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Makefile
View file @ 3dd2c856
CC=gcc
CFLAGS=-g -Wall -O2 -Wno-unused-function
BINDIR=/usr/local/bin
all:seqtk
seqtk:seqtk.c khash.h kseq.h
$(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm
install:all
install seqtk $(BINDIR)
clean:
rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session*
debian/changelog
View file @ 3dd2c856
seqtk (1.3-1) unstable; urgency=medium
* New upstream version
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
-- Andreas Tille <tille@debian.org> Thu, 20 Sep 2018 21:35:35 +0200
seqtk (1.2-2) unstable; urgency=medium
* Team upload.
......
debian/control
View file @ 3dd2c856
......@@ -4,11 +4,11 @@ Uploaders: Andreas Tille <tille@debian.org>,
Brad Chapman <chapmanb@50mail.com>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
Build-Depends: debhelper (>= 11~),
zlib1g-dev
Standards-Version: 4.0.0
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/seqtk.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/seqtk.git
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/seqtk
Vcs-Git: https://salsa.debian.org/med-team/seqtk.git
Homepage: https://github.com/lh3/seqtk
Package: seqtk
......
debian/patches/hardening.patch
View file @ 3dd2c856
......@@ -5,16 +5,12 @@ Description: Propagate hardening options
--- a/Makefile
+++ b/Makefile
@@ -1,10 +1,10 @@
CC=gcc
-CFLAGS=-g -Wall -O2 -Wno-unused-function
+CFLAGS+=-g -Wall -O2 -Wno-unused-function
@@ -5,7 +5,7 @@ BINDIR=/usr/local/bin
all:seqtk
seqtk:seqtk.c khash.h kseq.h
- $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm
+ $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm $(LDFLAGS)
clean:
rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session*
install:all
install seqtk $(BINDIR)
debian/rules
View file @ 3dd2c856
......@@ -11,3 +11,6 @@ createmanpage:
help2man --no-info --help-option=" " --no-discard-stderr \
--name='sampling, trimming, fastq2fasta, subsequence, reverse complement' \
--version-string="1.0" seqtk > seqtk.1
override_dh_auto_install:
echo "Ignore broken Makefile"
kseq.h
View file @ 3dd2c856
......@@ -23,7 +23,7 @@
SOFTWARE.
*/
/* Last Modified: 05MAR2012 */
/* Last Modified: 2017-02-11 */
#ifndef AC_KSEQ_H
#define AC_KSEQ_H
......@@ -44,6 +44,7 @@
type_t f; \
} kstream_t;
#define ks_err(ks) ((ks)->end < 0)
#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
......@@ -66,11 +67,13 @@
#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_err(ks)) return -3; \
if (ks_eof(ks)) 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; } \
else if (ks->end < 0) { ks->is_eof = 1; return -3; } \
} \
return (int)ks->buf[ks->begin++]; \
}
......@@ -95,11 +98,13 @@ typedef struct __kstring_t {
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) { \
......@@ -167,25 +172,26 @@ typedef struct __kstring_t {
>=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; \
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)) != -1 && c != '>' && c != '@'); \
if (c == -1) return -1; /* end of file */ \
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 (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
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)) != -1 && c != '>' && c != '+' && c != '@') { \
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 */ \
......@@ -197,14 +203,16 @@ typedef struct __kstring_t {
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 */ \
seq->is_fastq = (c == '+'); \
if (!seq->is_fastq) 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 */ \
while ((c = ks_getc(ks)) >= 0 && 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); \
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; \
......@@ -213,7 +221,7 @@ typedef struct __kstring_t {
#define __KSEQ_TYPE(type_t) \
typedef struct { \
kstring_t name, comment, seq, qual; \
int last_char; \
int last_char, is_fastq; \
kstream_t *f; \
} kseq_t;
......
ksort.h deleted 100644 → 0
View file @ 5c91f5d1
/* The MIT License
Copyright (c) 2008, 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.
*/
/*
2011-04-10 (0.1.6):
* Added sample
2011-03 (0.1.5):
* Added shuffle/permutation
2008-11-16 (0.1.4):
* Fixed a bug in introsort() that happens in rare cases.
2008-11-05 (0.1.3):
* Fixed a bug in introsort() for complex comparisons.
* Fixed a bug in mergesort(). The previous version is not stable.
2008-09-15 (0.1.2):
* Accelerated introsort. On my Mac (not on another Linux machine),
my implementation is as fast as std::sort on random input.
* Added combsort and in introsort, switch to combsort if the
recursion is too deep.
2008-09-13 (0.1.1):
* Added k-small algorithm
2008-09-05 (0.1.0):
* Initial version
*/
#ifndef AC_KSORT_H
#define AC_KSORT_H
#include <stdlib.h>
#include <string.h>
typedef struct {
void *left, *right;
int depth;
} ks_isort_stack_t;
#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
#define KSORT_INIT(name, type_t, __sort_lt) \
void ks_mergesort_##name(size_t n, type_t array[], type_t temp[]) \
{ \
type_t *a2[2], *a, *b; \
int curr, shift; \
\
a2[0] = array; \
a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n); \
for (curr = 0, shift = 0; (1ul<<shift) < n; ++shift) { \
a = a2[curr]; b = a2[1-curr]; \
if (shift == 0) { \
type_t *p = b, *i, *eb = a + n; \
for (i = a; i < eb; i += 2) { \
if (i == eb - 1) *p++ = *i; \
else { \
if (__sort_lt(*(i+1), *i)) { \
*p++ = *(i+1); *p++ = *i; \
} else { \
*p++ = *i; *p++ = *(i+1); \
} \
} \
} \
} else { \
size_t i, step = 1ul<<shift; \
for (i = 0; i < n; i += step<<1) { \
type_t *p, *j, *k, *ea, *eb; \
if (n < i + step) { \
ea = a + n; eb = a; \
} else { \
ea = a + i + step; \
eb = a + (n < i + (step<<1)? n : i + (step<<1)); \
} \
j = a + i; k = a + i + step; p = b + i; \
while (j < ea && k < eb) { \
if (__sort_lt(*k, *j)) *p++ = *k++; \
else *p++ = *j++; \
} \
while (j < ea) *p++ = *j++; \
while (k < eb) *p++ = *k++; \
} \
} \
curr = 1 - curr; \
} \
if (curr == 1) { \
type_t *p = a2[0], *i = a2[1], *eb = array + n; \
for (; p < eb; ++i) *p++ = *i; \
} \
if (temp == 0) free(a2[1]); \
} \
void ks_heapadjust_##name(size_t i, size_t n, type_t l[]) \
{ \
size_t k = i; \
type_t tmp = l[i]; \
while ((k = (k << 1) + 1) < n) { \
if (k != n - 1 && __sort_lt(l[k], l[k+1])) ++k; \
if (__sort_lt(l[k], tmp)) break; \
l[i] = l[k]; i = k; \
} \
l[i] = tmp; \
} \
void ks_heapmake_##name(size_t lsize, type_t l[]) \
{ \
size_t i; \
for (i = (lsize >> 1) - 1; i != (size_t)(-1); --i) \
ks_heapadjust_##name(i, lsize, l); \
} \
void ks_heapsort_##name(size_t lsize, type_t l[]) \
{ \
size_t i; \
for (i = lsize - 1; i > 0; --i) { \
type_t tmp; \
tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \
} \
} \
static inline void __ks_insertsort_##name(type_t *s, type_t *t) \
{ \
type_t *i, *j, swap_tmp; \
for (i = s + 1; i < t; ++i) \
for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \
swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp; \
} \
} \
void ks_combsort_##name(size_t n, type_t a[]) \
{ \
const double shrink_factor = 1.2473309501039786540366528676643; \
int do_swap; \
size_t gap = n; \
type_t tmp, *i, *j; \
do { \
if (gap > 2) { \
gap = (size_t)(gap / shrink_factor); \
if (gap == 9 || gap == 10) gap = 11; \
} \
do_swap = 0; \
for (i = a; i < a + n - gap; ++i) { \
j = i + gap; \
if (__sort_lt(*j, *i)) { \
tmp = *i; *i = *j; *j = tmp; \
do_swap = 1; \
} \
} \
} while (do_swap || gap > 2); \
if (gap != 1) __ks_insertsort_##name(a, a + n); \
} \
void ks_introsort_##name(size_t n, type_t a[]) \
{ \
int d; \
ks_isort_stack_t *top, *stack; \
type_t rp, swap_tmp; \
type_t *s, *t, *i, *j, *k; \
\
if (n < 1) return; \
else if (n == 2) { \
if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \
return; \
} \
for (d = 2; 1ul<<d < n; ++d); \
stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
top = stack; s = a; t = a + (n-1); d <<= 1; \
while (1) { \
if (s < t) { \
if (--d == 0) { \
ks_combsort_##name(t - s + 1, s); \
t = s; \
continue; \
} \
i = s; j = t; k = i + ((j-i)>>1) + 1; \
if (__sort_lt(*k, *i)) { \
if (__sort_lt(*k, *j)) k = j; \
} else k = __sort_lt(*j, *i)? i : j; \
rp = *k; \
if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; } \
for (;;) { \
do ++i; while (__sort_lt(*i, rp)); \
do --j; while (i <= j && __sort_lt(rp, *j)); \
if (j <= i) break; \
swap_tmp = *i; *i = *j; *j = swap_tmp; \
} \
swap_tmp = *i; *i = *t; *t = swap_tmp; \
if (i-s > t-i) { \
if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \
s = t-i > 16? i+1 : t; \
} else { \
if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \
t = i-s > 16? i-1 : s; \
} \
} else { \
if (top == stack) { \
free(stack); \
__ks_insertsort_##name(a, a+n); \
return; \
} else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \
} \
} \
} \
/* This function is adapted from: http://ndevilla.free.fr/median/ */ \
/* 0 <= kk < n */ \
type_t ks_ksmall_##name(size_t n, type_t arr[], size_t kk) \
{ \
type_t *low, *high, *k, *ll, *hh, *mid; \
low = arr; high = arr + n - 1; k = arr + kk; \
for (;;) { \
if (high <= low) return *k; \
if (high == low + 1) { \
if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
return *k; \
} \
mid = low + (high - low) / 2; \
if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \
KSORT_SWAP(type_t, *mid, *(low+1)); \
ll = low + 1; hh = high; \
for (;;) { \
do ++ll; while (__sort_lt(*ll, *low)); \
do --hh; while (__sort_lt(*low, *hh)); \
if (hh < ll) break; \
KSORT_SWAP(type_t, *ll, *hh); \
} \
KSORT_SWAP(type_t, *low, *hh); \
if (hh <= k) low = ll; \
if (hh >= k) high = hh - 1; \
} \
} \
void ks_shuffle_##name(size_t n, type_t a[]) \
{ \
int i, j; \
for (i = n; i > 1; --i) { \
type_t tmp; \
j = (int)(drand48() * i); \
tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp; \
} \
} \
void ks_sample_##name(size_t n, size_t r, type_t a[]) /* FIXME: NOT TESTED!!! */ \
{ /* reference: http://code.activestate.com/recipes/272884/ */ \
int i, k, pop = n; \
for (i = (int)r, k = 0; i >= 0; --i) { \
double z = 1., x = drand48(); \
type_t tmp; \
while (x < z) z -= z * i / (pop--); \
if (k != n - pop - 1) tmp = a[k], a[k] = a[n-pop-1], a[n-pop-1] = tmp; \
++k; \
} \
}
#define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t)
#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
#define ks_combsort(name, n, a) ks_combsort_##name(n, a)
#define ks_heapsort(name, n, a) ks_heapsort_##name(n, a)
#define ks_heapmake(name, n, a) ks_heapmake_##name(n, a)
#define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a)
#define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k)
#define ks_shuffle(name, n, a) ks_shuffle_##name(n, a)
#define ks_lt_generic(a, b) ((a) < (b))
#define ks_lt_str(a, b) (strcmp((a), (b)) < 0)
typedef const char *ksstr_t;
#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
#define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str)
#endif
kstring.h deleted 100644 → 0
View file @ 5c91f5d1
/* The MIT License
Copyright (c) by 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.
*/
#ifndef KSTRING_H
#define KSTRING_H
#include <stdlib.h>
#include <string.h>
#include <stdint.h>
#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif
#ifndef KSTRING_T
#define KSTRING_T kstring_t
typedef struct __kstring_t {
uint32_t l, m;
char *s;
} kstring_t;
#endif
typedef struct {
uint64_t tab[4];
int sep, finished;
const char *p; // end of the current token
} ks_tokaux_t;
#ifdef __cplusplus
extern "C" {
#endif
int ksprintf(kstring_t *s, const char *fmt, ...);
int ksprintf_fast(kstring_t *s, const char *fmt, ...);
int ksplit_core(char *s, int delimiter, int *_max, int **_offsets);
char *kstrstr(const char *str, const char *pat, int **_prep);
char *kstrnstr(const char *str, const char *pat, int n, int **_prep);
void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep);
/* kstrtok() is similar to strtok_r() except that str is not
* modified and both str and sep can be NULL. For efficiency, it is
* actually recommended to set both to NULL in the subsequent calls
* if sep is not changed. */
char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux);
#ifdef __cplusplus
}
#endif
static inline void ks_resize(kstring_t *s, size_t size)
{
if (s->m < size) {
s->m = size;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
}
}
static inline int kputsn(const char *p, int l, kstring_t *s)
{
if (s->l + l + 1 >= s->m) {
s->m = s->l + l + 2;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
}
memcpy(s->s + s->l, p, l);
s->l += l;
s->s[s->l] = 0;
return l;
}
static inline int kputs(const char *p, kstring_t *s)
{
return kputsn(p, strlen(p), s);
}
static inline int kputc(int c, kstring_t *s)
{
if (s->l + 1 >= s->m) {
s->m = s->l + 2;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
}
s->s[s->l++] = c;
s->s[s->l] = 0;
return c;
}
static inline int kputw(int c, kstring_t *s)
{
char buf[16];
int l, x;
if (c == 0) return kputc('0', s);
for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
if (c < 0) buf[l++] = '-';
if (s->l + l + 1 >= s->m) {
s->m = s->l + l + 2;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
}
for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
s->s[s->l] = 0;
return 0;
}
static inline int kputuw(unsigned c, kstring_t *s)
{
char buf[16];
int l, i;
unsigned x;
if (c == 0) return kputc('0', s);
for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
if (s->l + l + 1 >= s->m) {
s->m = s->l + l + 2;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
}
for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
s->s[s->l] = 0;
return 0;
}
static inline int kputl(long c, kstring_t *s)
{
char buf[32];
long l, x;
if (c == 0) return kputc('0', s);
for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
if (c < 0) buf[l++] = '-';
if (s->l + l + 1 >= s->m) {
s->m = s->l + l + 2;
kroundup32(s->m);
s->s = (char*)realloc(s->s, s->m);
}
for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
s->s[s->l] = 0;
return 0;
}
static inline int *ksplit(kstring_t *s, int delimiter, int *n)
{
int max = 0, *offsets = 0;
*n = ksplit_core(s->s, delimiter, &max, &offsets);
return offsets;
}
#endif
kvec.h deleted 100644 → 0
View file @ 5c91f5d1
/* The MIT License
Copyright (c) 2008, by 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.
*/
/*
An example:
#include "kvec.h"
int main() {
kvec_t(int) array;
kv_init(array);
kv_push(int, array, 10); // append
kv_a(int, array, 20) = 5; // dynamic
kv_A(array, 20) = 4; // static
kv_destroy(array);
return 0;
}
*/
/*
2008-09-22 (0.1.0):
* The initial version.
*/
#ifndef AC_KVEC_H
#define AC_KVEC_H
#include <stdlib.h>
#define kv_roundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#define kvec_t(type) struct { size_t n, m; type *a; }
#define kv_init(v) ((v).n = (v).m = 0, (v).a = 0)
#define kv_destroy(v) free((v).a)
#define kv_A(v, i) ((v).a[(i)])
#define kv_pop(v) ((v).a[--(v).n])
#define kv_size(v) ((v).n)
#define kv_max(v) ((v).m)
#define kv_resize(type, v, s) ((v).m = (s), (v).a = (type*)realloc((v).a, sizeof(type) * (v).m))
#define kv_copy(type, v1, v0) do { \
if ((v1).m < (v0).n) kv_resize(type, v1, (v0).n); \
(v1).n = (v0).n; \
memcpy((v1).a, (v0).a, sizeof(type) * (v0).n); \
} while (0) \
#define kv_push(type, v, x) do { \
if ((v).n == (v).m) { \
(v).m = (v).m? (v).m<<1 : 2; \
(v).a = (type*)realloc((v).a, sizeof(type) * (v).m); \
} \
(v).a[(v).n++] = (x); \
} while (0)
#define kv_pushp(type, v) (((v).n == (v).m)? \
((v).m = ((v).m? (v).m<<1 : 2), \
(v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0) \
: 0), ((v).a + ((v).n++))
#define kv_a(type, v, i) (((v).m <= (size_t)(i)? \
((v).m = (v).n = (i) + 1, kv_roundup32((v).m), \
(v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0) \
: (v).n <= (size_t)(i)? (v).n = (i) + 1 \
: 0), (v).a[(i)])
#endif
seqtk.c
View file @ 3dd2c856
/* The MIT License
Copyright (c) 20082-2012 by Heng Li <lh3@me.com>
Copyright (c) 2008-2016 Broad Institute
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
......@@ -57,9 +57,10 @@ reghash_t *stk_reg_read(const char *fn)
int dret;
kstring_t *str;
// read the list
str = calloc(1, sizeof(kstring_t));
fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) return 0;
ks = ks_init(fp);
str = calloc(1, sizeof(kstring_t));
while (ks_getuntil(ks, 0, str, &dret) >= 0) {
int beg = -1, end = -1;
reglist_t *p;
......@@ -298,10 +299,15 @@ int stk_trimfq(int argc, char *argv[])
fprintf(stderr, " -b INT trim INT bp from left (non-zero to disable -q/-l) [0]\n");
fprintf(stderr, " -e INT trim INT bp from right (non-zero to disable -q/-l) [0]\n");
fprintf(stderr, " -L INT retain at most INT bp from the 5'-end (non-zero to disable -q/-l) [0]\n");
fprintf(stderr, " -Q force FASTQ output\n");
fprintf(stderr, "\n");
return 1;
}
fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
for (i = 0; i < 128; ++i)
q_int2real[i] = pow(10., -(i - 33) / 10.);
......@@ -336,12 +342,12 @@ int stk_trimfq(int argc, char *argv[])
end = beg + min_len;
}
} else beg = 0, end = seq->seq.l;
putchar(seq->qual.l? '@' : '>'); fputs(seq->name.s, stdout);
putchar(seq->is_fastq? '@' : '>'); fputs(seq->name.s, stdout);
if (seq->comment.l) {
putchar(' '); puts(seq->comment.s);
} else putchar('\n');
fwrite(seq->seq.s + beg, 1, end - beg, stdout); putchar('\n');
if (seq->qual.l) {
if (seq->is_fastq) {
puts("+");
fwrite(seq->qual.s + beg, 1, end - beg, stdout); putchar('\n');
}
......@@ -372,6 +378,10 @@ int stk_comp(int argc, char *argv[])
return 1;
}
fp = optind < argc && strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
dummy.n= dummy.m = 1; dummy.a = calloc(1, 8);
while ((l = kseq_read(seq)) >= 0) {
......@@ -437,6 +447,10 @@ int stk_randbase(int argc, char *argv[])
return 1;
}
fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
while ((l = kseq_read(seq)) >= 0) {
int i;
......@@ -489,6 +503,10 @@ int stk_hety(int argc, char *argv[])
}
}
fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
win_step = win_size / n_start;
buf = calloc(win_size, 1);
......@@ -547,8 +565,16 @@ int stk_subseq(int argc, char *argv[])
return 1;
}
h = stk_reg_read(argv[optind+1]);
if (h == 0) {
fprintf(stderr, "[E::%s] failed to read the list of regions in file '%s'\n", __func__, argv[optind+1]);
return 1;
}
// subseq
fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream\n", __func__);
return 1;
}
seq = kseq_init(fp);
while ((l = kseq_read(seq)) >= 0) {
reglist_t *p;
......@@ -626,6 +652,10 @@ int stk_mergefa(int argc, char *argv[])
fp[i] = strcmp(argv[optind+i], "-")? gzopen(argv[optind+i], "r") : gzdopen(fileno(stdin), "r");
seq[i] = kseq_init(fp[i]);
}
if (fp[0] == 0 || fp[1] == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
cnt[0] = cnt[1] = cnt[2] = cnt[3] = cnt[4] = 0;
srand48(11);
while (kseq_read(seq[0]) >= 0) {
......@@ -707,6 +737,10 @@ int stk_famask(int argc, char *argv[])
fp[i] = strcmp(argv[optind+i], "-")? gzopen(argv[optind+i], "r") : gzdopen(fileno(stdin), "r");
seq[i] = kseq_init(fp[i]);
}
if (fp[0] == 0 || fp[1] == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
while (kseq_read(seq[0]) >= 0) {
int min_l, c[2];
kseq_read(seq[1]);
......@@ -746,6 +780,10 @@ int stk_mutfa(int argc, char *argv[])
// read the list
str = calloc(1, sizeof(kstring_t));
fp = strcmp(argv[2], "-")? gzopen(argv[2], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
ks = ks_init(fp);
while (ks_getuntil(ks, 0, str, &dret) >= 0) {
char *s = strdup(str->s);
......@@ -775,6 +813,10 @@ int stk_mutfa(int argc, char *argv[])
free(str->s); free(str);
// mutfa
fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
while ((l = kseq_read(seq)) >= 0) {
reglist_t *p;
......@@ -817,6 +859,10 @@ int stk_listhet(int argc, char *argv[])
return 1;
}
fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
while ((l = kseq_read(seq)) >= 0) {
for (i = 0; i < l; ++i) {
......@@ -902,6 +948,10 @@ int stk_cutN(int argc, char *argv[])
return 1;
}
fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
ks = kseq_init(fp);
while ((l = kseq_read(ks)) >= 0) {
int k = 0, begin = 0, end = 0;
......@@ -930,6 +980,10 @@ int stk_hrun(int argc, char *argv[])
}
if (argc == optind + 2) min_len = atoi(argv[optind+1]);
fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
ks = kseq_init(fp);
while (kseq_read(ks) >= 0) {
c = ks->seq.s[0]; l = 1; beg = 0;
......@@ -989,7 +1043,7 @@ int stk_sample(int argc, char *argv[])
return 1;
}
frac = atof(argv[optind+1]);
if (frac > 1.) num = (uint64_t)(frac + .499), frac = 0.;
if (frac >= 1.0) num = (uint64_t)(frac + .499), frac = 0.;
else if (twopass) {
fprintf(stderr, "[W::%s] when sampling a fraction, option -2 is ignored.", __func__);
twopass = 0;
......@@ -1006,6 +1060,10 @@ int stk_sample(int argc, char *argv[])
}
fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
n_seqs = 0;
while (kseq_read(seq) >= 0) {
......@@ -1037,6 +1095,10 @@ int stk_sample(int argc, char *argv[])
buf = malloc(num * 8);
for (i = 0; i < num; ++i) buf[i] = UINT64_MAX;
fp = gzopen(argv[optind], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
n_seqs = 0;
while (kseq_read(seq) >= 0) {
......@@ -1117,14 +1179,14 @@ int stk_seq(int argc, char *argv[])
{
gzFile fp;
kseq_t *seq;
int c, qual_thres = 0, flag = 0, qual_shift = 33, mask_chr = 0, min_len = 0, max_q = 255;
int c, qual_thres = 0, flag = 0, qual_shift = 33, mask_chr = 0, min_len = 0, max_q = 255, fake_qual = -1;
unsigned i, line_len = 0;
int64_t n_seqs = 0;
double frac = 1.;
khash_t(reg) *h = 0;
krand_t *kr = 0;
while ((c = getopt(argc, argv, "N12q:l:Q:aACrn:s:f:M:L:cVUX:S")) >= 0) {
while ((c = getopt(argc, argv, "N12q:l:Q:aACrn:s:f:M:L:cVUX:SF:")) >= 0) {
switch (c) {
case 'a':
case 'A': flag |= 1; break;
......@@ -1146,6 +1208,7 @@ int stk_seq(int argc, char *argv[])
case 'L': min_len = atoi(optarg); break;
case 's': kr = kr_srand(atol(optarg)); break;
case 'f': frac = atof(optarg); break;
case 'F': fake_qual = *optarg; break;
}
}
if (kr == 0) kr = kr_srand(11);
......@@ -1161,6 +1224,7 @@ int stk_seq(int argc, char *argv[])
fprintf(stderr, " -f FLOAT sample FLOAT fraction of sequences [1]\n");
fprintf(stderr, " -M FILE mask regions in BED or name list FILE [null]\n");
fprintf(stderr, " -L INT drop sequences with length shorter than INT [0]\n");
fprintf(stderr, " -F CHAR fake FASTQ quality []\n");
fprintf(stderr, " -c mask complement region (effective with -M)\n");
fprintf(stderr, " -r reverse complement\n");
fprintf(stderr, " -A force FASTA output (discard quality)\n");
......@@ -1177,6 +1241,10 @@ int stk_seq(int argc, char *argv[])
}
if (line_len == 0) line_len = UINT_MAX;
fp = optind < argc && strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
qual_thres += qual_shift;
while (kseq_read(seq) >= 0) {
......@@ -1215,6 +1283,15 @@ int stk_seq(int argc, char *argv[])
for (i = 0; i < seq->seq.l; ++i)
seq->seq.s[i] = toupper(seq->seq.s[i]);
if (flag & 1) seq->qual.l = 0; // option -a: fastq -> fasta
else if (fake_qual >= 33 && fake_qual <= 127) {
if (seq->qual.m < seq->seq.m) {
seq->qual.m = seq->seq.m;
seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m);
}
seq->qual.l = seq->seq.l;
memset(seq->qual.s, fake_qual, seq->qual.l);
seq->qual.s[seq->qual.l] = 0;
}
if (flag & 2) seq->comment.l = 0; // option -C: drop fasta/q comments
if (h) stk_mask(seq, h, flag&8, mask_chr); // masking
if (flag & 4) { // option -r: reverse complement
......@@ -1274,6 +1351,10 @@ int stk_gc(int argc, char *argv[])
q = (1.0f - frac) / frac;
fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
while (kseq_read(seq) >= 0) {
int i, start = 0, max_i = 0, n_hits = 0, start_hits = 0, max_hits = 0;
......@@ -1317,6 +1398,10 @@ int stk_mergepe(int argc, char *argv[])
}
fp1 = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
fp2 = strcmp(argv[2], "-")? gzopen(argv[2], "r") : gzdopen(fileno(stdin), "r");
if (fp1 == 0 || fp2 == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq[0] = kseq_init(fp1);
seq[1] = kseq_init(fp2);
while (kseq_read(seq[0]) >= 0) {
......@@ -1344,6 +1429,10 @@ int stk_dropse(int argc, char *argv[])
return 1;
}
fp = argc > 1 && strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
memset(&last, 0, sizeof(kseq_t));
......@@ -1381,6 +1470,10 @@ int stk_rename(int argc, char *argv[])
return 1;
}
fp = argc > 1 && strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
if (argc > 2) prefix = argv[2];
......@@ -1444,6 +1537,10 @@ int stk_kfreq(int argc, char *argv[])
}
fp = argc == 2 || strcmp(argv[2], "-") == 0? gzdopen(fileno(stdin), "r") : gzopen(argv[2], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
ks = kseq_init(fp);
while (kseq_read(ks) >= 0) {
int k, x[2], cnt[2], cnt_nei[2], which;
......@@ -1517,6 +1614,10 @@ int stk_fqchk(int argc, char *argv[])
return 1;
}
fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
for (k = 0; k <= 93; ++k)
perr[k] = pow(10., -.1 * k);
......@@ -1574,7 +1675,7 @@ static int usage()
{
fprintf(stderr, "\n");
fprintf(stderr, "Usage: seqtk <command> <arguments>\n");
fprintf(stderr, "Version: 1.2-r94\n\n");
fprintf(stderr, "Version: 1.3-r106\n\n");
fprintf(stderr, "Command: seq common transformation of FASTA/Q\n");
fprintf(stderr, " comp get the nucleotide composition of FASTA/Q\n");
fprintf(stderr, " sample subsample sequences\n");
......@@ -1599,28 +1700,27 @@ static int usage()
int main(int argc, char *argv[])
{
if (argc == 1) return usage();
if (strcmp(argv[1], "comp") == 0) stk_comp(argc-1, argv+1);
else if (strcmp(argv[1], "fqchk") == 0) stk_fqchk(argc-1, argv+1);
else if (strcmp(argv[1], "hety") == 0) stk_hety(argc-1, argv+1);
else if (strcmp(argv[1], "gc") == 0) stk_gc(argc-1, argv+1);
else if (strcmp(argv[1], "subseq") == 0) stk_subseq(argc-1, argv+1);
else if (strcmp(argv[1], "mutfa") == 0) stk_mutfa(argc-1, argv+1);
else if (strcmp(argv[1], "mergefa") == 0) stk_mergefa(argc-1, argv+1);
else if (strcmp(argv[1], "mergepe") == 0) stk_mergepe(argc-1, argv+1);
else if (strcmp(argv[1], "dropse") == 0) stk_dropse(argc-1, argv+1);
else if (strcmp(argv[1], "randbase") == 0) stk_randbase(argc-1, argv+1);
else if (strcmp(argv[1], "cutN") == 0) stk_cutN(argc-1, argv+1);
else if (strcmp(argv[1], "listhet") == 0) stk_listhet(argc-1, argv+1);
else if (strcmp(argv[1], "famask") == 0) stk_famask(argc-1, argv+1);
else if (strcmp(argv[1], "trimfq") == 0) stk_trimfq(argc-1, argv+1);
else if (strcmp(argv[1], "hrun") == 0) stk_hrun(argc-1, argv+1);
else if (strcmp(argv[1], "sample") == 0) stk_sample(argc-1, argv+1);
else if (strcmp(argv[1], "seq") == 0) stk_seq(argc-1, argv+1);
else if (strcmp(argv[1], "kfreq") == 0) stk_kfreq(argc-1, argv+1);
else if (strcmp(argv[1], "rename") == 0) stk_rename(argc-1, argv+1);
if (strcmp(argv[1], "comp") == 0) return stk_comp(argc-1, argv+1);
else if (strcmp(argv[1], "fqchk") == 0) return stk_fqchk(argc-1, argv+1);
else if (strcmp(argv[1], "hety") == 0) return stk_hety(argc-1, argv+1);
else if (strcmp(argv[1], "gc") == 0) return stk_gc(argc-1, argv+1);
else if (strcmp(argv[1], "subseq") == 0) return stk_subseq(argc-1, argv+1);
else if (strcmp(argv[1], "mutfa") == 0) return stk_mutfa(argc-1, argv+1);
else if (strcmp(argv[1], "mergefa") == 0) return stk_mergefa(argc-1, argv+1);
else if (strcmp(argv[1], "mergepe") == 0) return stk_mergepe(argc-1, argv+1);
else if (strcmp(argv[1], "dropse") == 0) return stk_dropse(argc-1, argv+1);
else if (strcmp(argv[1], "randbase") == 0) return stk_randbase(argc-1, argv+1);
else if (strcmp(argv[1], "cutN") == 0) return stk_cutN(argc-1, argv+1);
else if (strcmp(argv[1], "listhet") == 0) return stk_listhet(argc-1, argv+1);
else if (strcmp(argv[1], "famask") == 0) return stk_famask(argc-1, argv+1);
else if (strcmp(argv[1], "trimfq") == 0) return stk_trimfq(argc-1, argv+1);
else if (strcmp(argv[1], "hrun") == 0) return stk_hrun(argc-1, argv+1);
else if (strcmp(argv[1], "sample") == 0) return stk_sample(argc-1, argv+1);
else if (strcmp(argv[1], "seq") == 0) return stk_seq(argc-1, argv+1);
else if (strcmp(argv[1], "kfreq") == 0) return stk_kfreq(argc-1, argv+1);
else if (strcmp(argv[1], "rename") == 0) return stk_rename(argc-1, argv+1);
else {
fprintf(stderr, "[main] unrecognized command '%s'. Abort!\n", argv[1]);
return 1;
}
return 0;
}