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updated to the latest kseq.h

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1 parent a9292d6 commit 5a0b32bfd24e89f70460c85bdb03d7dd1d87045a @lh3 committed Feb 6, 2013
Showing with 138 additions and 62 deletions.
  1. +1 −1 Makefile
  2. +1 −1 bntseq.c
  3. +4 −0 bseq.c
  4. +15 −0 bseq.h
  5. +30 −0 bwamem.c
  6. +1 −1 bwamem.h
  7. +1 −1 bwaseqio.c
  8. +1 −1 bwtsw2_aux.c
  9. +1 −1 fastmap.c
  10. +82 −55 kseq.h
  11. +1 −1 simple_dp.c
View
@@ -5,7 +5,7 @@ CXXFLAGS= $(CFLAGS)
AR= ar
DFLAGS= -DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
LOBJS= bwa.o bamlite.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o bntseq.o bwamem.o stdaln.o \
- bwaseqio.o bwase.o kstring.o
+ bseq.o bwaseqio.o bwase.o kstring.o
AOBJS= QSufSort.o bwt_gen.o \
is.o bwtmisc.o bwtindex.o ksw.o simple_dp.o \
bwape.o cs2nt.o \
View
@@ -35,7 +35,7 @@
#include "utils.h"
#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
+KSEQ_DECLARE(gzFile)
unsigned char nst_nt4_table[256] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
View
4 bseq.c
@@ -0,0 +1,4 @@
+#include <zlib.h>
+#include "bseq.h"
+#include "kseq.h"
+KSEQ_INIT2(, gzFile, gzread)
View
15 bseq.h
@@ -0,0 +1,15 @@
+#ifndef BATCHSEQ_H_
+#define BATCHSEQ_H_
+
+typedef struct {
+ char *name, *comment, *seq, *qual;
+} bseq1_t;
+
+typedef struct {
+ int n, m;
+ bseq1_t *seqs;
+} bseq_t;
+
+int bseq_read(int chunk_size, bseq_t *bs);
+
+#endif
View
@@ -274,6 +274,32 @@ int mem_chain_flt(const mem_opt_t *opt, int n_chn, mem_chain1_t *chains)
return n;
}
+#define alnreg_lt(a, b) ((a).score > (b).score)
+KSORT_INIT(mem_ar, mem_alnreg_t, alnreg_lt)
+
+int mem_choose_alnreg_se(const mem_opt_t *opt, int n, mem_alnreg_t *a)
+{ // similar to the loop in mem_chain_flt()
+ int i, j, m;
+ if (n <= 1) return n;
+ ks_introsort(mem_ar, n, a);
+ for (i = 0; i < n; ++i) a[i].sub = 0;
+ for (i = 1, m = 1; i < n; ++i) {
+ for (j = 0; j < m; ++j) {
+ int b_max = a[j].qb > a[i].qb? a[j].qb : a[i].qb;
+ int e_min = a[j].qe < a[i].qe? a[j].qe : a[i].qe;
+ if (e_min > b_max) { // have overlap
+ int min_l = a[i].qe - a[i].qb < a[j].qe - a[j].qb? a[i].qe - a[i].qb : a[j].qe - a[j].qb;
+ if (e_min - b_max >= min_l * opt->mask_level) { // significant overlap
+ if (a[j].sub == 0) a[j].sub = a[i].score;
+ break;
+ }
+ }
+ }
+ if (j == m) a[m++] = a[i];
+ }
+ return m;
+}
+
/****************************************
* Construct the alignment from a chain *
****************************************/
@@ -388,3 +414,7 @@ uint32_t *mem_gen_cigar(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac,
free(rseq);
return cigar;
}
+
+/****************
+ * Sequence I/O *
+ ****************/
View
@@ -31,7 +31,7 @@ typedef struct {
typedef struct {
int64_t rb, re;
- int score, qb, qe;
+ int score, qb, qe, sub;
} mem_alnreg_t;
#ifdef __cplusplus
View
@@ -5,7 +5,7 @@
#include "bamlite.h"
#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
+KSEQ_DECLARE(gzFile)
extern unsigned char nst_nt4_table[256];
static char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
View
@@ -15,7 +15,7 @@
#include "kstring.h"
#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
+KSEQ_DECLARE(gzFile)
#include "ksort.h"
#define __left_lt(a, b) ((a).end > (b).end)
View
@@ -7,7 +7,7 @@
#include "bwamem.h"
#include "kvec.h"
#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
+KSEQ_DECLARE(gzFile)
extern unsigned char nst_nt4_table[256];
View
137 kseq.h
@@ -1,6 +1,6 @@
/* The MIT License
- Copyright (c) 2008, by Heng Li <lh3@sanger.ac.uk>
+ 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
@@ -23,16 +23,23 @@
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 { \
- char *buf; \
+ unsigned char *buf; \
int begin, end, is_eof; \
type_t f; \
} kstream_t;
@@ -45,7 +52,7 @@
{ \
kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
ks->f = f; \
- ks->buf = (char*)malloc(__bufsize); \
+ ks->buf = (unsigned char*)malloc(__bufsize); \
return ks; \
} \
static inline void ks_destroy(kstream_t *ks) \
@@ -82,10 +89,10 @@ typedef struct __kstring_t {
#endif
#define __KS_GETUNTIL(__read, __bufsize) \
- static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
+ static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
{ \
if (dret) *dret = 0; \
- str->l = 0; \
+ str->l = append? str->l : 0; \
if (ks->begin >= ks->end && ks->is_eof) return -1; \
for (;;) { \
int i; \
@@ -97,14 +104,20 @@ typedef struct __kstring_t {
if (ks->end == 0) break; \
} else break; \
} \
- if (delimiter) { \
+ 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 { \
+ } else if (delimiter == KS_SEP_SPACE) { \
for (i = ks->begin; i < ks->end; ++i) \
if (isspace(ks->buf[i])) break; \
- } \
- if (str->m - str->l < i - ks->begin + 1) { \
+ } 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); \
@@ -117,29 +130,32 @@ typedef struct __kstring_t {
break; \
} \
} \
+ 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_BASIC(type_t) \
- static inline kseq_t *kseq_init(type_t fd) \
+#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; \
} \
- 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) \
+ 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); \
@@ -152,44 +168,46 @@ typedef struct __kstring_t {
-1 end-of-file
-2 truncated quality string
*/
-#define __KSEQ_READ \
- static int kseq_read(kseq_t *seq) \
- { \
- int c; \
- kstream_t *ks = seq->f; \
+#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; \
- } /* the first header char has been read */ \
- 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 != '@'); \
+ 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 (isgraph(c)) { /* printable non-space character */ \
- if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \
- seq->seq.m = seq->seq.l + 2; \
- kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \
- seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
- } \
- seq->seq.s[seq->seq.l++] = (char)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 */ \
- 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 enough memory */ \
- seq->qual.m = seq->seq.m; \
- seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
- } \
+ 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; /* we should not stop here */ \
- 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; /* null terminated string */ \
+ 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; /* qual string is shorter than seq string */ \
- return seq->seq.l; \
+ 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) \
@@ -199,10 +217,19 @@ typedef struct __kstring_t {
kstream_t *f; \
} kseq_t;
-#define KSEQ_INIT(type_t, __read) \
- KSTREAM_INIT(type_t, __read, 4096) \
+#define KSEQ_INIT2(SCOPE, type_t, __read) \
+ KSTREAM_INIT(type_t, __read, 16384) \
__KSEQ_TYPE(type_t) \
- __KSEQ_BASIC(type_t) \
- __KSEQ_READ
+ __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
View
@@ -8,7 +8,7 @@
#include "utils.h"
#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
+KSEQ_DECLARE(gzFile)
typedef struct {
int l;

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