Mercurial > repos > siyuan > prada
comparison pyPRADA_1.2/tools/samtools-0.1.16/bcftools/call1.c @ 0:acc2ca1a3ba4
Uploaded
author | siyuan |
---|---|
date | Thu, 20 Feb 2014 00:44:58 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:acc2ca1a3ba4 |
---|---|
1 #include <unistd.h> | |
2 #include <stdlib.h> | |
3 #include <math.h> | |
4 #include <zlib.h> | |
5 #include <errno.h> | |
6 #include "bcf.h" | |
7 #include "prob1.h" | |
8 #include "kstring.h" | |
9 #include "time.h" | |
10 | |
11 #include "kseq.h" | |
12 KSTREAM_INIT(gzFile, gzread, 16384) | |
13 | |
14 #define VC_NO_GENO 2 | |
15 #define VC_BCFOUT 4 | |
16 #define VC_CALL 8 | |
17 #define VC_VARONLY 16 | |
18 #define VC_VCFIN 32 | |
19 #define VC_UNCOMP 64 | |
20 #define VC_KEEPALT 256 | |
21 #define VC_ACGT_ONLY 512 | |
22 #define VC_QCALL 1024 | |
23 #define VC_CALL_GT 2048 | |
24 #define VC_ADJLD 4096 | |
25 #define VC_NO_INDEL 8192 | |
26 #define VC_ANNO_MAX 16384 | |
27 #define VC_FIX_PL 32768 | |
28 #define VC_EM 0x10000 | |
29 | |
30 typedef struct { | |
31 int flag, prior_type, n1, n_sub, *sublist, n_perm; | |
32 char *prior_file, **subsam, *fn_dict; | |
33 uint8_t *ploidy; | |
34 double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt; | |
35 void *bed; | |
36 } viewconf_t; | |
37 | |
38 void *bed_read(const char *fn); | |
39 void bed_destroy(void *_h); | |
40 int bed_overlap(const void *_h, const char *chr, int beg, int end); | |
41 | |
42 typedef struct { | |
43 double p[4]; | |
44 int mq, depth, is_tested, d[4]; | |
45 } anno16_t; | |
46 | |
47 static double ttest(int n1, int n2, int a[4]) | |
48 { | |
49 extern double kf_betai(double a, double b, double x); | |
50 double t, v, u1, u2; | |
51 if (n1 == 0 || n2 == 0 || n1 + n2 < 3) return 1.0; | |
52 u1 = (double)a[0] / n1; u2 = (double)a[2] / n2; | |
53 if (u1 <= u2) return 1.; | |
54 t = (u1 - u2) / sqrt(((a[1] - n1 * u1 * u1) + (a[3] - n2 * u2 * u2)) / (n1 + n2 - 2) * (1./n1 + 1./n2)); | |
55 v = n1 + n2 - 2; | |
56 // printf("%d,%d,%d,%d,%lf,%lf,%lf\n", a[0], a[1], a[2], a[3], t, u1, u2); | |
57 return t < 0.? 1. : .5 * kf_betai(.5*v, .5, v/(v+t*t)); | |
58 } | |
59 | |
60 static int test16_core(int anno[16], anno16_t *a) | |
61 { | |
62 extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two); | |
63 double left, right; | |
64 int i; | |
65 a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.; | |
66 memcpy(a->d, anno, 4 * sizeof(int)); | |
67 a->depth = anno[0] + anno[1] + anno[2] + anno[3]; | |
68 a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0); | |
69 if (a->depth == 0) return -1; | |
70 a->mq = (int)(sqrt((anno[9] + anno[11]) / a->depth) + .499); | |
71 kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]); | |
72 for (i = 1; i < 4; ++i) | |
73 a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i); | |
74 return 0; | |
75 } | |
76 | |
77 static int test16(bcf1_t *b, anno16_t *a) | |
78 { | |
79 char *p; | |
80 int i, anno[16]; | |
81 a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.; | |
82 a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.; | |
83 a->mq = a->depth = a->is_tested = 0; | |
84 if ((p = strstr(b->info, "I16=")) == 0) return -1; | |
85 p += 4; | |
86 for (i = 0; i < 16; ++i) { | |
87 errno = 0; anno[i] = strtol(p, &p, 10); | |
88 if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2; | |
89 ++p; | |
90 } | |
91 return test16_core(anno, a); | |
92 } | |
93 | |
94 static void rm_info(bcf1_t *b, const char *key) | |
95 { | |
96 char *p, *q; | |
97 if ((p = strstr(b->info, key)) == 0) return; | |
98 for (q = p; *q && *q != ';'; ++q); | |
99 if (p > b->info && *(p-1) == ';') --p; | |
100 memmove(p, q, b->l_str - (q - b->str)); | |
101 b->l_str -= q - p; | |
102 bcf_sync(b); | |
103 } | |
104 | |
105 static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[9]) | |
106 { | |
107 kstring_t s; | |
108 int has_I16, is_var; | |
109 double fq, r; | |
110 anno16_t a; | |
111 | |
112 has_I16 = test16(b, &a) >= 0? 1 : 0; | |
113 rm_info(b, "I16="); // FIXME: probably this function has a bug. If I move it below, I16 will not be removed! | |
114 | |
115 memset(&s, 0, sizeof(kstring_t)); | |
116 kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s); | |
117 kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s); | |
118 kputs(b->info, &s); | |
119 if (b->info[0]) kputc(';', &s); | |
120 { // print EM | |
121 if (em[0] >= 0) ksprintf(&s, "AF1=%.4g", 1 - em[0]); | |
122 if (em[4] >= 0 && em[4] <= 0.05) ksprintf(&s, ";G3=%.4g,%.4g,%.4g;HWE=%.3g", em[3], em[2], em[1], em[4]); | |
123 if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]); | |
124 if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]); | |
125 } | |
126 if (pr == 0) { // if pr is unset, return | |
127 kputc('\0', &s); kputs(b->fmt, &s); kputc('\0', &s); | |
128 free(b->str); | |
129 b->m_str = s.m; b->l_str = s.l; b->str = s.s; | |
130 bcf_sync(b); | |
131 return 1; | |
132 } | |
133 | |
134 is_var = (pr->p_ref < pref); | |
135 r = is_var? pr->p_ref : pr->p_var; | |
136 | |
137 ksprintf(&s, ";CI95=%.4g,%.4g", pr->cil, pr->cih); // FIXME: when EM is not used, ";" should be omitted! | |
138 if (has_I16) ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq); | |
139 fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded); | |
140 if (fq < -999) fq = -999; | |
141 if (fq > 999) fq = 999; | |
142 ksprintf(&s, ";FQ=%.3g", fq); | |
143 if (pr->cmp[0] >= 0.) { // two sample groups | |
144 int i, q[3]; | |
145 for (i = 1; i < 3; ++i) { | |
146 double x = pr->cmp[i] + pr->cmp[0]/2.; | |
147 q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499); | |
148 if (q[i] > 255) q[i] = 255; | |
149 } | |
150 if (pr->perm_rank >= 0) ksprintf(&s, ";PR=%d", pr->perm_rank); | |
151 ksprintf(&s, ";PCHI2=%.3g;PC2=%d,%d", q[1], q[2], pr->p_chi2); | |
152 } | |
153 if (has_I16 && a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]); | |
154 kputc('\0', &s); | |
155 kputs(b->fmt, &s); kputc('\0', &s); | |
156 free(b->str); | |
157 b->m_str = s.m; b->l_str = s.l; b->str = s.s; | |
158 b->qual = r < 1e-100? 999 : -4.343 * log(r); | |
159 if (b->qual > 999) b->qual = 999; | |
160 bcf_sync(b); | |
161 if (!is_var) bcf_shrink_alt(b, 1); | |
162 else if (!(flag&VC_KEEPALT)) | |
163 bcf_shrink_alt(b, pr->rank0 < 2? 2 : pr->rank0+1); | |
164 if (is_var && (flag&VC_CALL_GT)) { // call individual genotype | |
165 int i, x, old_n_gi = b->n_gi; | |
166 s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str; | |
167 kputs(":GT:GQ", &s); kputc('\0', &s); | |
168 b->m_str = s.m; b->l_str = s.l; b->str = s.s; | |
169 bcf_sync(b); | |
170 for (i = 0; i < b->n_smpl; ++i) { | |
171 x = bcf_p1_call_gt(pa, pr->f_exp, i); | |
172 ((uint8_t*)b->gi[old_n_gi].data)[i] = (x&3) == 0? 1<<3|1 : (x&3) == 1? 1 : 0; | |
173 ((uint8_t*)b->gi[old_n_gi+1].data)[i] = x>>2; | |
174 } | |
175 } | |
176 return is_var; | |
177 } | |
178 | |
179 static char **read_samples(const char *fn, int *_n) | |
180 { | |
181 gzFile fp; | |
182 kstream_t *ks; | |
183 kstring_t s; | |
184 int dret, n = 0, max = 0; | |
185 char **sam = 0; | |
186 *_n = 0; | |
187 s.l = s.m = 0; s.s = 0; | |
188 fp = gzopen(fn, "r"); | |
189 if (fp == 0) return 0; // fail to open file | |
190 ks = ks_init(fp); | |
191 while (ks_getuntil(ks, 0, &s, &dret) >= 0) { | |
192 int l; | |
193 if (max == n) { | |
194 max = max? max<<1 : 4; | |
195 sam = realloc(sam, sizeof(void*)*max); | |
196 } | |
197 l = s.l; | |
198 sam[n] = malloc(s.l + 2); | |
199 strcpy(sam[n], s.s); | |
200 sam[n][l+1] = 2; // by default, diploid | |
201 if (dret != '\n') { | |
202 if (ks_getuntil(ks, 0, &s, &dret) >= 0) { // read ploidy, 1 or 2 | |
203 int x = (int)s.s[0] - '0'; | |
204 if (x == 1 || x == 2) sam[n][l+1] = x; | |
205 else fprintf(stderr, "(%s) ploidy can only be 1 or 2; assume diploid\n", __func__); | |
206 } | |
207 if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); | |
208 } | |
209 ++n; | |
210 } | |
211 ks_destroy(ks); | |
212 gzclose(fp); | |
213 free(s.s); | |
214 *_n = n; | |
215 return sam; | |
216 } | |
217 | |
218 static void write_header(bcf_hdr_t *h) | |
219 { | |
220 kstring_t str; | |
221 str.l = h->l_txt? h->l_txt - 1 : 0; | |
222 str.m = str.l + 1; str.s = h->txt; | |
223 if (!strstr(str.s, "##INFO=<ID=DP,")) | |
224 kputs("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">\n", &str); | |
225 if (!strstr(str.s, "##INFO=<ID=DP4,")) | |
226 kputs("##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\n", &str); | |
227 if (!strstr(str.s, "##INFO=<ID=MQ,")) | |
228 kputs("##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Root-mean-square mapping quality of covering reads\">\n", &str); | |
229 if (!strstr(str.s, "##INFO=<ID=FQ,")) | |
230 kputs("##INFO=<ID=FQ,Number=1,Type=Float,Description=\"Phred probability of all samples being the same\">\n", &str); | |
231 if (!strstr(str.s, "##INFO=<ID=AF1,")) | |
232 kputs("##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the site allele frequency of the first ALT allele\">\n", &str); | |
233 if (!strstr(str.s, "##INFO=<ID=G3,")) | |
234 kputs("##INFO=<ID=G3,Number=3,Type=Float,Description=\"ML estimate of genotype frequencies\">\n", &str); | |
235 if (!strstr(str.s, "##INFO=<ID=HWE,")) | |
236 kputs("##INFO=<ID=HWE,Number=1,Type=Float,Description=\"Chi^2 based HWE test P-value based on G3\">\n", &str); | |
237 if (!strstr(str.s, "##INFO=<ID=CI95,")) | |
238 kputs("##INFO=<ID=CI95,Number=2,Type=Float,Description=\"Equal-tail Bayesian credible interval of the site allele frequency at the 95% level\">\n", &str); | |
239 if (!strstr(str.s, "##INFO=<ID=PV4,")) | |
240 kputs("##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n", &str); | |
241 if (!strstr(str.s, "##INFO=<ID=INDEL,")) | |
242 kputs("##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">\n", &str); | |
243 if (!strstr(str.s, "##INFO=<ID=PC2,")) | |
244 kputs("##INFO=<ID=PC2,Number=2,Type=Integer,Description=\"Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.\">\n", &str); | |
245 if (!strstr(str.s, "##INFO=<ID=PCHI2,")) | |
246 kputs("##INFO=<ID=PCHI2,Number=1,Type=Float,Description=\"Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.\">\n", &str); | |
247 if (!strstr(str.s, "##INFO=<ID=QCHI2,")) | |
248 kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str); | |
249 if (!strstr(str.s, "##INFO=<ID=RP,")) | |
250 kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str); | |
251 if (!strstr(str.s, "##FORMAT=<ID=GT,")) | |
252 kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str); | |
253 if (!strstr(str.s, "##FORMAT=<ID=GQ,")) | |
254 kputs("##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\n", &str); | |
255 if (!strstr(str.s, "##FORMAT=<ID=GL,")) | |
256 kputs("##FORMAT=<ID=GL,Number=3,Type=Float,Description=\"Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)\">\n", &str); | |
257 if (!strstr(str.s, "##FORMAT=<ID=DP,")) | |
258 kputs("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"# high-quality bases\">\n", &str); | |
259 if (!strstr(str.s, "##FORMAT=<ID=SP,")) | |
260 kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str); | |
261 if (!strstr(str.s, "##FORMAT=<ID=PL,")) | |
262 kputs("##FORMAT=<ID=PL,Number=-1,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2\">\n", &str); | |
263 h->l_txt = str.l + 1; h->txt = str.s; | |
264 } | |
265 | |
266 double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]); | |
267 | |
268 int bcfview(int argc, char *argv[]) | |
269 { | |
270 extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b); | |
271 extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x); | |
272 extern int bcf_fix_gt(bcf1_t *b); | |
273 extern int bcf_anno_max(bcf1_t *b); | |
274 extern int bcf_shuffle(bcf1_t *b, int seed); | |
275 bcf_t *bp, *bout = 0; | |
276 bcf1_t *b, *blast; | |
277 int c, *seeds = 0; | |
278 uint64_t n_processed = 0; | |
279 viewconf_t vc; | |
280 bcf_p1aux_t *p1 = 0; | |
281 bcf_hdr_t *hin, *hout; | |
282 int tid, begin, end; | |
283 char moder[4], modew[4]; | |
284 | |
285 tid = begin = end = -1; | |
286 memset(&vc, 0, sizeof(viewconf_t)); | |
287 vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1; | |
288 while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:")) >= 0) { | |
289 switch (c) { | |
290 case '1': vc.n1 = atoi(optarg); break; | |
291 case 'l': vc.bed = bed_read(optarg); break; | |
292 case 'D': vc.fn_dict = strdup(optarg); break; | |
293 case 'F': vc.flag |= VC_FIX_PL; break; | |
294 case 'N': vc.flag |= VC_ACGT_ONLY; break; | |
295 case 'G': vc.flag |= VC_NO_GENO; break; | |
296 case 'A': vc.flag |= VC_KEEPALT; break; | |
297 case 'b': vc.flag |= VC_BCFOUT; break; | |
298 case 'S': vc.flag |= VC_VCFIN; break; | |
299 case 'c': vc.flag |= VC_CALL; break; | |
300 case 'e': vc.flag |= VC_EM; break; | |
301 case 'v': vc.flag |= VC_VARONLY | VC_CALL; break; | |
302 case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break; | |
303 case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break; | |
304 case 'I': vc.flag |= VC_NO_INDEL; break; | |
305 case 'M': vc.flag |= VC_ANNO_MAX; break; | |
306 case 't': vc.theta = atof(optarg); break; | |
307 case 'p': vc.pref = atof(optarg); break; | |
308 case 'i': vc.indel_frac = atof(optarg); break; | |
309 case 'Q': vc.flag |= VC_QCALL; break; | |
310 case 'L': vc.flag |= VC_ADJLD; break; | |
311 case 'U': vc.n_perm = atoi(optarg); break; | |
312 case 'C': vc.min_lrt = atof(optarg); break; | |
313 case 'X': vc.min_perm_p = atof(optarg); break; | |
314 case 'd': vc.min_smpl_frac = atof(optarg); break; | |
315 case 's': vc.subsam = read_samples(optarg, &vc.n_sub); | |
316 vc.ploidy = calloc(vc.n_sub + 1, 1); | |
317 for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1]; | |
318 tid = -1; | |
319 break; | |
320 case 'P': | |
321 if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL; | |
322 else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2; | |
323 else if (strcmp(optarg, "flat") == 0) vc.prior_type = MC_PTYPE_FLAT; | |
324 else vc.prior_file = strdup(optarg); | |
325 break; | |
326 } | |
327 } | |
328 if (argc == optind) { | |
329 fprintf(stderr, "\n"); | |
330 fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n"); | |
331 fprintf(stderr, "Input/output options:\n\n"); | |
332 fprintf(stderr, " -A keep all possible alternate alleles at variant sites\n"); | |
333 fprintf(stderr, " -b output BCF instead of VCF\n"); | |
334 fprintf(stderr, " -D FILE sequence dictionary for VCF->BCF conversion [null]\n"); | |
335 fprintf(stderr, " -F PL generated by r921 or before (which generate old ordering)\n"); | |
336 fprintf(stderr, " -G suppress all individual genotype information\n"); | |
337 fprintf(stderr, " -l FILE list of sites (chr pos) or regions (BED) to output [all sites]\n"); | |
338 fprintf(stderr, " -L calculate LD for adjacent sites\n"); | |
339 fprintf(stderr, " -N skip sites where REF is not A/C/G/T\n"); | |
340 fprintf(stderr, " -Q output the QCALL likelihood format\n"); | |
341 fprintf(stderr, " -s FILE list of samples to use [all samples]\n"); | |
342 fprintf(stderr, " -S input is VCF\n"); | |
343 fprintf(stderr, " -u uncompressed BCF output (force -b)\n"); | |
344 fprintf(stderr, "\nConsensus/variant calling options:\n\n"); | |
345 fprintf(stderr, " -c SNP calling (force -e)\n"); | |
346 fprintf(stderr, " -d FLOAT skip loci where less than FLOAT fraction of samples covered [0]\n"); | |
347 fprintf(stderr, " -e likelihood based analyses\n"); | |
348 fprintf(stderr, " -g call genotypes at variant sites (force -c)\n"); | |
349 fprintf(stderr, " -i FLOAT indel-to-substitution ratio [%.4g]\n", vc.indel_frac); | |
350 fprintf(stderr, " -I skip indels\n"); | |
351 fprintf(stderr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref); | |
352 fprintf(stderr, " -P STR type of prior: full, cond2, flat [full]\n"); | |
353 fprintf(stderr, " -t FLOAT scaled substitution mutation rate [%.4g]\n", vc.theta); | |
354 fprintf(stderr, " -v output potential variant sites only (force -c)\n"); | |
355 fprintf(stderr, "\nContrast calling and association test options:\n\n"); | |
356 fprintf(stderr, " -1 INT number of group-1 samples [0]\n"); | |
357 fprintf(stderr, " -C FLOAT posterior constrast for LRT<FLOAT and P(ref|D)<0.5 [%g]\n", vc.min_lrt); | |
358 fprintf(stderr, " -U INT number of permutations for association testing (effective with -1) [0]\n"); | |
359 fprintf(stderr, " -X FLOAT only perform permutations for P(chi^2)<FLOAT [%g]\n", vc.min_perm_p); | |
360 fprintf(stderr, "\n"); | |
361 return 1; | |
362 } | |
363 | |
364 if (vc.flag & VC_CALL) vc.flag |= VC_EM; | |
365 if ((vc.flag & VC_VCFIN) && (vc.flag & VC_BCFOUT) && vc.fn_dict == 0) { | |
366 fprintf(stderr, "[%s] For VCF->BCF conversion please specify the sequence dictionary with -D\n", __func__); | |
367 return 1; | |
368 } | |
369 if (vc.n1 <= 0) vc.n_perm = 0; // TODO: give a warning here! | |
370 if (vc.n_perm > 0) { | |
371 seeds = malloc(vc.n_perm * sizeof(int)); | |
372 srand48(time(0)); | |
373 for (c = 0; c < vc.n_perm; ++c) seeds[c] = lrand48(); | |
374 } | |
375 b = calloc(1, sizeof(bcf1_t)); | |
376 blast = calloc(1, sizeof(bcf1_t)); | |
377 strcpy(moder, "r"); | |
378 if (!(vc.flag & VC_VCFIN)) strcat(moder, "b"); | |
379 strcpy(modew, "w"); | |
380 if (vc.flag & VC_BCFOUT) strcat(modew, "b"); | |
381 if (vc.flag & VC_UNCOMP) strcat(modew, "u"); | |
382 bp = vcf_open(argv[optind], moder); | |
383 hin = hout = vcf_hdr_read(bp); | |
384 if (vc.fn_dict && (vc.flag & VC_VCFIN)) | |
385 vcf_dictread(bp, hin, vc.fn_dict); | |
386 bout = vcf_open("-", modew); | |
387 if (!(vc.flag & VC_QCALL)) { | |
388 if (vc.n_sub) { | |
389 vc.sublist = calloc(vc.n_sub, sizeof(int)); | |
390 hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist); | |
391 } | |
392 if (vc.flag & VC_CALL) write_header(hout); | |
393 vcf_hdr_write(bout, hout); | |
394 } | |
395 if (vc.flag & VC_CALL) { | |
396 p1 = bcf_p1_init(hout->n_smpl, vc.ploidy); | |
397 if (vc.prior_file) { | |
398 if (bcf_p1_read_prior(p1, vc.prior_file) < 0) { | |
399 fprintf(stderr, "[%s] fail to read the prior AFS.\n", __func__); | |
400 return 1; | |
401 } | |
402 } else bcf_p1_init_prior(p1, vc.prior_type, vc.theta); | |
403 if (vc.n1 > 0 && vc.min_lrt > 0.) { // set n1 | |
404 bcf_p1_set_n1(p1, vc.n1); | |
405 bcf_p1_init_subprior(p1, vc.prior_type, vc.theta); | |
406 } | |
407 if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac | |
408 } | |
409 if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) { | |
410 void *str2id = bcf_build_refhash(hout); | |
411 if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) { | |
412 bcf_idx_t *idx; | |
413 idx = bcf_idx_load(argv[optind]); | |
414 if (idx) { | |
415 uint64_t off; | |
416 off = bcf_idx_query(idx, tid, begin); | |
417 if (off == 0) { | |
418 fprintf(stderr, "[%s] no records in the query region.\n", __func__); | |
419 return 1; // FIXME: a lot of memory leaks... | |
420 } | |
421 bgzf_seek(bp->fp, off, SEEK_SET); | |
422 bcf_idx_destroy(idx); | |
423 } | |
424 } | |
425 } | |
426 while (vcf_read(bp, hin, b) > 0) { | |
427 int is_indel; | |
428 double em[9]; | |
429 if ((vc.flag & VC_VARONLY) && strcmp(b->alt, "X") == 0) continue; | |
430 if ((vc.flag & VC_VARONLY) && vc.min_smpl_frac > 0.) { | |
431 extern int bcf_smpl_covered(const bcf1_t *b); | |
432 int n = bcf_smpl_covered(b); | |
433 if ((double)n / b->n_smpl < vc.min_smpl_frac) continue; | |
434 } | |
435 if (vc.n_sub) bcf_subsam(vc.n_sub, vc.sublist, b); | |
436 if (vc.flag & VC_FIX_PL) bcf_fix_pl(b); | |
437 is_indel = bcf_is_indel(b); | |
438 if ((vc.flag & VC_NO_INDEL) && is_indel) continue; | |
439 if ((vc.flag & VC_ACGT_ONLY) && !is_indel) { | |
440 int x; | |
441 if (b->ref[0] == 0 || b->ref[1] != 0) continue; | |
442 x = toupper(b->ref[0]); | |
443 if (x != 'A' && x != 'C' && x != 'G' && x != 'T') continue; | |
444 } | |
445 if (vc.bed && !bed_overlap(vc.bed, hin->ns[b->tid], b->pos, b->pos + strlen(b->ref))) continue; | |
446 if (tid >= 0) { | |
447 int l = strlen(b->ref); | |
448 l = b->pos + (l > 0? l : 1); | |
449 if (b->tid != tid || b->pos >= end) break; | |
450 if (!(l > begin && end > b->pos)) continue; | |
451 } | |
452 ++n_processed; | |
453 if (vc.flag & VC_QCALL) { // output QCALL format; STOP here | |
454 bcf_2qcall(hout, b); | |
455 continue; | |
456 } | |
457 if (vc.flag & VC_EM) bcf_em1(b, vc.n1, 0xff, em); | |
458 else { | |
459 int i; | |
460 for (i = 0; i < 9; ++i) em[i] = -1.; | |
461 } | |
462 if (vc.flag & (VC_CALL|VC_ADJLD)) bcf_gl2pl(b); | |
463 if (vc.flag & VC_CALL) { // call variants | |
464 bcf_p1rst_t pr; | |
465 int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr); | |
466 if (n_processed % 100000 == 0) { | |
467 fprintf(stderr, "[%s] %ld sites processed.\n", __func__, (long)n_processed); | |
468 bcf_p1_dump_afs(p1); | |
469 } | |
470 if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue; | |
471 if (vc.n_perm && vc.n1 > 0 && pr.p_chi2 < vc.min_perm_p) { // permutation test | |
472 bcf_p1rst_t r; | |
473 int i, n = 0; | |
474 for (i = 0; i < vc.n_perm; ++i) { | |
475 #ifdef BCF_PERM_LRT // LRT based permutation is much faster but less robust to artifacts | |
476 double x[9]; | |
477 bcf_shuffle(b, seeds[i]); | |
478 bcf_em1(b, vc.n1, 1<<7, x); | |
479 if (x[7] < em[7]) ++n; | |
480 #else | |
481 bcf_shuffle(b, seeds[i]); | |
482 bcf_p1_cal(b, 1, p1, &r); | |
483 if (pr.p_chi2 >= r.p_chi2) ++n; | |
484 #endif | |
485 } | |
486 pr.perm_rank = n; | |
487 } | |
488 if (calret >= 0) update_bcf1(b, p1, &pr, vc.pref, vc.flag, em); | |
489 } else if (vc.flag & VC_EM) update_bcf1(b, 0, 0, 0, vc.flag, em); | |
490 if (vc.flag & VC_ADJLD) { // compute LD | |
491 double f[4], r2; | |
492 if ((r2 = bcf_pair_freq(blast, b, f)) >= 0) { | |
493 kstring_t s; | |
494 s.m = s.l = 0; s.s = 0; | |
495 if (*b->info) kputc(';', &s); | |
496 ksprintf(&s, "NEIR=%.3f;NEIF4=%.3f,%.3f,%.3f,%.3f", r2, f[0], f[1], f[2], f[3]); | |
497 bcf_append_info(b, s.s, s.l); | |
498 free(s.s); | |
499 } | |
500 bcf_cpy(blast, b); | |
501 } | |
502 if (vc.flag & VC_ANNO_MAX) bcf_anno_max(b); | |
503 if (vc.flag & VC_NO_GENO) { // do not output GENO fields | |
504 b->n_gi = 0; | |
505 b->fmt[0] = '\0'; | |
506 b->l_str = b->fmt - b->str + 1; | |
507 } else bcf_fix_gt(b); | |
508 vcf_write(bout, hout, b); | |
509 } | |
510 if (vc.prior_file) free(vc.prior_file); | |
511 if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1); | |
512 if (hin != hout) bcf_hdr_destroy(hout); | |
513 bcf_hdr_destroy(hin); | |
514 bcf_destroy(b); bcf_destroy(blast); | |
515 vcf_close(bp); vcf_close(bout); | |
516 if (vc.fn_dict) free(vc.fn_dict); | |
517 if (vc.ploidy) free(vc.ploidy); | |
518 if (vc.n_sub) { | |
519 int i; | |
520 for (i = 0; i < vc.n_sub; ++i) free(vc.subsam[i]); | |
521 free(vc.subsam); free(vc.sublist); | |
522 } | |
523 if (vc.bed) bed_destroy(vc.bed); | |
524 if (seeds) free(seeds); | |
525 if (p1) bcf_p1_destroy(p1); | |
526 return 0; | |
527 } |