X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fcall1.c;h=415426abcd1511f1e2cadd987501efcbf21bcb74;hb=74e6aebb5c07d14cdccc5f8abb40fd4a00b2be86;hp=b0baee2ea1b346e24eadd2d9bccea0ed6e886f6a;hpb=23e43ef6778e51eb2a71046282d1c21431520857;p=samtools.git

diff --git a/bcftools/call1.c b/bcftools/call1.c
index b0baee2..415426a 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -33,13 +33,14 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 #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;
 
@@ -131,7 +132,6 @@ static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr,
 		if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
 		if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
 		if (em[8] >= 0) ksprintf(&s, ";LRT2=%.3g", em[8]);
-		//if (em[9] >= 0) ksprintf(&s, ";LRT1=%.3g", em[9]);
 	}
 	if (cons_llr > 0) {
 		ksprintf(&s, ";CLR=%d", cons_llr);
@@ -250,6 +250,12 @@ static void write_header(bcf_hdr_t *h)
 		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,"))
@@ -274,6 +280,8 @@ static void write_header(bcf_hdr_t *h)
         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=VDB,"))
+        kputs("##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias\">\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,"))
@@ -282,10 +290,12 @@ static void write_header(bcf_hdr_t *h)
         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,"))
-		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);
+		kputs("##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">\n", &str);
 	h->l_txt = str.l + 1; h->txt = str.s;
 }
 
@@ -315,9 +325,9 @@ int bcfview(int argc, char *argv[])
 
 	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:")) >= 0) {
 		switch (c) {
 		case '1': vc.n1 = atoi(optarg); break;
 		case 'l': vc.bed = bed_read(optarg); break;
@@ -334,8 +344,10 @@ int bcfview(int argc, char *argv[])
 		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;
@@ -391,6 +403,7 @@ int bcfview(int argc, char *argv[])
 		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);
@@ -481,6 +494,7 @@ int bcfview(int argc, char *argv[])
 		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;
@@ -514,7 +528,13 @@ int bcfview(int argc, char *argv[])
 			int i;
 			for (i = 0; i < 9; ++i) em[i] = -1.;
 		}
-		if (vc.flag & VC_CALL) { // call variants
+        bcf_p1_set_ploidy(b, p1); // could be improved: do this per site to allow pseudo-autosomal regions
+        if ( !(vc.flag&VC_KEEPALT) && vc.flag&VC_CALL && vc.min_ma_lrt>=0 )
+        {
+            int gts = call_multiallelic_gt(b,p1,vc.min_ma_lrt);
+            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);
 			if (n_processed % 100000 == 0) {