/usr/include/fml.h is in libfml-dev 0.1-2+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 | #ifndef FML_H
#define FML_H
#define FML_VERSION "r41"
#include <stdint.h>
typedef struct {
int32_t l_seq;
char *seq, *qual;
} bseq1_t;
#define MAG_F_AGGRESSIVE 0x20
#define MAG_F_NO_SIMPL 0x80
typedef struct {
int flag, min_ovlp, min_elen, min_ensr, min_insr, max_bdist, max_bvtx, min_merge_len, trim_len, trim_depth;
float min_dratio1, max_bcov, max_bfrac;
} magopt_t;
typedef struct {
int n_threads; // number of threads; don't use multi-threading for small data sets
int ec_k; // k-mer length for error correction; 0 for auto estimate
int min_cnt, max_cnt; // both occ threshold in ec and tip threshold in cleaning lie in [min_cnt,max_cnt]
int min_asm_ovlp; // min overlap length during assembly
int min_merge_len; // during assembly, don't explicitly merge an overlap if shorter than this value
magopt_t mag_opt; // graph cleaning options
} fml_opt_t;
struct rld_t;
struct mag_t;
typedef struct {
uint32_t tid;
uint32_t len:31, from:1;
} fml_ovlp_t;
typedef struct {
int32_t len; // length of sequence
int32_t nsr; // number of supporting reads
char *seq; // unitig sequence
char *cov; // cov[i]-33 gives per-base coverage at i
int n_ovlp[2]; // number of 5'-end [0] and 3'-end [1] overlaps
fml_ovlp_t *ovlp; // overlaps, of size n_ovlp[0]+n_ovlp[1]
} fml_utg_t;
#ifdef __cplusplus
extern "C" {
#endif
/************************
* High-level functions *
************************/
/**
* Read all sequences from a FASTA/FASTQ file
*
* @param fn filename; NULL or "-" for stdin
* @param n (out) number of sequences read into RAM
*
* @return array of sequences
*/
bseq1_t *bseq_read(const char *fn, int *n);
/**
* Initialize default parameters
*
* @param opt (out) pointer to parameters
*/
void fml_opt_init(fml_opt_t *opt);
/**
* Assemble a list of sequences
*
* @param opt parameters
* @param n_seqs number of input sequences
* @param seqs sequences to assemble; FREED on return
* @param n_utg (out) number of unitigs in return
*
* @return array of unitigs
*/
fml_utg_t *fml_assemble(const fml_opt_t *opt, int n_seqs, bseq1_t *seqs, int *n_utg);
/**
* Free unitigs
*
* @param n_utg number of unitigs
* @param utg array of unitigs
*/
void fml_utg_destroy(int n_utg, fml_utg_t *utg);
/************************************************
* Mid-level functions called by fml_assemble() *
************************************************/
/**
* Adjust parameters based on input sequences
*
* @param opt parameters to update IN PLACE
* @param n_seqs number of sequences
* @param seqs array of sequences
*/
void fml_opt_adjust(fml_opt_t *opt, int n_seqs, const bseq1_t *seqs);
/**
* Error correction
*
* @param opt parameters
* @param n number of sequences
* @param seq array of sequences; corrected IN PLACE
*
* @return k-mer coverage
*/
float fml_correct(const fml_opt_t *opt, int n, bseq1_t *seq);
float fml_fltuniq(const fml_opt_t *opt, int n, bseq1_t *seq);
/**
* Construct FMD-index
*
* @param opt parameters
* @param n number of sequences
* @param seq array of sequences; FREED on return
*
* @return FMD-index
*/
struct rld_t *fml_seq2fmi(const fml_opt_t *opt, int n, bseq1_t *seq);
/**
* Generate initial overlap graph
*
* @param opt parameters
* @param e FMD-index; FREED on return
*
* @return overlap graph in the "mag" structure
*/
struct mag_t *fml_fmi2mag(const fml_opt_t *opt, struct rld_t *e);
/**
* Clean a mag graph
*
* @param opt parameters
* @param g overlap graph; modified IN PLACE
*/
void fml_mag_clean(const fml_opt_t *opt, struct mag_t *g);
/**
* Convert a graph in mag to fml_utg_t
*
* @param g graph in the "mag" structure; FREED on return
* @param n_utg (out) number of unitigs
*
* @return array of unitigs
*/
fml_utg_t *fml_mag2utg(struct mag_t *g, int *n_utg);
/**
* Output unitig graph in the mag format
*
* @param n_utg number of unitigs
* @param utg array of unitigs
*/
void fml_utg_print(int n_utgs, const fml_utg_t *utg);
/**
* Deallocate an FM-index
*
* @param e pointer to the FM-index
*/
void fml_fmi_destroy(struct rld_t *e);
/**
* Deallocate a mag graph
*
* @param g pointer to the mag graph
*/
void fml_mag_destroy(struct mag_t *g);
#ifdef __cplusplus
}
#endif
#endif
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