
__KSEQ_TYPE(type_t) \
extern kseq_t *kseq_init(type_t fd); \
void kseq_destroy(kseq_t *ks); \
int kseq_read(kseq_t *seq);
#endif
main.cpp
+4 -6
View File
@@ -11,17 +11,15 @@ int main(int argc, char *argv[])
if (!CommandLine_process(argc, argv))
return 1;
init_kseq(read_file_name);
if (!initiReadAllReads(read_file_name))
{
fprintf(stdout, "Cannot open read files. \n");
return 1;
}
Counting();
destory_kseq();
return 1;