Codebase list fermi-lite / 57245fb
Update patches Andreas Tille 3 years ago
1 changed file(s) with 20 addition(s) and 20 deletion(s). Raw diff Collapse all Expand all
+20
-20
debian/patches/rename_bseq1_t.patch less more
108108 --- a/misc.c
109109 +++ b/misc.c
110110 @@ -40,7 +40,7 @@ void fml_opt_init(fml_opt_t *opt)
111 opt->mag_opt.flag = MAG_F_NO_SIMPL;
111 opt->mag_opt.flag = MAG_F_NO_SIMPL | MAG_F_POPOPEN;
112112 }
113113
114114 -void fml_opt_adjust(fml_opt_t *opt, int n_seqs, const bseq1_t *seqs)
125125 {
126126 mrope_t *mr;
127127 kstring_t str = {0,0,0};
128 @@ -75,7 +75,7 @@ struct rld_t *fml_fmi_gen(int n, bseq1_t
128 @@ -80,7 +80,7 @@ struct rld_t *fml_fmi_gen(int n, bseq1_t
129129 mr = mr_init(ROPE_DEF_MAX_NODES, ROPE_DEF_BLOCK_LEN, MR_SO_RCLO);
130130 for (k = 0; k < n; ++k) {
131131 int i;
134134 if (s->l_seq == 0) continue;
135135 free(s->qual);
136136 for (i = 0; i < s->l_seq; ++i)
137 @@ -116,7 +116,7 @@ struct rld_t *fml_fmi_gen(int n, bseq1_t
137 @@ -121,7 +121,7 @@ struct rld_t *fml_fmi_gen(int n, bseq1_t
138138 return e;
139139 }
140140
143143 {
144144 return fml_fmi_gen(n, seq, opt->n_threads > 1? 1 : 0);
145145 }
146 @@ -251,7 +251,7 @@ void fml_utg_destroy(int n, fml_utg_t *u
146 @@ -277,7 +277,7 @@ void fml_utg_destroy(int n, fml_utg_t *u
147147
148148 #define MAG_MIN_NSR_COEF .1
149149
157157 @@ -7,7 +7,7 @@ int main(int argc, char *argv[])
158158 {
159159 fml_opt_t opt;
160 int c, n_seqs, n_utg;
160 int c, n_seqs, n_utg, gfa_out = 0;
161161 - bseq1_t *seqs;
162162 + fml_seq1_t *seqs;
163163 fml_utg_t *utg;
164164
165165 fml_opt_init(&opt);
166 @@ -34,7 +34,7 @@ int main(int argc, char *argv[])
167 fprintf(stderr, " -A discard heterozygotes (apply this to assemble bacterial genomes)\n");
166 @@ -41,7 +41,7 @@ int main(int argc, char *argv[])
167 fprintf(stderr, " -g output the assembly graph in the GFA format\n");
168168 return 1;
169169 }
170170 - seqs = bseq_read(argv[optind], &n_seqs);
171171 + seqs = fml_seq_read(argv[optind], &n_seqs);
172172 utg = fml_assemble(&opt, n_seqs, seqs, &n_utg);
173 fml_utg_print(n_utg, utg);
174 fml_utg_destroy(n_utg, utg);
173 if (!gfa_out) fml_utg_print(n_utg, utg);
174 else fml_utg_print_gfa(n_utg, utg);
175175 --- a/internal.h
176176 +++ b/internal.h
177177 @@ -12,7 +12,7 @@ extern "C" {
188188 @@ -8,7 +8,7 @@
189189 typedef struct {
190190 int32_t l_seq;
191 char *seq, *qual;
191 char *seq, *qual; // NULL-terminated strings; length expected to match $l_seq
192192 -} bseq1_t;
193193 +} fml_seq1_t;
194194
195 #define MAG_F_AGGRESSIVE 0x20
196 #define MAG_F_NO_SIMPL 0x80
197 @@ -60,7 +60,7 @@ extern "C" {
195 #define MAG_F_AGGRESSIVE 0x20 // pop variant bubbles (not default)
196 #define MAG_F_POPOPEN 0x40 // aggressive tip trimming (default)
197 @@ -63,7 +63,7 @@ extern "C" {
198198 *
199199 * @return array of sequences
200200 */
203203
204204 /**
205205 * Initialize default parameters
206 @@ -79,7 +79,7 @@ void fml_opt_init(fml_opt_t *opt);
206 @@ -82,7 +82,7 @@ void fml_opt_init(fml_opt_t *opt);
207207 *
208208 * @return array of unitigs
209209 */
212212
213213 /**
214214 * Free unitigs
215 @@ -100,7 +100,7 @@ void fml_utg_destroy(int n_utg, fml_utg_
215 @@ -103,7 +103,7 @@ void fml_utg_destroy(int n_utg, fml_utg_
216216 * @param n_seqs number of sequences
217217 * @param seqs array of sequences
218218 */
221221
222222 /**
223223 * Error correction
224 @@ -111,8 +111,8 @@ void fml_opt_adjust(fml_opt_t *opt, int
224 @@ -114,8 +114,8 @@ void fml_opt_adjust(fml_opt_t *opt, int
225225 *
226226 * @return k-mer coverage
227227 */
232232
233233 /**
234234 * Construct FMD-index
235 @@ -123,7 +123,7 @@ float fml_fltuniq(const fml_opt_t *opt,
236 *
237 * @return FMD-index
235 @@ -126,7 +126,7 @@ float fml_fltuniq(const fml_opt_t *opt,
236 *
237 * @return FMD-index on success; NULL if all input sequences are zero in length
238238 */
239239 -struct rld_t *fml_seq2fmi(const fml_opt_t *opt, int n, bseq1_t *seq);
240240 +struct rld_t *fml_seq2fmi(const fml_opt_t *opt, int n, fml_seq1_t *seq);
243243 * Generate initial overlap graph
244244 --- a/README.md
245245 +++ b/README.md
246 @@ -29,11 +29,11 @@ sketch of the example:
246 @@ -34,11 +34,11 @@ sketch of the example:
247247 int main(int argc, char *argv[])
248248 {
249249 int i, n_seqs, n_utgs;