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Revert "FMSI supports masked superstrings longer than 2^31 chars."
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This reverts commit 3fa4f66.
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@OndrejSladky
OndrejSladky committed Aug 11, 2024
1 parent 3fa4f66 commit 2230770
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2 changes: 1 addition & 1 deletion src/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ CXXFLAGS= -g -Wall -Wno-unused-function -std=c++17 -g3
PROG= ../fmsi
INCLUDES-PATH?=.
INCLUDES= -I$(INCLUDES-PATH)/include -L$(INCLUDES-PATH)/lib
LIBS= -lsdsl -ldivsufsort -ldivsufsort64
LIBS= -lz -lsdsl -ldivsufsort -ldivsufsort64

all:$(PROG)

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279 changes: 279 additions & 0 deletions src/kseq.h
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@@ -0,0 +1,279 @@
/* 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 <stdlib.h>
#include <string.h>

#ifdef USE_MALLOC_WRAPPERS
#include "malloc_wrap.h"
#endif

#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_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->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; \
} \
} \
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->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; \
} \
} 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
*/
#define __KSEQ_READ(SCOPE) \
SCOPE int kseq_read(kseq_t *seq) { \
int c; \
kstream_t *ks = seq->f; \
if (seq->last_char == 0) { /* then jump to the next header line */ \
while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@') \
; \
if (c == -1) \
return -1; /* end of file */ \
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 (ks_getuntil(ks, 0, &seq->name, &c) < 0) \
return -1; /* normal exit: EOF */ \
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)) != -1 && 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)) != -1 && c != '\n') \
; /* skip the rest of '+' line */ \
if (c == -1) \
return -2; /* error: no quality string */ \
while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && \
seq->qual.l < seq->seq.l) \
; \
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
44 changes: 22 additions & 22 deletions src/parser.h
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@@ -1,33 +1,33 @@
#pragma once

#include "kseq.h"
#include <stdexcept>
#include <stdio.h>
#include <string>
#include <zlib.h>
#include <vector>

KSEQ_INIT(gzFile, gzread)

/// Load masked superstring from the fasta file in the mask-cased format.
std::string read_masked_superstring(std::string fn) {
std::vector<char> masked_superstring;
std::ifstream fasta(fn);
if (fasta.is_open()) {
char c;
bool readingHeader = false;
while (fasta >> std::noskipws >> c) {
if (c == '>') {
readingHeader = true;
}
else if (c == '\n') readingHeader = false;
if (readingHeader) continue;
// Disregard white space.
if (c == '\n' || c == '\r' || c == ' ') continue;
if (c != 'A' && c != 'C' && c != 'G' && c != 'T' && c != 'a' && c != 'c' && c != 'g' && c != 't') {
throw std::invalid_argument("invalid character in masked superstring");
}
masked_superstring.push_back(c);
}
fasta.close();
} else {
throw std::invalid_argument("couldn't open file " + fn);
gzFile fp;
kseq_t *seq;

fp = gzopen(fn.c_str(), "r");
if (fp == 0) {
throw std::invalid_argument("couldn't open file " + fn);
}

seq = kseq_init(fp);
std::vector<char> ret;
int l;
while ((l = kseq_read(seq)) >= 0) {
for (int i = 0; i < l; ++i) {
ret.push_back(seq->seq.s[i]);
}
return std::string(masked_superstring.begin(), masked_superstring.end());
}
kseq_destroy(seq);
gzclose(fp);
return std::string(ret.begin(), ret.end());
}
2 changes: 1 addition & 1 deletion tests/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ CXX = g++
CXXFLAGS= -g -Wall -Wno-unused-function -std=c++17 -O2
INCLUDES-PATH?=../src
INCLUDES= -I$(INCLUDES-PATH)/include -L$(INCLUDES-PATH)/lib
LIBS= -lsdsl -ldivsufsort -ldivsufsort64
LIBS= -lz -lsdsl -ldivsufsort -ldivsufsort64
GTEST= googletest/googletest
SRC= ../src

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