X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=a5bcdf560a5bfdfd14a9a2eccffb46be1164e8cc;hb=0c48be00cefea7373a8b5ec5dad821ceee6c960d;hp=2afebeadf85bc2ee020e3c8aecd0209dccebc51d;hpb=d763698cc12d7daa7361d610db3c9c9e83e7655b;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 2afebea..a5bcdf5 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -450,7 +450,8 @@ int bam_pileup(int argc, char *argv[])
  ***********/
 
 typedef struct {
-	int vcf, max_mq, min_mq, var_only;
+	int vcf, max_mq, min_mq, var_only, prior_type;
+	double theta;
 	char *reg, *fn_pos;
 	faidx_t *fai;
 	kh_64_t *hash;
@@ -521,6 +522,10 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 		kstring_t s;
 		s.l = s.m = 0; s.s = 0;
 		puts("##fileformat=VCFv4.0");
+		puts("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">");
+		puts("##INFO=<ID=AF,Number=1,Type=Float,Description=\"Posterior non-reference allele frequency\">");
+		puts("##INFO=<ID=AFEM,Number=1,Type=Float,Description=\"Prior-free non-reference allele frequency by EM\">");
+		puts("##FILTER=<ID=Q13,Description=\"All min{baseQ,mapQ} below 13\">");
 		kputs("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", &s);
 		for (i = 0; i < n; ++i) {
 			const char *p;
@@ -533,7 +538,10 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 		free(s.s);
 	}
 	// mpileup
-	if (conf->vcf) ma = mc_init(n);
+	if (conf->vcf) {
+		ma = mc_init(n);
+		mc_init_prior(ma, conf->prior_type, conf->theta);
+	}
 	ref_tid = -1; ref = 0;
 	iter = bam_mplp_init(n, mplp_func, (void**)data);
 	while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
@@ -549,12 +557,12 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 			ref_tid = tid;
 		}
 		if (conf->vcf) {
-			double f0, f, pref = -1.0; // the reference allele frequency
-			int j, _ref, _alt, _ref0, depth, rms_q, _ref0b, is_var = 0, qref = 0;
+			double f0, f, fpost, pref = -1.0; // the reference allele frequency
+			int j, _ref, _alt, _ref0, depth, rms_q, _ref0b, is_var = 0, qref = 0, filtered = 0;
 			uint64_t sqr_sum;
 			_ref0 = _ref0b = (ref && pos < ref_len)? ref[pos] : 'N';
 			_ref0 = bam_nt16_nt4_table[bam_nt16_table[_ref0]];
-			f = f0 = mc_freq0(_ref0, n_plp, plp, ma, &_ref, &_alt);
+			f = f0 = fpost = mc_freq0(_ref0, n_plp, plp, ma, &_ref, &_alt);
 			if (f >= 0.0) {
 				double q, flast = f;
 				for (j = 0; j < 10; ++j) {
@@ -563,14 +571,17 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 					if (fabs(f - flast) < 1e-3) break;
 					flast = f;
 				}
-				if (1. - f < 1e-4) f = 1.;
 				pref = mc_ref_prob(ma);
+				fpost = mc_freq_post(ma);
+				if (1. - f < 1e-4) f = 1.;
+				if (1. - fpost < 1e-4) fpost = 1.;
 				is_var = (pref < .5);
 				q = is_var? pref : 1. - pref;
 				if (q < 1e-308) q = 1e-308;
 				qref = (int)(-3.434 * log(q) + .499);
 				if (qref > 99) qref = 99;
 			}
+			filtered = (f >= 0. && f <= 1.)? 0 : 1;
 			if (conf->var_only && !is_var) continue;
 			printf("%s\t%d\t.\t%c\t", h->target_name[tid], pos + 1, _ref0b);
 			if (is_var) {
@@ -578,7 +589,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 				else printf("%c,%c", "ACGTN"[_ref], "ACGTN"[_alt]);
 			} else putchar('.');
 			printf("\t%d\t", qref);
-			if (f0 < 0.) printf("Q13\t");
+			if (filtered) printf("Q13\t");
 			else printf(".\t");
 			for (i = depth = 0, sqr_sum = 0; i < n; ++i) {
 				depth += n_plp[i];
@@ -589,13 +600,16 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 				}
 			}
 			rms_q = (int)(sqrt((double)sqr_sum / depth) + .499);
-			printf("DP=%d;MQ=%d;AF=%.3lg", depth, rms_q, f0<0.?0.:1.-f);
+			printf("DP=%d;MQ=%d", depth, rms_q);
+			if (fpost >= 0. && fpost <= 1.) printf(";AF=%.3lg", 1. - fpost);
+			if (f >= 0. && f <= 1.) printf(";AFEM=%.3lg", 1. - f);
 			printf("\tGT:GQ:DP");
-			// output genotype information; FIXME: to be implmented...
-			for (i = 0; i < n; ++i) {
-				int x = mc_call_gt(ma, f, i);
-				printf("\t%c/%c:%d:%d", "10"[((x&3)==2)], "10"[((x&3)>0)], x>>2, n_plp[i]);
-			}
+			if (fpost >= 0. && fpost <= 1.) {
+				for (i = 0; i < n; ++i) {
+					int x = mc_call_gt(ma, fpost, i);
+					printf("\t%c/%c:%d:%d", "10"[((x&3)==2)], "10"[((x&3)>0)], x>>2, n_plp[i]);
+				}
+			} else for (i = 0; i < n; ++i) printf("\t./.:0:0");
 			putchar('\n');
 		} else {
 			printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
@@ -642,8 +656,12 @@ int bam_mpileup(int argc, char *argv[])
 	mplp_conf_t mplp;
 	memset(&mplp, 0, sizeof(mplp_conf_t));
 	mplp.max_mq = 60;
-	while ((c = getopt(argc, argv, "f:r:l:VvM:q:")) >= 0) {
+	mplp.prior_type = MC_PTYPE_FULL;
+	mplp.theta = 1e-3;
+	while ((c = getopt(argc, argv, "f:r:l:VvM:q:t:2")) >= 0) {
 		switch (c) {
+		case 't': mplp.theta = atof(optarg); break;
+		case '2': mplp.prior_type = MC_PTYPE_COND2; break;
 		case 'f':
 			mplp.fai = fai_load(optarg);
 			if (mplp.fai == 0) return 1;
@@ -664,8 +682,10 @@ int bam_mpileup(int argc, char *argv[])
 		fprintf(stderr, "         -l FILE     list of positions (format: chr pos) [null]\n");
 		fprintf(stderr, "         -M INT      cap mapping quality at INT [%d]\n", mplp.max_mq);
 		fprintf(stderr, "         -q INT      filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
+		fprintf(stderr, "         -t FLOAT    scaled mutation rate [%lg]\n", mplp.theta);
 		fprintf(stderr, "         -V          generate VCF output (SNP calling)\n");
 		fprintf(stderr, "         -v          show variant sites only\n");
+		fprintf(stderr, "         -2          conditional prior\n");
 		fprintf(stderr, "\n");
 		fprintf(stderr, "Notes: Assuming error independency and diploid individuals.\n\n");
 		return 1;