#include "kmer.h"
#include "internal.h"
#include "fml.h"
+#include "bfc.h"
/*******************
*** BFC options ***
*******************/
-typedef struct {
- int n_threads, q, k, l_pre;
- int min_cov; // a k-mer is considered solid if the count is no less than this
-
- int max_end_ext;
- int win_multi_ec;
- float min_trim_frac;
-
- // these ec options cannot be changed on the command line
- int w_ec, w_ec_high, w_absent, w_absent_high;
- int max_path_diff, max_heap;
-} bfc_opt_t;
-
void bfc_opt_init(bfc_opt_t *opt)
{
memset(opt, 0, sizeof(bfc_opt_t));
opt->max_heap = 100;
}
-/**********************
- *** K-mer counting ***
- **********************/
-
-#define CNT_BUF_SIZE 256
-
-typedef struct { // cache to reduce locking
- uint64_t y[2];
- int is_high;
-} insbuf_t;
-
-typedef struct {
- int k, q;
- int n_seqs;
- const fml_seq1_t *seqs;
- bfc_ch_t *ch;
- int *n_buf;
- insbuf_t **buf;
-} cnt_step_t;
-
bfc_kmer_t bfc_kmer_null = {{0,0,0,0}};
static int bfc_kmer_bufclear(cnt_step_t *cs, int forced, int tid)
return cs.ch;
}
-/***************
- *** Correct ***
- ***************/
-
-#define BFC_MAX_KMER 63
-#define BFC_MAX_BF_SHIFT 37
-
-#define BFC_MAX_PATHS 4
-#define BFC_EC_HIST 5
-#define BFC_EC_HIST_HIGH 2
-
-#define BFC_EC_MIN_COV_COEF .1
-
-/**************************
- * Sequence struct for ec *
- **************************/
-
-#include "kvec.h"
-
-typedef struct { // NOTE: unaligned memory
- uint8_t b:3, q:1, ob:3, oq:1;
- uint8_t dummy;
- uint16_t lcov:6, hcov:6, solid_end:1, high_end:1, ec:1, absent:1;
- int i;
-} ecbase_t;
-
-typedef kvec_t(ecbase_t) ecseq_t;
-
static int bfc_seq_conv(const char *s, const char *q, int qthres, ecseq_t *seq)
{
int i, l;
return max > 0? (uint64_t)(max_i - max - k + 1) << 32 | max_i : 0;
}
-/********************
- * Correct one read *
- ********************/
-
-#include "ksort.h"
-
-#define ECCODE_MISC 1
-#define ECCODE_MANY_N 2
-#define ECCODE_NO_SOLID 3
-#define ECCODE_UNCORR_N 4
-#define ECCODE_MANY_FAIL 5
-
-typedef struct {
- uint32_t ec_code:3, brute:1, n_ec:14, n_ec_high:14;
- uint32_t n_absent:24, max_heap:8;
-} ecstat_t;
-
-typedef struct {
- uint8_t ec:1, ec_high:1, absent:1, absent_high:1, b:4;
-} bfc_penalty_t;
-
-typedef struct {
- int tot_pen;
- int i; // base position
- int k; // position in the stack
- int32_t ecpos_high[BFC_EC_HIST_HIGH];
- int32_t ecpos[BFC_EC_HIST];
- bfc_kmer_t x;
-} echeap1_t;
-
-typedef struct {
- int parent, i, tot_pen;
- uint8_t b;
- bfc_penalty_t pen;
- uint16_t cnt;
-} ecstack1_t;
-
-typedef struct {
- const bfc_opt_t *opt;
- const bfc_ch_t *ch;
- kvec_t(echeap1_t) heap;
- kvec_t(ecstack1_t) stack;
- ecseq_t seq, tmp, ec[2];
- int mode;
- ecstat_t ori_st;
-} bfc_ec1buf_t;
-
#define heap_lt(a, b) ((a).tot_pen > (b).tot_pen)
KSORT_INIT(ec, echeap1_t, heap_lt)
return s;
}
-/********************
- * Error correction *
- ********************/
-
-typedef struct {
- const bfc_opt_t *opt;
- const bfc_ch_t *ch;
- bfc_ec1buf_t **e;
- int64_t n_processed;
- int n_seqs, flt_uniq;
- fml_seq1_t *seqs;
-} ec_step_t;
-
static uint64_t max_streak(int k, const bfc_ch_t *ch, const fml_seq1_t *s)
{
int i, l;
return kcov;
}
+// Added by jwala for use in libSeqLib
+void kmer_correct(ec_step_t * es, int mode, bfc_ch_t * ch) {
+ int i = 0;
+ es->e = (bfc_ec1buf_t**)calloc(es->opt->n_threads, sizeof(void*)); //jwala added cast
+ for (i = 0; i < es->opt->n_threads; ++i)
+ es->e[i] = ec1buf_init(es->opt, ch), es->e[i]->mode = mode;
+ kt_for(es->opt->n_threads, worker_ec, es, es->n_seqs);
+ for (i = 0; i < es->opt->n_threads; ++i)
+ ec1buf_destroy(es->e[i]);
+ free(es->e);
+}
+
float fml_correct(const fml_opt_t *opt, int n, fml_seq1_t *seq)
{
return fml_correct_core(opt, 0, n, seq);
--- /dev/null
+#ifndef AC_BFC_H__
+#define AC_BFC_H__
+
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <limits.h>
+#include <stdio.h>
+#include "htab.h"
+/* #include "kmer.h" ... this is actually included by htab.h */
+#include "internal.h"
+#include "fml.h"
+#include "khash.h"
+
+/* Andreas Tille <tille@debian.org>: Its not clear where jwala took this from and what its purpose might be - commenting out for the moment
+#define _cnt_eq(a, b) ((a)>>14 == (b)>>14)
+#define _cnt_hash(a) ((a)>>14)
+KHASH_INIT(cnt, uint64_t, char, 0, _cnt_hash, _cnt_eq)
+typedef khash_t(cnt) cnthash_t;
+
+struct bfc_ch_s {
+ int k;
+ cnthash_t **h;
+ // private
+ int l_pre;
+};
+*/
+
+typedef struct {
+ int n_threads, q, k, l_pre;
+ int min_cov; // a k-mer is considered solid if the count is no less than this
+
+ int max_end_ext;
+ int win_multi_ec;
+ float min_trim_frac;
+
+ // these ec options cannot be changed on the command line
+ int w_ec, w_ec_high, w_absent, w_absent_high;
+ int max_path_diff, max_heap;
+} bfc_opt_t;
+
+/**********************
+ *** K-mer counting ***
+ **********************/
+
+#define CNT_BUF_SIZE 256
+
+typedef struct { // cache to reduce locking
+ uint64_t y[2];
+ int is_high;
+} insbuf_t;
+
+typedef struct {
+ int k, q;
+ int n_seqs;
+ const fml_seq1_t *seqs;
+ bfc_ch_t *ch;
+ int *n_buf;
+ insbuf_t **buf;
+} cnt_step_t;
+
+/***************
+ *** Correct ***
+ ***************/
+
+#define BFC_MAX_KMER 63
+#define BFC_MAX_BF_SHIFT 37
+
+#define BFC_MAX_PATHS 4
+#define BFC_EC_HIST 5
+#define BFC_EC_HIST_HIGH 2
+
+#define BFC_EC_MIN_COV_COEF .1
+
+/**************************
+ * Sequence struct for ec *
+ **************************/
+
+#include "kvec.h"
+
+typedef struct { // NOTE: unaligned memory
+ uint8_t b:3, q:1, ob:3, oq:1;
+ uint8_t dummy;
+ uint16_t lcov:6, hcov:6, solid_end:1, high_end:1, ec:1, absent:1;
+ int i;
+} ecbase_t;
+
+typedef kvec_t(ecbase_t) ecseq_t;
+
+/********************
+ * Correct one read *
+ ********************/
+
+#include "ksort.h"
+
+#define ECCODE_MISC 1
+#define ECCODE_MANY_N 2
+#define ECCODE_NO_SOLID 3
+#define ECCODE_UNCORR_N 4
+#define ECCODE_MANY_FAIL 5
+
+typedef struct {
+ uint32_t ec_code:3, brute:1, n_ec:14, n_ec_high:14;
+ uint32_t n_absent:24, max_heap:8;
+} ecstat_t;
+
+typedef struct {
+ uint8_t ec:1, ec_high:1, absent:1, absent_high:1, b:4;
+} bfc_penalty_t;
+
+typedef struct {
+ int tot_pen;
+ int i; // base position
+ int k; // position in the stack
+ int32_t ecpos_high[BFC_EC_HIST_HIGH];
+ int32_t ecpos[BFC_EC_HIST];
+ bfc_kmer_t x;
+} echeap1_t;
+
+typedef struct {
+ int parent, i, tot_pen;
+ uint8_t b;
+ bfc_penalty_t pen;
+ uint16_t cnt;
+} ecstack1_t;
+
+typedef struct {
+ const bfc_opt_t *opt;
+ const bfc_ch_t *ch;
+ kvec_t(echeap1_t) heap;
+ kvec_t(ecstack1_t) stack;
+ ecseq_t seq, tmp, ec[2];
+ int mode;
+ ecstat_t ori_st;
+} bfc_ec1buf_t;
+
+/********************
+ * Error correction *
+ ********************/
+
+typedef struct {
+ const bfc_opt_t *opt;
+ const bfc_ch_t *ch;
+ bfc_ec1buf_t **e;
+ int64_t n_processed;
+ int n_seqs, flt_uniq;
+ fml_seq1_t *seqs;
+} ec_step_t;
+
+void kmer_correct(ec_step_t * es, int mode, bfc_ch_t * ch);
+void bfc_opt_init(bfc_opt_t *opt);
+
+#endif
projects / fermi-lite.git / commitdiff