Avoid name space conflict with bwa

README.md

@@ -34,11 +34,11 @@ sketch of the example:
 int main(int argc, char *argv[])
 {
 	int i, n_seqs, n_utgs;
-	bseq1_t *seqs;                      // array of input sequences
+	fml_seq1_t *seqs;                   // array of input sequences
 	fml_utg_t *utgs;                    // array of output unitigs
 	fml_opt_t opt;
 	if (argc == 1) return 1;            // do nothing if there is no input file
-	seqs = bseq_read(argv[1], &n_seqs); // or fill the array with callers' functions
+	seqs = fml_seq_read(argv[1], &n_seqs); // or fill the array with callers' functions
 	fml_opt_init(&opt);                 // initialize parameters
 	utgs = fml_assemble(&opt, n_seqs, seqs, &n_utgs); // assemble!
 	for (i = 0; i < n_utgs; ++i)        // output in fasta

bfc.c

@@ -7,24 +7,12 @@
 #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));
@@ -46,26 +34,6 @@ void bfc_opt_init(bfc_opt_t *opt)
 	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 bseq1_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)
@@ -97,7 +65,7 @@ static void bfc_kmer_insert(cnt_step_t *cs, const bfc_kmer_t *x, int is_high, in
 static void worker_count(void *_data, long k, int tid)
 {
 	cnt_step_t *cs = (cnt_step_t*)_data;
-	const bseq1_t *s = &cs->seqs[k];
+	const fml_seq1_t *s = &cs->seqs[k];
 	int i, l;
 	bfc_kmer_t x = bfc_kmer_null;
 	uint64_t qmer = 0, mask = (1ULL<<cs->k) - 1;
@@ -111,7 +79,7 @@ static void worker_count(void *_data, long k, int tid)
 	}
 }
 
-struct bfc_ch_s *fml_count(int n, const bseq1_t *seq, int k, int q, int l_pre, int n_threads)
+struct bfc_ch_s *fml_count(int n, const fml_seq1_t *seq, int k, int q, int l_pre, int n_threads)
 {
 	int i;
 	cnt_step_t cs;
@@ -127,34 +95,6 @@ struct bfc_ch_s *fml_count(int n, const bseq1_t *seq, int k, int q, int l_pre, i
 	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;
@@ -264,53 +204,6 @@ uint64_t bfc_ec_best_island(int k, const ecseq_t *s)
 	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)
 
@@ -567,20 +460,7 @@ ecstat_t bfc_ec1(bfc_ec1buf_t *e, char *seq, char *qual)
 	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;
-	bseq1_t *seqs;
-} ec_step_t;
-
-static uint64_t max_streak(int k, const bfc_ch_t *ch, const bseq1_t *s)
+static uint64_t max_streak(int k, const bfc_ch_t *ch, const fml_seq1_t *s)
 {
 	int i, l;
 	uint64_t max = 0, t = 0;
@@ -602,7 +482,7 @@ static uint64_t max_streak(int k, const bfc_ch_t *ch, const bseq1_t *s)
 static void worker_ec(void *_data, long k, int tid)
 {
 	ec_step_t *es = (ec_step_t*)_data;
-	bseq1_t *s = &es->seqs[k];
+	fml_seq1_t *s = &es->seqs[k];
 	if (es->flt_uniq) {
 		uint64_t max;
 		max = max_streak(es->opt->k, es->ch, s);
@@ -624,7 +504,7 @@ static void worker_ec(void *_data, long k, int tid)
 	} else bfc_ec1(es->e[tid], s->seq, s->qual);
 }
 
-float fml_correct_core(const fml_opt_t *opt, int flt_uniq, int n, bseq1_t *seq)
+float fml_correct_core(const fml_opt_t *opt, int flt_uniq, int n, fml_seq1_t *seq)
 {
 	bfc_ch_t *ch;
 	int i, mode;
@@ -663,12 +543,24 @@ float fml_correct_core(const fml_opt_t *opt, int flt_uniq, int n, bseq1_t *seq)
 	return kcov;
 }
 
-float fml_correct(const fml_opt_t *opt, int n, bseq1_t *seq)
+// 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);
 }
 
-float fml_fltuniq(const fml_opt_t *opt, int n, bseq1_t *seq)
+float fml_fltuniq(const fml_opt_t *opt, int n, fml_seq1_t *seq)
 {
 	return fml_correct_core(opt, 1, n, seq);
 }

bfc.h

@@ -0,0 +1,153 @@
+#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 <[email protected]>: 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