X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_plcmd.c;h=cbf6ae8c13754be0c441b311eb14dfb9f04452a3;hp=e3f73aaddd03a14343a82084ee060d9c41ba42d4;hb=9a36c994ed991f79cc191ece6cbc5f1bf6410da2;hpb=e3b3a0177339fb8c099346986e965e3bd5b85999

diff --git a/bam_plcmd.c b/bam_plcmd.c
index e3f73aa..cbf6ae8 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -6,93 +6,8 @@
 #include <errno.h>
 #include "sam.h"
 #include "faidx.h"
-#include "bam_maqcns.h"
-#include "khash.h"
-#include "glf.h"
 #include "kstring.h"
 
-typedef int *indel_list_t;
-KHASH_MAP_INIT_INT64(64, indel_list_t)
-
-#define BAM_PLF_SIMPLE     0x01
-#define BAM_PLF_CNS        0x02
-#define BAM_PLF_INDEL_ONLY 0x04
-#define BAM_PLF_GLF        0x08
-#define BAM_PLF_VAR_ONLY   0x10
-#define BAM_PLF_2ND        0x20
-#define BAM_PLF_RANBASE    0x40
-#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;
-	bam_maqcns_t *c;
-	bam_maqindel_opt_t *ido;
-	faidx_t *fai;
-	khash_t(64) *hash;
-	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
-} pu_data_t;
-
-char **__bam_get_lines(const char *fn, int *_n);
-void bam_init_header_hash(bam_header_t *header);
-int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
-
-static khash_t(64) *load_pos(const char *fn, bam_header_t *h)
-{
-	char **list;
-	int i, j, n, *fields, max_fields;
-	khash_t(64) *hash;
-	bam_init_header_hash(h);
-	list = __bam_get_lines(fn, &n);
-	hash = kh_init(64);
-	max_fields = 0; fields = 0;
-	for (i = 0; i < n; ++i) {
-		char *str = list[i];
-		int chr, n_fields, ret;
-		khint_t k;
-		uint64_t x;
-		n_fields = ksplit_core(str, 0, &max_fields, &fields);
-		if (n_fields < 2) continue;
-		chr = bam_get_tid(h, str + fields[0]);
-		if (chr < 0) {
-			fprintf(stderr, "[load_pos] unknown reference sequence name: %s\n", str + fields[0]);
-			continue;
-		}
-		x = (uint64_t)chr << 32 | (atoi(str + fields[1]) - 1);
-		k = kh_put(64, hash, x, &ret);
-		if (ret == 0) {
-			fprintf(stderr, "[load_pos] position %s:%s has been loaded.\n", str+fields[0], str+fields[1]);
-			continue;
-		}
-		kh_val(hash, k) = 0;
-		if (n_fields > 2) {
-			// count
-			for (j = 2; j < n_fields; ++j) {
-				char *s = str + fields[j];
-				if ((*s != '+' && *s != '-') || !isdigit(s[1])) break;
- 			}
-			if (j > 2) { // update kh_val()
-				int *q, y, z;
-				q = kh_val(hash, k) = (int*)calloc(j - 1, sizeof(int));
-				q[0] = j - 2; z = j; y = 1;
-				for (j = 2; j < z; ++j)
-					q[y++] = atoi(str + fields[j]);
-			}
-		}
-		free(str);
-	}
-	free(list); free(fields);
-	return hash;
-}
-
 static inline int printw(int c, FILE *fp)
 {
 	char buf[16];
@@ -108,75 +23,6 @@ static inline int printw(int c, FILE *fp)
 	return 0;
 }
 
-// an analogy to pileup_func() below
-static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
-{
-	pu_data_t *d = (pu_data_t*)data;
-	bam_maqindel_ret_t *r = 0;
-	int rb, *proposed_indels = 0;
-	glf1_t *g;
-	glf3_t *g3;
-
-	if (d->fai == 0) {
-		fprintf(stderr, "[glt3_func] reference sequence is required for generating GLT. Abort!\n");
-		exit(1);
-	}
-	if (d->hash) { // only output a list of sites
-		khint_t k = kh_get(64, d->hash, (uint64_t)tid<<32|pos);
-		if (k == kh_end(d->hash)) return 0;
-		proposed_indels = kh_val(d->hash, k);
-	}
-	g3 = glf3_init1();
-	if (d->fai && (int)tid != d->tid) {
-		if (d->ref) { // then write the end mark
-			g3->rtype = GLF3_RTYPE_END;
-			glf3_write1(d->fp_glf, g3);
-		}
-		glf3_ref_write(d->fp_glf, d->h->target_name[tid], d->h->target_len[tid]); // write reference
-		free(d->ref);
-		d->ref = fai_fetch(d->fai, d->h->target_name[tid], &d->len);
-		d->tid = tid;
-		d->last_pos = 0;
-	}
-	rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N';
-	g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c);
-	memcpy(g3, g, sizeof(glf1_t));
-	g3->rtype = GLF3_RTYPE_SUB;
-	g3->offset = pos - d->last_pos;
-	d->last_pos = pos;
-	glf3_write1(d->fp_glf, g3);
-    if (pos < d->len) {
-        int m = (!d->max_depth || d->max_depth>n) ? n : d->max_depth;
-		if (proposed_indels)
-			r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
-		else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0);
-	}
-	if (r) { // then write indel line
-		int het = 3 * n, min;
-		min = het;
-		if (min > r->gl[0]) min = r->gl[0];
-		if (min > r->gl[1]) min = r->gl[1];
-		g3->ref_base = 0;
-		g3->rtype = GLF3_RTYPE_INDEL;
-		memset(g3->lk, 0, 10);
-		g3->lk[0] = r->gl[0] - min < 255? r->gl[0] - min : 255;
-		g3->lk[1] = r->gl[1] - min < 255? r->gl[1] - min : 255;
-		g3->lk[2] = het - min < 255? het - min : 255;
-		g3->offset = 0;
-		g3->indel_len[0] = r->indel1;
-		g3->indel_len[1] = r->indel2;
-		g3->min_lk = min < 255? min : 255;
-		g3->max_len = (abs(r->indel1) > abs(r->indel2)? abs(r->indel1) : abs(r->indel2)) + 1;
-		g3->indel_seq[0] = strdup(r->s[0]+1);
-		g3->indel_seq[1] = strdup(r->s[1]+1);
-		glf3_write1(d->fp_glf, g3);
-		bam_maqindel_ret_destroy(r);
-	}
-	free(g);
-	glf3_destroy1(g3);
-	return 0;
-}
-
 static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
 {
 	int j;
@@ -212,316 +58,6 @@ static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, cons
 	if (p->is_tail) putchar('$');
 }
 
-static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
-{
-	pu_data_t *d = (pu_data_t*)data;
-	bam_maqindel_ret_t *r = 0;
-	int i, rb, rms_mapq = -1, *proposed_indels = 0;
-	uint64_t rms_aux;
-	uint32_t cns = 0;
-
-	// if GLF is required, suppress -c completely
-	if (d->format & BAM_PLF_GLF) return glt3_func(tid, pos, n, pu, data);
-	// if d->hash is initialized, only output the sites in the hash table
-	if (d->hash) {
-		khint_t k = kh_get(64, d->hash, (uint64_t)tid<<32|pos);
-		if (k == kh_end(d->hash)) return 0;
-		proposed_indels = kh_val(d->hash, k);
-	}
-	// update d->ref if necessary
-	if (d->fai && (int)tid != d->tid) {
-		free(d->ref);
-		d->ref = faidx_fetch_seq(d->fai, d->h->target_name[tid], 0, 0x7fffffff, &d->len);
-		d->tid = tid;
-	}
-	rb = (d->ref && (int)pos < d->len)? d->ref[pos] : 'N';
-	// when the indel-only mode is asked for, return if no reads mapped with indels
-	if (d->format & BAM_PLF_INDEL_ONLY) {
-		for (i = 0; i < n; ++i)
-			if (pu[i].indel != 0) break;
-		if (i == n) return 0;
-	}
-	// call the consensus and indel
-	if (d->format & BAM_PLF_CNS) { // call consensus
-		if (d->format & (BAM_PLF_RANBASE|BAM_PLF_1STBASE)) { // use a random base or the 1st base as the consensus call
-			const bam_pileup1_t *p = (d->format & BAM_PLF_1STBASE)? pu : pu + (int)(drand48() * n);
-			int q = bam1_qual(p->b)[p->qpos];
-			int mapQ = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
-			uint32_t b = bam1_seqi(bam1_seq(p->b), p->qpos);
-			cns = b<<28 | 0xf<<24 | mapQ<<16 | q<<8;
-		} else if (d->format & BAM_PLF_ALLBASE) { // collapse all bases
-			uint64_t rmsQ = 0;
-			uint32_t b = 0;
-			for (i = 0; i < n; ++i) {
-				const bam_pileup1_t *p = pu + i;
-				int q = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
-				b |= bam1_seqi(bam1_seq(p->b), p->qpos);
-				rmsQ += q * q;
-			}
-			rmsQ = (uint64_t)(sqrt((double)rmsQ / n) + .499);
-			cns = b<<28 | 0xf<<24 | rmsQ<<16 | 60<<8;
-		} 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;
-        if (proposed_indels) // the first element gives the size of the array
-            r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
-        else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0);
-	}
-	// 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 != 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;
-			}
-		}
-	}
-	// print the first 3 columns
-	fputs(d->h->target_name[tid], stdout); putchar('\t');
-	printw(pos+1, stdout); putchar('\t'); putchar(rb); putchar('\t');
-	// print consensus information if required
-	if (d->format & BAM_PLF_CNS) {
-		putchar(bam_nt16_rev_table[cns>>28]); putchar('\t');
-		printw(cns>>8&0xff, stdout); putchar('\t');
-		printw(cns&0xff, stdout); putchar('\t');
-		printw(cns>>16&0xff, stdout); putchar('\t');
-	}
-	// print pileup sequences
-	printw(n, stdout); putchar('\t');
-	for (i = 0; i < n; ++i)
-		pileup_seq(pu + i, pos, d->len, d->ref);
-	// finalize rms_mapq
-	if (d->format & BAM_PLF_CNS) {
-		for (i = rms_aux = 0; i < n; ++i) {
-			const bam_pileup1_t *p = pu + i;
-			int tmp = p->b->core.qual < d->c->cap_mapQ? p->b->core.qual : d->c->cap_mapQ;
-			rms_aux += tmp * tmp;
-		}
-		rms_aux = (uint64_t)(sqrt((double)rms_aux / n) + .499);
-		if (rms_mapq < 0) rms_mapq = rms_aux;
-	}
-	putchar('\t');
-	// print quality
-	for (i = 0; i < n; ++i) {
-		const bam_pileup1_t *p = pu + i;
-		int c = bam1_qual(p->b)[p->qpos] + 33;
-		if (c > 126) c = 126;
-		putchar(c);
-	}
-	if (d->format & BAM_PLF_2ND) { // print 2nd calls and qualities
-		const unsigned char *q;
-		putchar('\t');
-		for (i = 0; i < n; ++i) {
-			const bam_pileup1_t *p = pu + i;
-			q = bam_aux_get(p->b, "E2");
-			putchar(q? q[p->qpos + 1] : 'N');
-		}
-		putchar('\t');
-		for (i = 0; i < n; ++i) {
-			const bam_pileup1_t *p = pu + i;
-			q = bam_aux_get(p->b, "U2");
-			putchar(q? q[p->qpos + 1] : '!');
-		}
-	}
-	// print mapping quality if -s is flagged on the command line
-	if (d->format & BAM_PLF_SIMPLE) {
-		putchar('\t');
-		for (i = 0; i < n; ++i) {
-			int c = pu[i].b->core.qual + 33;
-			if (c > 126) c = 126;
-			putchar(c);
-		}
-	}
-	// print read position
-	if (d->format & BAM_PLF_READPOS) {
-		putchar('\t');
-		for (i = 0; i < n; ++i) {
-			int x = pu[i].qpos;
-			int l = pu[i].b->core.l_qseq;
-			printw(x < l/2? x+1 : -((l-1)-x+1), stdout); putchar(',');
-		}
-	}
-	putchar('\n');
-	// print the indel line if r has been calculated. This only happens if:
-	// a) -c or -i are flagged, AND b) the reference sequence is available
-	if (r) {
-		printf("%s\t%d\t*\t", d->h->target_name[tid], pos + 1);
-		if (r->gt < 2) printf("%s/%s\t", r->s[r->gt], r->s[r->gt]);
-		else printf("%s/%s\t", r->s[0], r->s[1]);
-		printf("%d\t%d\t", r->q_cns, r->q_ref);
-		printf("%d\t%d\t", rms_mapq, n);
-		printf("%s\t%s\t", r->s[0], r->s[1]);
-		//printf("%d\t%d\t", r->gl[0], r->gl[1]);
-		printf("%d\t%d\t%d\t", r->cnt1, r->cnt2, r->cnt_anti);
-		printf("%d\t%d\n", r->cnt_ref, r->cnt_ambi);
-		bam_maqindel_ret_destroy(r);
-	}
-	return 0;
-}
-
-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 = 1024; d->tid = -1; d->mask = BAM_DEF_MASK; d->min_baseQ = 13;
-	d->c = bam_maqcns_init();
-	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:PAQ:C:B")) >= 0) {
-		switch (c) {
-		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;
-		case 'f': fn_fa = strdup(optarg); break;
-		case 'T': d->c->theta = atof(optarg); break;
-		case 'N': d->c->n_hap = atoi(optarg); break;
-		case 'r': d->c->het_rate = atof(optarg); d->ido->r_snp = d->c->het_rate; break;
-		case 'M': d->c->cap_mapQ = atoi(optarg); break;
-		case 'd': d->max_depth = atoi(optarg); break;
-		case 'c': d->format |= BAM_PLF_CNS; break;
-		case 'i': d->format |= BAM_PLF_INDEL_ONLY; break;
-		case 'v': d->format |= BAM_PLF_VAR_ONLY; break;
-		case 'm': d->mask = strtol(optarg, 0, 0); break;
-		case 'g': d->format |= BAM_PLF_GLF; break;
-		case '2': d->format |= BAM_PLF_2ND; break;
-		case 'P': d->format |= BAM_PLF_READPOS; break;
-		case 'I': d->ido->q_indel = atoi(optarg); break;
-		case 'G': d->ido->r_indel = atof(optarg); break;
-		case 'S': is_SAM = 1; break;
-		case 'R':
-			if (strcmp(optarg, "random") == 0) d->format |= BAM_PLF_RANBASE;
-			else if (strcmp(optarg, "first") == 0) d->format |= BAM_PLF_1STBASE;
-			else if (strcmp(optarg, "all") == 0) d->format |= BAM_PLF_ALLBASE;
-			else fprintf(stderr, "[bam_pileup] unrecognized -R\n");
-			break;
-		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, "        -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, "        -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 [%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        compute the consensus sequence\n");
-		fprintf(stderr, "        -v        print variants only (for -c)\n");
-		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;
-	}
-	if (d->format & (BAM_PLF_RANBASE|BAM_PLF_1STBASE|BAM_PLF_ALLBASE)) d->format |= BAM_PLF_CNS;
-	if (fn_fa) d->fai = fai_load(fn_fa);
-	if (d->format & (BAM_PLF_CNS|BAM_PLF_GLF)) bam_maqcns_prepare(d->c); // consensus calling
-	if (d->format & BAM_PLF_GLF) { // for glf output
-		glf3_header_t *h;
-		h = glf3_header_init();
-		d->fp_glf = bgzf_fdopen(fileno(stdout), "w");
-		glf3_header_write(d->fp_glf, h);
-		glf3_header_destroy(h);
-	}
-	if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)))
-		fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n");
-	if (fn_fa && is_SAM && fn_list == 0) fn_list = samfaipath(fn_fa);
-
-	{
-		samfile_t *fp;
-		fp = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);
-		if (fp == 0 || fp->header == 0) {
-			fprintf(stderr, "[bam_pileup] fail to read the header: non-exisiting file or wrong format.\n");
-			return 1;
-		}
-		d->h = fp->header;
-		if (fn_pos) d->hash = load_pos(fn_pos, d->h);
-		{ // 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;
-				if ((int)b->core.tid < 0) break;
-				// 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
-	}
-
-	// free
-	if (d->format & BAM_PLF_GLF) bgzf_close(d->fp_glf);
-	if (fn_pos) { // free the hash table
-		khint_t k;
-		for (k = kh_begin(d->hash); k < kh_end(d->hash); ++k)
-			if (kh_exist(d->hash, k)) free(kh_val(d->hash, k));
-		kh_destroy(64, d->hash);
-	}
-	free(fn_pos); free(fn_list); free(fn_fa);
-	if (d->fai) fai_destroy(d->fai);
-	bam_maqcns_destroy(d->c);
-	free(d->ido); free(d->ref); free(d);
-	return 0;
-}
-
-/***********
- * mpileup *
- ***********/
-
 #include <assert.h>
 #include "bam2bcf.h"
 #include "sample.h"
@@ -533,20 +69,32 @@ int bam_pileup(int argc, char *argv[])
 #define MPLP_FMT_DP 0x100
 #define MPLP_FMT_SP 0x200
 #define MPLP_NO_INDEL 0x400
+#define MPLP_EXT_BAQ 0x800
+#define MPLP_ILLUMINA13 0x1000
+#define MPLP_IGNORE_RG 0x2000
+#define MPLP_PRINT_POS 0x4000
+#define MPLP_PRINT_MAPQ 0x8000
+
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);
 
 typedef struct {
-	int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth;
-	int openQ, extQ, tandemQ;
-	char *reg, *fn_pos, *pl_list;
+	int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth;
+	int openQ, extQ, tandemQ, min_support; // for indels
+	double min_frac; // for indels
+	char *reg, *pl_list;
 	faidx_t *fai;
-	kh_64_t *hash;
+	void *bed, *rghash;
 } mplp_conf_t;
 
 typedef struct {
 	bamFile fp;
 	bam_iter_t iter;
-	int min_mq, flag, ref_id, capQ_thres;
+	bam_header_t *h;
+	int ref_id;
 	char *ref;
+	const mplp_conf_t *conf;
 } mplp_aux_t;
 
 typedef struct {
@@ -563,24 +111,44 @@ static int mplp_func(void *data, bam1_t *b)
 	mplp_aux_t *ma = (mplp_aux_t*)data;
 	int ret, skip = 0;
 	do {
-		int has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
+		int has_ref;
 		ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
 		if (ret < 0) break;
+		if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads
+			skip = 1;
+			continue;
+		}
+		if (ma->conf->bed) { // test overlap
+			skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
+			if (skip) continue;
+		}
+		if (ma->conf->rghash) { // exclude read groups
+			uint8_t *rg = bam_aux_get(b, "RG");
+			skip = (rg && bcf_str2id(ma->conf->rghash, (const char*)(rg+1)) >= 0);
+			if (skip) continue;
+		}
+		if (ma->conf->flag & MPLP_ILLUMINA13) {
+			int i;
+			uint8_t *qual = bam1_qual(b);
+			for (i = 0; i < b->core.l_qseq; ++i)
+				qual[i] = qual[i] > 31? qual[i] - 31 : 0;
+		}
+		has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
 		skip = 0;
-		if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, 1);
-		if (has_ref && ma->capQ_thres > 10) {
-			int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres);
+		if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_EXT_BAQ)? 3 : 1);
+		if (has_ref && ma->conf->capQ_thres > 10) {
+			int q = bam_cap_mapQ(b, ma->ref, ma->conf->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;
+		}
+		else if (b->core.qual < ma->conf->min_mq) skip = 1; 
+		else if ((ma->conf->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 n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg)
 {
 	int i, j;
 	memset(m->n_plp, 0, m->n * sizeof(int));
@@ -589,10 +157,14 @@ static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
 			const bam_pileup1_t *p = plp[i] + j;
 			uint8_t *q;
 			int id = -1;
-			q = bam_aux_get(p->b, "RG");
+			q = ignore_rg? 0 : 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 (id < 0 || id >= m->n) {
+				assert(q); // otherwise a bug
+				fprintf(stderr, "[%s] Read group %s used in file %s but absent from the header or an alignment missing read group.\n", __func__, (char*)q+1, fn[i]);
+				exit(1);
+			}
 			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]);
@@ -607,12 +179,11 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 	extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
 	extern void bcf_call_del_rghash(void *rghash);
 	mplp_aux_t **data;
-	int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid, max_depth;
+	int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth;
 	const bam_pileup1_t **plp;
 	bam_mplp_t iter;
 	bam_header_t *h = 0;
 	char *ref;
-	khash_t(64) *hash = 0;
 	void *rghash = 0;
 
 	bcf_callaux_t *bca = 0;
@@ -637,12 +208,11 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 	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]->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");
+		data[i]->conf = conf;
 		h_tmp = bam_header_read(data[i]->fp);
-		bam_smpl_add(sm, fn[i], h_tmp->text);
+		data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
+		bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
 		rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
 		if (conf->reg) {
 			int beg, end;
@@ -656,7 +226,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 				fprintf(stderr, "[%s] malformatted region or wrong seqname for %d-th input.\n", __func__, i+1);
 				exit(1);
 			}
-			if (i == 0) beg0 = beg, end0 = end;
+			if (i == 0) tid0 = tid, beg0 = beg, end0 = end;
 			data[i]->iter = bam_iter_query(idx, tid, beg, end);
 			bam_index_destroy(idx);
 		}
@@ -672,7 +242,6 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 	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->flag & MPLP_GLF) {
 		kstring_t s;
@@ -693,7 +262,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 		bh->l_smpl = s.l;
 		bh->sname = malloc(s.l);
 		memcpy(bh->sname, s.s, s.l);
-		bh->l_txt = 0;
+		bh->txt = malloc(strlen(BAM_VERSION) + 64);
+		bh->l_txt = 1 + sprintf(bh->txt, "##samtoolsVersion=%s\n", BAM_VERSION);
 		free(s.s);
 		bcf_hdr_sync(bh);
 		bcf_hdr_write(bp, bh);
@@ -701,34 +271,38 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 		bcr = calloc(sm->n, sizeof(bcf_callret1_t));
 		bca->rghash = rghash;
 		bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
-	}
-	ref_tid = -1; ref = 0;
+		bca->min_frac = conf->min_frac;
+		bca->min_support = conf->min_support;
+	}
+	if (tid0 >= 0 && conf->fai) { // region is set
+		ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
+		ref_tid = tid0;
+		for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0;
+	} else ref_tid = -1, ref = 0;
 	iter = bam_mplp_init(n, mplp_func, (void**)data);
 	max_depth = conf->max_depth;
 	if (max_depth * sm->n > 1<<20)
 		fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__);
 	if (max_depth * sm->n < 8000) {
 		max_depth = 8000 / sm->n;
-		fprintf(stderr, "<%s> Set max per-sample depth to %d\n", __func__, max_depth);
+		fprintf(stderr, "<%s> Set max per-file depth to %d\n", __func__, max_depth);
 	}
+	max_indel_depth = conf->max_indel_depth * sm->n;
 	bam_mplp_set_maxcnt(iter, max_depth);
 	while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
 		if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
-		if (hash) {
-			khint_t k;
-			k = kh_get(64, hash, (uint64_t)tid<<32 | pos);
-			if (k == kh_end(hash)) continue;
-		}
+		if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
 		if (tid != ref_tid) {
 			free(ref); ref = 0;
-			if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
+			if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len);
 			for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid;
 			ref_tid = tid;
 		}
 		if (conf->flag & MPLP_GLF) {
-			int _ref0, ref16;
+			int total_depth, _ref0, ref16;
 			bcf1_t *b = calloc(1, sizeof(bcf1_t));
-			group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp);
+			for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
+			group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG);
 			_ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
 			ref16 = bam_nt16_table[_ref0];
 			for (i = 0; i < gplp.n; ++i)
@@ -739,7 +313,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 			bcf_write(bp, bh, b);
 			bcf_destroy(b);
 			// call indels
-			if (!(conf->flag&MPLP_NO_INDEL) && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
+			if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
 				for (i = 0; i < gplp.n; ++i)
 					bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
 				if (bcf_call_combine(gplp.n, bcr, -1, &bc) >= 0) {
@@ -755,8 +329,10 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 			for (i = 0; i < n; ++i) {
 				int j;
 				printf("\t%d\t", n_plp[i]);
-				if (n_plp[i] == 0) printf("*\t*");
-				else {
+				if (n_plp[i] == 0) {
+					printf("*\t*"); // FIXME: printf() is very slow...
+					if (conf->flag & MPLP_PRINT_POS) printf("\t*");
+				} else {
 					for (j = 0; j < n_plp[i]; ++j)
 						pileup_seq(plp[i] + j, pos, ref_len, ref);
 					putchar('\t');
@@ -766,6 +342,21 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 						if (c > 126) c = 126;
 						putchar(c);
 					}
+					if (conf->flag & MPLP_PRINT_MAPQ) {
+						putchar('\t');
+						for (j = 0; j < n_plp[i]; ++j) {
+							int c = plp[i][j].b->core.qual + 33;
+							if (c > 126) c = 126;
+							putchar(c);
+						}
+					}
+					if (conf->flag & MPLP_PRINT_POS) {
+						putchar('\t');
+						for (j = 0; j < n_plp[i]; ++j) {
+							if (j > 0) putchar(',');
+							printf("%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow...
+						}
+					}
 				}
 			}
 			putchar('\n');
@@ -777,12 +368,6 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 	for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
 	free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
 	bcf_call_del_rghash(rghash);
-	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);
-	}
 	bcf_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr);
 	bam_mplp_destroy(iter);
 	bam_header_destroy(h);
@@ -796,7 +381,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 }
 
 #define MAX_PATH_LEN 1024
-int read_file_list(const char *file_list,int *n,char **argv[])
+static int read_file_list(const char *file_list,int *n,char **argv[])
 {
     char buf[MAX_PATH_LEN];
     int len, nfiles;
@@ -849,16 +434,18 @@ int bam_mpileup(int argc, char *argv[])
 	int c;
     const char *file_list = NULL;
     char **fn = NULL;
-    int nfiles = 0;
+    int nfiles = 0, use_orphan = 0;
 	mplp_conf_t mplp;
 	memset(&mplp, 0, sizeof(mplp_conf_t));
+	#define MPLP_PRINT_POS 0x4000
 	mplp.max_mq = 60;
 	mplp.min_baseQ = 13;
 	mplp.capQ_thres = 0;
-	mplp.max_depth = 250;
+	mplp.max_depth = 250; mplp.max_indel_depth = 250;
 	mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
+	mplp.min_frac = 0.002; mplp.min_support = 1;
 	mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
-	while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDSd:b:P:o:e:h:I")) >= 0) {
+	while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6Os")) >= 0) {
 		switch (c) {
 		case 'f':
 			mplp.fai = fai_load(optarg);
@@ -866,17 +453,20 @@ int bam_mpileup(int argc, char *argv[])
 			break;
 		case 'd': mplp.max_depth = atoi(optarg); break;
 		case 'r': mplp.reg = strdup(optarg); break;
-		case 'l': mplp.fn_pos = strdup(optarg); break;
+		case 'l': mplp.bed = bed_read(optarg); break;
 		case 'P': mplp.pl_list = strdup(optarg); 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 'B': mplp.flag &= ~MPLP_REALN & ~MPLP_NO_ORPHAN; break;
-		case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
-		case 'R': mplp.flag |= MPLP_REALN; break;
+		case 'B': mplp.flag &= ~MPLP_REALN; break;
 		case 'D': mplp.flag |= MPLP_FMT_DP; break;
 		case 'S': mplp.flag |= MPLP_FMT_SP; break;
 		case 'I': mplp.flag |= MPLP_NO_INDEL; break;
+		case 'E': mplp.flag |= MPLP_EXT_BAQ; break;
+		case '6': mplp.flag |= MPLP_ILLUMINA13; break;
+		case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
+		case 's': mplp.flag |= MPLP_PRINT_MAPQ; break;
+		case 'O': mplp.flag |= MPLP_PRINT_POS; 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;
@@ -885,43 +475,72 @@ int bam_mpileup(int argc, char *argv[])
 		case 'o': mplp.openQ = atoi(optarg); break;
 		case 'e': mplp.extQ = atoi(optarg); break;
 		case 'h': mplp.tandemQ = atoi(optarg); break;
+		case 'A': use_orphan = 1; break;
+		case 'F': mplp.min_frac = atof(optarg); break;
+		case 'm': mplp.min_support = atoi(optarg); break;
+		case 'L': mplp.max_indel_depth = atoi(optarg); break;
+		case 'G': {
+				FILE *fp_rg;
+				char buf[1024];
+				mplp.rghash = bcf_str2id_init();
+				if ((fp_rg = fopen(optarg, "r")) == 0)
+					fprintf(stderr, "(%s) Fail to open file %s. Continue anyway.\n", __func__, optarg);
+				while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me...
+					bcf_str2id_add(mplp.rghash, strdup(buf));
+				fclose(fp_rg);
+			}
+			break;
 		}
 	}
+	if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
 	if (argc == 1) {
 		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, "         -b FILE     list of input BAM files [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, "         -d INT      max per-sample depth [%d]\n", mplp.max_depth);
-		fprintf(stderr, "         -P STR      comma separated list of platforms for indels [all]\n");
-		fprintf(stderr, "         -o INT      Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
-		fprintf(stderr, "         -e INT      Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
-		fprintf(stderr, "         -h INT      coefficient for homopolyer errors [%d]\n", mplp.tandemQ);
-		fprintf(stderr, "         -g          generate BCF output\n");
-		fprintf(stderr, "         -u          do not compress BCF output\n");
-		fprintf(stderr, "         -B          disable BAQ computation\n");
-		fprintf(stderr, "         -D          output per-sample DP\n");
-		fprintf(stderr, "         -S          output per-sample SP (strand bias P-value, slow)\n");
-		fprintf(stderr, "         -I          do not perform indel calling\n");
+		fprintf(stderr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
+		fprintf(stderr, "Input options:\n\n");
+		fprintf(stderr, "       -6           assume the quality is in the Illumina-1.3+ encoding\n");
+		fprintf(stderr, "       -A           count anomalous read pairs\n");
+		fprintf(stderr, "       -B           disable BAQ computation\n");
+		fprintf(stderr, "       -b FILE      list of input BAM files [null]\n");
+		fprintf(stderr, "       -C INT       parameter for adjusting mapQ; 0 to disable [0]\n");
+		fprintf(stderr, "       -d INT       max per-BAM depth to avoid excessive memory usage [%d]\n", mplp.max_depth);
+		fprintf(stderr, "       -E           extended BAQ for higher sensitivity but lower specificity\n");
+		fprintf(stderr, "       -f FILE      faidx indexed reference sequence file [null]\n");
+		fprintf(stderr, "       -G FILE      exclude read groups listed in FILE [null]\n");
+		fprintf(stderr, "       -l FILE      list of positions (chr pos) or regions (BED) [null]\n");
+		fprintf(stderr, "       -M INT       cap mapping quality at INT [%d]\n", mplp.max_mq);
+		fprintf(stderr, "       -r STR       region in which pileup is generated [null]\n");
+		fprintf(stderr, "       -R           ignore RG tags\n");
+		fprintf(stderr, "       -q INT       skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq);
+		fprintf(stderr, "       -Q INT       skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ);
+		fprintf(stderr, "\nOutput options:\n\n");
+		fprintf(stderr, "       -D           output per-sample DP in BCF (require -g/-u)\n");
+		fprintf(stderr, "       -g           generate BCF output (genotype likelihoods)\n");
+		fprintf(stderr, "       -O           output base positions on reads (disabled by -g/-u)\n");
+		fprintf(stderr, "       -s           output mapping quality (disabled by -g/-u)\n");
+		fprintf(stderr, "       -S           output per-sample strand bias P-value in BCF (require -g/-u)\n");
+		fprintf(stderr, "       -u           generate uncompress BCF output\n");
+		fprintf(stderr, "\nSNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):\n\n");
+		fprintf(stderr, "       -e INT       Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
+		fprintf(stderr, "       -F FLOAT     minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac);
+		fprintf(stderr, "       -h INT       coefficient for homopolymer errors [%d]\n", mplp.tandemQ);
+		fprintf(stderr, "       -I           do not perform indel calling\n");
+		fprintf(stderr, "       -L INT       max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth);
+		fprintf(stderr, "       -m INT       minimum gapped reads for indel candidates [%d]\n", mplp.min_support);
+		fprintf(stderr, "       -o INT       Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
+		fprintf(stderr, "       -P STR       comma separated list of platforms for indels [all]\n");
 		fprintf(stderr, "\n");
 		fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
 		return 1;
 	}
-    if ( file_list )
-    {
+    if (file_list) {
         if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
         mpileup(&mplp,nfiles,fn);
         for (c=0; c<nfiles; c++) free(fn[c]);
         free(fn);
-    }
-    else
-	    mpileup(&mplp, argc - optind, argv + optind);
+    } else mpileup(&mplp, argc - optind, argv + optind);
+	if (mplp.rghash) bcf_str2id_thorough_destroy(mplp.rghash);
 	free(mplp.reg); free(mplp.pl_list);
 	if (mplp.fai) fai_destroy(mplp.fai);
+	if (mplp.bed) bed_destroy(mplp.bed);
 	return 0;
 }