#define VC_EM 0x10000
#define VC_PAIRCALL 0x20000
#define VC_QCNT 0x40000
+#define VC_INDEL_ONLY 0x80000
typedef struct {
int flag, prior_type, n1, n_sub, *sublist, n_perm;
uint32_t *trio_aux;
char *prior_file, **subsam, *fn_dict;
uint8_t *ploidy;
- double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt;
+ double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt, min_ma_lrt;
void *bed;
} viewconf_t;
void bed_destroy(void *_h);
int bed_overlap(const void *_h, const char *chr, int beg, int end);
-typedef struct {
- double p[4];
- int mq, depth, is_tested, d[4];
-} anno16_t;
-
static double ttest(int n1, int n2, int a[4])
{
extern double kf_betai(double a, double b, double x);
return 0;
}
-static int test16(bcf1_t *b, anno16_t *a)
+int test16(bcf1_t *b, anno16_t *a)
{
char *p;
int i, anno[16];
return test16_core(anno, a);
}
-static void rm_info(bcf1_t *b, const char *key)
-{
- char *p, *q;
- if ((p = strstr(b->info, key)) == 0) return;
- for (q = p; *q && *q != ';'; ++q);
- if (p > b->info && *(p-1) == ';') --p;
- memmove(p, q, b->l_str - (q - b->str));
- b->l_str -= q - p;
- bcf_sync(b);
-}
-
static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[10], int cons_llr, int64_t cons_gt)
{
kstring_t s;
anno16_t a;
has_I16 = test16(b, &a) >= 0? 1 : 0;
- rm_info(b, "I16="); // FIXME: probably this function has a bug. If I move it below, I16 will not be removed!
+ //rm_info(b, "I16="); // FIXME: probably this function has a bug. If I move it below, I16 will not be removed!
memset(&s, 0, sizeof(kstring_t));
kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
}
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]);
kputc('\0', &s);
+ rm_info(&s, "QS=");
+ rm_info(&s, "I16=");
kputs(b->fmt, &s); kputc('\0', &s);
free(b->str);
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
*_n = 0;
s.l = s.m = 0; s.s = 0;
fp = gzopen(fn, "r");
- if (fp == 0) return 0; // fail to open file
+ if (fp == 0)
+ {
+ // interpret as sample names, not as a file name
+ const char *t = fn, *p = t;
+ while (*t)
+ {
+ t++;
+ if ( *t==',' || !*t )
+ {
+ sam = realloc(sam, sizeof(void*)*(n+1));
+ sam[n] = (char*) malloc(sizeof(char)*(t-p+2));
+ memcpy(sam[n], p, t-p);
+ sam[n][t-p] = 0;
+ sam[n][t-p+1] = 2; // assume diploid
+ p = t+1;
+ n++;
+ }
+ }
+ *_n = n;
+ return sam; // fail to open file
+ }
ks = ks_init(fp);
while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
int l;
kputs("##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele frequency (assuming HWE)\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=AC1,"))
kputs("##INFO=<ID=AC1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele count (no HWE assumption)\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=AN,"))
+ kputs("##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=IS,"))
+ kputs("##INFO=<ID=IS,Number=2,Type=Float,Description=\"Maximum number of reads supporting an indel and fraction of indel reads\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=AC,"))
+ kputs("##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes for each ALT allele, in the same order as listed\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=G3,"))
kputs("##INFO=<ID=G3,Number=3,Type=Float,Description=\"ML estimate of genotype frequencies\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=HWE,"))
kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=RP,"))
kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=QBD,"))
+ kputs("##INFO=<ID=QBD,Number=1,Type=Float,Description=\"Quality by Depth: QUAL/#reads\">\n", &str);
+ //if (!strstr(str.s, "##INFO=<ID=RPS,"))
+ // kputs("##INFO=<ID=RPS,Number=3,Type=Float,Description=\"Read Position Stats: depth, average, stddev\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=RPB,"))
+ kputs("##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Read Position Bias\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=MDV,"))
+ kputs("##INFO=<ID=MDV,Number=1,Type=Integer,Description=\"Maximum number of high-quality nonRef reads in samples\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=VDB,"))
- kputs("##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias\">\n", &str);
+ kputs("##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias (v2) for filtering splice-site artefacts in RNA-seq data. Note: this version may be broken.\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=GT,"))
kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
kputs("##FORMAT=<ID=GL,Number=3,Type=Float,Description=\"Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=DP,"))
kputs("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"# high-quality bases\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=DV,"))
+ kputs("##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"# high-quality non-reference bases\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=SP,"))
kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=PL,"))
extern int bcf_trio_call(uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt);
extern int bcf_pair_call(const bcf1_t *b);
extern int bcf_min_diff(const bcf1_t *b);
+ extern int bcf_p1_get_M(bcf_p1aux_t *b);
+
+ extern gzFile bcf_p1_fp_lk;
bcf_t *bp, *bout = 0;
bcf1_t *b, *blast;
tid = begin = end = -1;
memset(&vc, 0, sizeof(viewconf_t));
- 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;
+ 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; vc.min_ma_lrt = -1;
memset(qcnt, 0, 8 * 256);
- while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Y")) >= 0) {
+ while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Ywm:K:")) >= 0) {
switch (c) {
case '1': vc.n1 = atoi(optarg); break;
- case 'l': vc.bed = bed_read(optarg); break;
+ case 'l': vc.bed = bed_read(optarg); if (!vc.bed) { fprintf(stderr,"Could not read \"%s\"\n", optarg); return 1; } break;
case 'D': vc.fn_dict = strdup(optarg); break;
case 'F': vc.flag |= VC_FIX_PL; break;
case 'N': vc.flag |= VC_ACGT_ONLY; break;
case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
case 'I': vc.flag |= VC_NO_INDEL; break;
+ case 'w': vc.flag |= VC_INDEL_ONLY; break;
case 'M': vc.flag |= VC_ANNO_MAX; break;
case 'Y': vc.flag |= VC_QCNT; break;
+ case 'm': vc.min_ma_lrt = atof(optarg); break;
case 't': vc.theta = atof(optarg); break;
case 'p': vc.pref = atof(optarg); break;
case 'i': vc.indel_frac = atof(optarg); break;
case 'C': vc.min_lrt = atof(optarg); break;
case 'X': vc.min_perm_p = atof(optarg); break;
case 'd': vc.min_smpl_frac = atof(optarg); break;
+ case 'K': bcf_p1_fp_lk = gzopen(optarg, "w"); break;
case 's': vc.subsam = read_samples(optarg, &vc.n_sub);
vc.ploidy = calloc(vc.n_sub + 1, 1);
for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
fprintf(stderr, " -g call genotypes at variant sites (force -c)\n");
fprintf(stderr, " -i FLOAT indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
fprintf(stderr, " -I skip indels\n");
+ fprintf(stderr, " -m FLOAT alternative model for multiallelic and rare-variant calling, include if P(chi^2)>=FLOAT\n");
fprintf(stderr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
fprintf(stderr, " -P STR type of prior: full, cond2, flat [full]\n");
fprintf(stderr, " -t FLOAT scaled substitution mutation rate [%.4g]\n", vc.theta);
vc.sublist = calloc(vc.n_sub, sizeof(int));
hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
}
- if (vc.flag & VC_CALL) write_header(hout);
+ write_header(hout); // always print the header
vcf_hdr_write(bout, hout);
}
if (vc.flag & VC_CALL) {
}
}
}
+ if (bcf_p1_fp_lk && p1) {
+ int32_t M = bcf_p1_get_M(p1);
+ gzwrite(bcf_p1_fp_lk, &M, 4);
+ }
while (vcf_read(bp, hin, b) > 0) {
int is_indel, cons_llr = -1;
int64_t cons_gt = -1;
if (vc.flag & VC_FIX_PL) bcf_fix_pl(b);
is_indel = bcf_is_indel(b);
if ((vc.flag & VC_NO_INDEL) && is_indel) continue;
+ if ((vc.flag & VC_INDEL_ONLY) && !is_indel) continue;
if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
int x;
if (b->ref[0] == 0 || b->ref[1] != 0) continue;
int i;
for (i = 0; i < 9; ++i) em[i] = -1.;
}
- if (vc.flag & VC_CALL) { // call variants
+ if ( !(vc.flag&VC_KEEPALT) && (vc.flag&VC_CALL) && vc.min_ma_lrt>=0 )
+ {
+ bcf_p1_set_ploidy(b, p1); // could be improved: do this per site to allow pseudo-autosomal regions
+ int gts = call_multiallelic_gt(b, p1, vc.min_ma_lrt, vc.flag&VC_VARONLY);
+ if ( gts<=1 && vc.flag & VC_VARONLY ) continue;
+ }
+ else if (vc.flag & VC_CALL) { // call variants
bcf_p1rst_t pr;
- int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
+ int calret;
+ gzwrite(bcf_p1_fp_lk, &b->tid, 4);
+ gzwrite(bcf_p1_fp_lk, &b->pos, 4);
+ gzwrite(bcf_p1_fp_lk, &em[0], sizeof(double));
+ calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
if (n_processed % 100000 == 0) {
fprintf(stderr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
bcf_p1_dump_afs(p1);
} else bcf_fix_gt(b);
vcf_write(bout, hout, b);
}
+
+ if (bcf_p1_fp_lk) gzclose(bcf_p1_fp_lk);
if (vc.prior_file) free(vc.prior_file);
if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
if (hin != hout) bcf_hdr_destroy(hout);
projects / rsem.git / blobdiff