X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_plcmd.c;h=4bdc351e18a38322bd39dac30433aea3212b3b5a;hb=0993e913dc402cbb11783bf5d3f96eed1c437e06;hp=285477050d19f489d7be34722846eca8e6407e14;hpb=d73a1b3b94255044787c0e4bfeba37df66e99770;p=samtools.git

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 2854770..4bdc351 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -5,7 +5,6 @@
 #include "sam.h"
 #include "faidx.h"
 #include "bam_maqcns.h"
-#include "bam_mcns.h"
 #include "khash.h"
 #include "glf.h"
 #include "kstring.h"
@@ -23,6 +22,7 @@ KHASH_MAP_INIT_INT64(64, indel_list_t)
 #define BAM_PLF_1STBASE    0x80
 #define BAM_PLF_ALLBASE    0x100
 #define BAM_PLF_READPOS    0x200
+#define BAM_PLF_NOBAQ      0x400
 
 typedef struct {
 	bam_header_t *h;
@@ -33,6 +33,7 @@ typedef struct {
 	uint32_t format;
 	int tid, len, last_pos;
 	int mask;
+	int capQ_thres, min_baseQ;
     int max_depth;  // for indel calling, ignore reads with the depth too high. 0 for unlimited
 	char *ref;
 	glfFile fp_glf; // for glf output only
@@ -233,7 +234,11 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 			}
 			rmsQ = (uint64_t)(sqrt((double)rmsQ / n) + .499);
 			cns = b<<28 | 0xf<<24 | rmsQ<<16 | 60<<8;
-		} else cns = bam_maqcns_call(n, pu, d->c);
+		} else {
+			glf1_t *g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c);
+			cns = g->depth == 0? (0xfu<<28 | 0xf<<24) : glf2cns(g, (int)(d->c->q_r + .499));
+			free(g);
+		}
 	}
     if ((d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)) && d->ref && pos < d->len) { // call indels
         int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth;
@@ -243,7 +248,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 	}
 	// when only variant sites are asked for, test if the site is a variant
 	if ((d->format & BAM_PLF_CNS) && (d->format & BAM_PLF_VAR_ONLY)) {
-		if (!(bam_nt16_table[rb] != 15 && cns>>28 != bam_nt16_table[rb])) { // not a SNP
+		if (!(bam_nt16_table[rb] != 15 && cns>>28 != 15 && cns>>28 != bam_nt16_table[rb])) { // not a SNP
 			if (!(r && (r->gt == 2 || strcmp(r->s[r->gt], "*")))) { // not an indel
 				if (r) bam_maqindel_ret_destroy(r);
 				return 0;
@@ -253,16 +258,8 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
 	// print the first 3 columns
 	printf("%s\t%d\t%c\t", d->h->target_name[tid], pos + 1, rb);
 	// print consensus information if required
-	if (d->format & BAM_PLF_CNS) {
-		int ref_q, rb4 = bam_nt16_table[rb];
-		ref_q = 0;
-		if (rb4 != 15 && cns>>28 != 15 && cns>>28 != rb4) { // a SNP
-			ref_q = ((cns>>24&0xf) == rb4)? cns>>8&0xff : (cns>>8&0xff) + (cns&0xff);
-			if (ref_q > 255) ref_q = 255;
-		}
-		rms_mapq = cns>>16&0xff;
-		printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[cns>>28], cns>>8&0xff, ref_q, rms_mapq);
-	}
+	if (d->format & BAM_PLF_CNS)
+		printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[cns>>28], cns>>8&0xff, cns&0xff, cns>>16&0xff);
 	// print pileup sequences
 	printf("%d\t", n);
 	rms_aux = 0; // we need to recalculate rms_mapq when -c is not flagged on the command line
@@ -339,15 +336,17 @@ int bam_pileup(int argc, char *argv[])
 	int c, is_SAM = 0;
 	char *fn_list = 0, *fn_fa = 0, *fn_pos = 0;
 	pu_data_t *d = (pu_data_t*)calloc(1, sizeof(pu_data_t));
-    d->max_depth = 0;
-	d->tid = -1; d->mask = BAM_DEF_MASK;
+    d->max_depth = 1024; d->tid = -1; d->mask = BAM_DEF_MASK; d->min_baseQ = 13;
 	d->c = bam_maqcns_init();
-	d->c->is_soap = 1; // change the default model
+	d->c->errmod = BAM_ERRMOD_MAQ2; // change the default model
 	d->ido = bam_maqindel_opt_init();
-	while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:PA")) >= 0) {
+	while ((c = getopt(argc, argv, "st:f:cT:N:r:l:d:im:gI:G:vM:S2aR:PAQ:C:B")) >= 0) {
 		switch (c) {
-		case 'a': d->c->is_soap = 1; break;
-		case 'A': d->c->is_soap = 0; break;
+		case 'Q': d->c->min_baseQ = atoi(optarg); break;
+		case 'C': d->capQ_thres = atoi(optarg); break;
+		case 'B': d->format |= BAM_PLF_NOBAQ; break;
+		case 'a': d->c->errmod = BAM_ERRMOD_SOAP; break;
+		case 'A': d->c->errmod = BAM_ERRMOD_MAQ; break;
 		case 's': d->format |= BAM_PLF_SIMPLE; break;
 		case 't': fn_list = strdup(optarg); break;
 		case 'l': fn_pos = strdup(optarg); break;
@@ -376,29 +375,34 @@ int bam_pileup(int argc, char *argv[])
 		default: fprintf(stderr, "Unrecognizd option '-%c'.\n", c); return 1;
 		}
 	}
+	if (d->c->errmod != BAM_ERRMOD_MAQ2) d->c->theta += 0.02;
+	if (d->c->theta > 1.0) d->c->theta = 1.0;
 	if (fn_list) is_SAM = 1;
 	if (optind == argc) {
 		fprintf(stderr, "\n");
 		fprintf(stderr, "Usage:  samtools pileup [options] <in.bam>|<in.sam>\n\n");
 		fprintf(stderr, "Option: -s        simple (yet incomplete) pileup format\n");
 		fprintf(stderr, "        -S        the input is in SAM\n");
-		fprintf(stderr, "        -A        use the MAQ model for SNP calling\n");
+		fprintf(stderr, "        -B        disable BAQ computation\n");
+		fprintf(stderr, "        -A        use the original MAQ model for SNP calling (DEPRECATED)\n");
 		fprintf(stderr, "        -2        output the 2nd best call and quality\n");
 		fprintf(stderr, "        -i        only show lines/consensus with indels\n");
-		fprintf(stderr, "        -m INT    filtering reads with bits in INT [%d]\n", d->mask);
+		fprintf(stderr, "        -Q INT    min base quality (possibly capped by BAQ) [%d]\n", d->c->min_baseQ);
+		fprintf(stderr, "        -C INT    coefficient for adjusting mapQ of poor mappings [%d]\n", d->capQ_thres);
+		fprintf(stderr, "        -m INT    filtering reads with bits in INT [0x%x]\n", d->mask);
 		fprintf(stderr, "        -M INT    cap mapping quality at INT [%d]\n", d->c->cap_mapQ);
-        fprintf(stderr, "        -d INT    limit maximum depth for indels [unlimited]\n");
+        fprintf(stderr, "        -d INT    limit maximum depth for indels [%d]\n", d->max_depth);
 		fprintf(stderr, "        -t FILE   list of reference sequences (force -S)\n");
 		fprintf(stderr, "        -l FILE   list of sites at which pileup is output\n");
 		fprintf(stderr, "        -f FILE   reference sequence in the FASTA format\n\n");
-		fprintf(stderr, "        -c        output the SOAPsnp consensus sequence\n");
+		fprintf(stderr, "        -c        compute the consensus sequence\n");
 		fprintf(stderr, "        -v        print variants only (for -c)\n");
-		fprintf(stderr, "        -g        output in the GLFv3 format (suppressing -c/-i/-s)\n");
-		fprintf(stderr, "        -T FLOAT  theta in maq consensus calling model (for -c/-g) [%f]\n", d->c->theta);
-		fprintf(stderr, "        -N INT    number of haplotypes in the sample (for -c/-g) [%d]\n", d->c->n_hap);
-		fprintf(stderr, "        -r FLOAT  prior of a difference between two haplotypes (for -c/-g) [%f]\n", d->c->het_rate);
-		fprintf(stderr, "        -G FLOAT  prior of an indel between two haplotypes (for -c/-g) [%f]\n", d->ido->r_indel);
-		fprintf(stderr, "        -I INT    phred prob. of an indel in sequencing/prep. (for -c/-g) [%d]\n", d->ido->q_indel);
+		fprintf(stderr, "        -g        output in the GLFv3 format (DEPRECATED)\n");
+		fprintf(stderr, "        -T FLOAT  theta in maq consensus calling model (for -c) [%.4g]\n", d->c->theta);
+		fprintf(stderr, "        -N INT    number of haplotypes in the sample (for -c) [%d]\n", d->c->n_hap);
+		fprintf(stderr, "        -r FLOAT  prior of a difference between two haplotypes (for -c) [%.4g]\n", d->c->het_rate);
+		fprintf(stderr, "        -G FLOAT  prior of an indel between two haplotypes (for -c) [%.4g]\n", d->ido->r_indel);
+		fprintf(stderr, "        -I INT    phred prob. of an indel in sequencing/prep. (for -c) [%d]\n", d->ido->q_indel);
 		fprintf(stderr, "\n");
 		free(fn_list); free(fn_fa); free(d);
 		return 1;
@@ -426,7 +430,42 @@ int bam_pileup(int argc, char *argv[])
 		}
 		d->h = fp->header;
 		if (fn_pos) d->hash = load_pos(fn_pos, d->h);
-		sampileup(fp, d->mask, pileup_func, d);
+		{ // run pileup
+			extern int bam_prob_realn(bam1_t *b, const char *ref);
+			extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
+			bam1_t *b;
+			int ret, tid, pos, n_plp;
+			bam_plp_t iter;
+			const bam_pileup1_t *plp;
+			b = bam_init1();
+			iter = bam_plp_init(0, 0);
+			bam_plp_set_mask(iter, d->mask);
+			while ((ret = samread(fp, b)) >= 0) {
+				int skip = 0;
+				// update d->ref if necessary
+				if (d->fai && (int)b->core.tid != d->tid) {
+					free(d->ref);
+					d->ref = faidx_fetch_seq(d->fai, d->h->target_name[b->core.tid], 0, 0x7fffffff, &d->len);
+					d->tid = b->core.tid;
+				}
+				if (d->ref && (d->format&BAM_PLF_CNS) && !(d->format&BAM_PLF_NOBAQ)) bam_prob_realn(b, d->ref);
+				if (d->ref && (d->format&BAM_PLF_CNS) && d->capQ_thres > 10) {
+					int q = bam_cap_mapQ(b, d->ref, d->capQ_thres);
+					if (q < 0) skip = 1;
+					else if (b->core.qual > q) b->core.qual = q;
+				} else if (b->core.flag&BAM_FUNMAP) skip = 1;
+				else if ((d->format&BAM_PLF_CNS) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1;
+				if (skip) continue;
+				bam_plp_push(iter, b);
+				while ((plp = bam_plp_next(iter, &tid, &pos, &n_plp)) != 0)
+					pileup_func(tid, pos, n_plp, plp, d);
+			}
+			bam_plp_push(iter, 0);
+			while ((plp = bam_plp_next(iter, &tid, &pos, &n_plp)) != 0)
+				pileup_func(tid, pos, n_plp, plp, d);
+			bam_plp_destroy(iter);
+			bam_destroy1(b);
+		}
 		samclose(fp); // d->h will be destroyed here
 	}
 
@@ -449,8 +488,17 @@ int bam_pileup(int argc, char *argv[])
  * mpileup *
  ***********/
 
+#include <assert.h>
+#include "bam2bcf.h"
+#include "sample.h"
+
+#define MPLP_GLF   0x10
+#define MPLP_NO_COMP 0x20
+#define MPLP_NO_ORPHAN 0x40
+#define MPLP_REALN   0x80
+
 typedef struct {
-	int vcf, max_mq, min_mq, var_only;
+	int max_mq, min_mq, flag, min_baseQ, capQ_thres;
 	char *reg, *fn_pos;
 	faidx_t *fai;
 	kh_64_t *hash;
@@ -459,40 +507,101 @@ typedef struct {
 typedef struct {
 	bamFile fp;
 	bam_iter_t iter;
-	int min_mq;
+	int min_mq, flag, ref_id, capQ_thres;
+	char *ref;
 } mplp_aux_t;
 
+typedef struct {
+	int n;
+	int *n_plp, *m_plp;
+	bam_pileup1_t **plp;
+} mplp_pileup_t;
+
 static int mplp_func(void *data, bam1_t *b)
 {
+	extern int bam_realn(bam1_t *b, const char *ref);
+	extern int bam_prob_realn(bam1_t *b, const char *ref);
+	extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
 	mplp_aux_t *ma = (mplp_aux_t*)data;
-	int ret;
+	int ret, skip = 0;
 	do {
+		int has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
 		ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
-	} while (b->core.qual < ma->min_mq && ret >= 0);
+		if (ret < 0) break;
+		skip = 0;
+		if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn(b, ma->ref);
+		if (has_ref && ma->capQ_thres > 10) {
+			int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres);
+			if (q < 0) skip = 1;
+			else if (b->core.qual > q) b->core.qual = q;
+		} else if (b->core.flag&BAM_FUNMAP) skip = 1;
+		else if (b->core.qual < ma->min_mq) skip = 1; 
+		else if ((ma->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1;
+	} while (skip);
 	return ret;
 }
 
+static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
+					   int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp)
+{
+	int i, j;
+	memset(m->n_plp, 0, m->n * sizeof(int));
+	for (i = 0; i < n; ++i) {
+		for (j = 0; j < n_plp[i]; ++j) {
+			const bam_pileup1_t *p = plp[i] + j;
+			uint8_t *q;
+			int id = -1;
+			q = bam_aux_get(p->b, "RG");
+			if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf);
+			if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf);
+			assert(id >= 0 && id < m->n);
+			if (m->n_plp[id] == m->m_plp[id]) {
+				m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
+				m->plp[id] = realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
+			}
+			m->plp[id][m->n_plp[id]++] = *p;
+		}
+	}
+}
+
 static int mpileup(mplp_conf_t *conf, int n, char **fn)
 {
 	mplp_aux_t **data;
-	mc_aux_t *ma = 0;
 	int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid;
 	const bam_pileup1_t **plp;
 	bam_mplp_t iter;
 	bam_header_t *h = 0;
 	char *ref;
 	khash_t(64) *hash = 0;
-	// allocate
+
+	bcf_callaux_t *bca = 0;
+	bcf_callret1_t *bcr = 0;
+	bcf_call_t bc;
+	bcf_t *bp = 0;
+	bcf_hdr_t *bh = 0;
+
+	bam_sample_t *sm = 0;
+	kstring_t buf;
+	mplp_pileup_t gplp;
+
+	memset(&gplp, 0, sizeof(mplp_pileup_t));
+	memset(&buf, 0, sizeof(kstring_t));
+	memset(&bc, 0, sizeof(bcf_call_t));
 	data = calloc(n, sizeof(void*));
 	plp = calloc(n, sizeof(void*));
 	n_plp = calloc(n, sizeof(int*));
+	sm = bam_smpl_init();
+
 	// read the header and initialize data
 	for (i = 0; i < n; ++i) {
 		bam_header_t *h_tmp;
 		data[i] = calloc(1, sizeof(mplp_aux_t));
 		data[i]->min_mq = conf->min_mq;
-		data[i]->fp = bam_open(fn[i], "r");
+		data[i]->flag = conf->flag;
+		data[i]->capQ_thres = conf->capQ_thres;
+		data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
 		h_tmp = bam_header_read(data[i]->fp);
+		bam_smpl_add(sm, fn[i], h_tmp->text);
 		if (conf->reg) {
 			int beg, end;
 			bam_index_t *idx;
@@ -515,25 +624,40 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 			bam_header_destroy(h_tmp);
 		}
 	}
+	gplp.n = sm->n;
+	gplp.n_plp = calloc(sm->n, sizeof(int));
+	gplp.m_plp = calloc(sm->n, sizeof(int));
+	gplp.plp = calloc(sm->n, sizeof(void*));
+
+	fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
 	if (conf->fn_pos) hash = load_pos(conf->fn_pos, h);
 	// write the VCF header
-	if (conf->vcf) {
+	if (conf->flag & MPLP_GLF) {
 		kstring_t s;
+		bh = calloc(1, sizeof(bcf_hdr_t));
 		s.l = s.m = 0; s.s = 0;
-		puts("##fileformat=VCFv4.0");
-		kputs("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", &s);
-		for (i = 0; i < n; ++i) {
-			const char *p;
-			kputc('\t', &s);
-			if ((p = strstr(fn[i], ".bam")) != 0)
-				kputsn(fn[i], p - fn[i], &s);
-			else kputs(fn[i], &s);
+		bp = bcf_open("-", (conf->flag&MPLP_NO_COMP)? "wu" : "w");
+		for (i = 0; i < h->n_targets; ++i) {
+			kputs(h->target_name[i], &s);
+			kputc('\0', &s);
 		}
-		puts(s.s);
+		bh->l_nm = s.l;
+		bh->name = malloc(s.l);
+		memcpy(bh->name, s.s, s.l);
+		s.l = 0;
+		for (i = 0; i < sm->n; ++i) {
+			kputs(sm->smpl[i], &s); kputc('\0', &s);
+		}
+		bh->l_smpl = s.l;
+		bh->sname = malloc(s.l);
+		memcpy(bh->sname, s.s, s.l);
+		bh->l_txt = 0;
 		free(s.s);
+		bcf_hdr_sync(bh);
+		bcf_hdr_write(bp, bh);
+		bca = bcf_call_init(-1., conf->min_baseQ);
+		bcr = calloc(sm->n, sizeof(bcf_callret1_t));
 	}
-	// mpileup
-	if (conf->vcf) ma = mc_init(n);
 	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) {
@@ -544,57 +668,23 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 			if (k == kh_end(hash)) continue;
 		}
 		if (tid != ref_tid) {
-			free(ref);
+			free(ref); ref = 0;
 			if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
+			for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid;
 			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;
-			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);
-			if (f >= 0.0) {
-				double q, flast = f;
-				for (j = 0; j < 10; ++j){
-					f = mc_freq_iter(flast, ma);
-					if (fabs(f - flast) < 1e-3) break;
-					flast = f;
-				}
-				pref = mc_ref_prob(ma);
-				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;
-			}
-			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) {
-				if (_ref0 == _ref) putchar("ACGTN"[_alt]);
-				else printf("%c,%c", "ACGTN"[_ref], "ACGTN"[_alt]);
-			} else putchar('.');
-			printf("\t%d\t", qref);
-			if (f0 < 0.) printf("Q13\t");
-			else printf(".\t");
-			for (i = depth = 0, sqr_sum = 0; i < n; ++i) {
-				depth += n_plp[i];
-				for (j = 0; j < n_plp[i]; ++j) {
-					int q = plp[i][j].b->core.qual;
-					if (q > conf->max_mq) q = conf->max_mq;
-					sqr_sum += q * q;
-				}
-			}
-			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("\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]);
-			}
-			putchar('\n');
+		if (conf->flag & MPLP_GLF) {
+			int _ref0, ref16;
+			bcf1_t *b = calloc(1, sizeof(bcf1_t));
+			group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp);
+			_ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
+			ref16 = bam_nt16_table[_ref0];
+			for (i = 0; i < gplp.n; ++i)
+				bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
+			bcf_call_combine(gplp.n, bcr, ref16, &bc);
+			bcf_call2bcf(tid, pos, &bc, b);
+			bcf_write(bp, bh, b);
+			bcf_destroy(b);
 		} else {
 			printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
 			for (i = 0; i < n; ++i) {
@@ -616,13 +706,18 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 			putchar('\n');
 		}
 	}
+
+	bcf_close(bp);
+	bam_smpl_destroy(sm); free(buf.s);
+	for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
+	free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
 	if (hash) { // free the hash table
 		khint_t k;
 		for (k = kh_begin(hash); k < kh_end(hash); ++k)
 			if (kh_exist(hash, k)) free(kh_val(hash, k));
 		kh_destroy(64, hash);
 	}
-	mc_destroy(ma);
+	bcf_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr);
 	bam_mplp_destroy(iter);
 	bam_header_destroy(h);
 	for (i = 0; i < n; ++i) {
@@ -640,7 +735,9 @@ 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.min_baseQ = 13;
+	mplp.capQ_thres = 0;
+	while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:")) >= 0) {
 		switch (c) {
 		case 'f':
 			mplp.fai = fai_load(optarg);
@@ -648,14 +745,30 @@ int bam_mpileup(int argc, char *argv[])
 			break;
 		case 'r': mplp.reg = strdup(optarg); break;
 		case 'l': mplp.fn_pos = strdup(optarg); break;
-		case 'v': mplp.var_only = 1; break;
-		case 'V': mplp.vcf = 1; break;
+		case 'g': mplp.flag |= MPLP_GLF; break;
+		case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
+		case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
+		case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
+		case 'R': mplp.flag |= MPLP_REALN; break;
+		case 'C': mplp.capQ_thres = atoi(optarg); break;
 		case 'M': mplp.max_mq = atoi(optarg); break;
 		case 'q': mplp.min_mq = atoi(optarg); break;
+		case 'Q': mplp.min_baseQ = atoi(optarg); break;
 		}
 	}
 	if (argc == 1) {
-		fprintf(stderr, "Usage: samtools mpileup [-r reg] [-f in.fa] [-l pos] in1.bam [in2.bam [...]]\n");
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:   samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
+		fprintf(stderr, "Options: -f FILE     reference sequence file [null]\n");
+		fprintf(stderr, "         -r STR      region in which pileup is generated [null]\n");
+		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      min base quality [%d]\n", mplp.min_baseQ);
+		fprintf(stderr, "         -q INT      filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
+		fprintf(stderr, "         -g          generate BCF output\n");
+		fprintf(stderr, "         -u          do not compress BCF output\n");
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
 		return 1;
 	}
 	mpileup(&mplp, argc - optind, argv + optind);