diff PsiCLASS-1.0.2/samtools-0.1.19/bam_plcmd.c @ 0:903fc43d6227 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/bam_plcmd.c	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,606 @@
+#include <math.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <string.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <getopt.h>
+#include "sam.h"
+#include "faidx.h"
+#include "kstring.h"
+#include "sam_header.h"
+
+static inline int printw(int c, FILE *fp)
+{
+	char buf[16];
+	int l, x;
+	if (c == 0) return fputc('0', fp);
+	for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+	if (c < 0) buf[l++] = '-';
+	buf[l] = 0;
+	for (x = 0; x < l/2; ++x) {
+		int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y;
+	}
+	fputs(buf, fp);
+	return 0;
+}
+
+static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
+{
+	int j;
+	if (p->is_head) {
+		putchar('^');
+		putchar(p->b->core.qual > 93? 126 : p->b->core.qual + 33);
+	}
+	if (!p->is_del) {
+		int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
+		if (ref) {
+			int rb = pos < ref_len? ref[pos] : 'N';
+			if (c == '=' || bam_nt16_table[c] == bam_nt16_table[rb]) c = bam1_strand(p->b)? ',' : '.';
+			else c = bam1_strand(p->b)? tolower(c) : toupper(c);
+		} else {
+			if (c == '=') c = bam1_strand(p->b)? ',' : '.';
+			else c = bam1_strand(p->b)? tolower(c) : toupper(c);
+		}
+		putchar(c);
+	} else putchar(p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*');
+	if (p->indel > 0) {
+		putchar('+'); printw(p->indel, stdout);
+		for (j = 1; j <= p->indel; ++j) {
+			int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
+			putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
+		}
+	} else if (p->indel < 0) {
+		printw(p->indel, stdout);
+		for (j = 1; j <= -p->indel; ++j) {
+			int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
+			putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
+		}
+	}
+	if (p->is_tail) putchar('$');
+}
+
+#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
+#define MPLP_NO_INDEL 0x400
+#define MPLP_REDO_BAQ 0x800
+#define MPLP_ILLUMINA13 0x1000
+#define MPLP_IGNORE_RG 0x2000
+#define MPLP_PRINT_POS 0x4000
+#define MPLP_PRINT_MAPQ 0x8000
+#define MPLP_PER_SAMPLE 0x10000
+
+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, max_indel_depth, fmt_flag;
+    int rflag_require, rflag_filter;
+	int openQ, extQ, tandemQ, min_support; // for indels
+	double min_frac; // for indels
+	char *reg, *pl_list, *fai_fname;
+	faidx_t *fai;
+	void *bed, *rghash;
+} mplp_conf_t;
+
+typedef struct {
+	bamFile fp;
+	bam_iter_t iter;
+	bam_header_t *h;
+	int ref_id;
+	char *ref;
+	const mplp_conf_t *conf;
+} 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_core(bam1_t *b, const char *ref, int);
+	extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
+	mplp_aux_t *ma = (mplp_aux_t*)data;
+	int ret, skip = 0;
+	do {
+		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->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; }
+        if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { 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->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
+		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.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 ignore_rg)
+{
+	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 = 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);
+			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]);
+			}
+			m->plp[id][m->n_plp[id]++] = *p;
+		}
+	}
+}
+
+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, 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;
+	void *rghash = 0;
+
+	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]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
+        if ( !data[i]->fp )
+        {
+            fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno));
+            exit(1);
+        }
+		data[i]->conf = conf;
+		h_tmp = bam_header_read(data[i]->fp);
+        if ( !h_tmp ) {
+            fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
+            exit(1);
+        }
+		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;
+			bam_index_t *idx;
+			idx = bam_index_load(fn[i]);
+			if (idx == 0) {
+				fprintf(stderr, "[%s] fail to load index for %s\n", __func__, fn[i]);
+				exit(1);
+			}
+			if (bam_parse_region(h_tmp, conf->reg, &tid, &beg, &end) < 0) {
+				fprintf(stderr, "[%s] malformatted region or wrong seqname for %s\n", __func__, fn[i]);
+				exit(1);
+			}
+			if (i == 0) tid0 = tid, beg0 = beg, end0 = end;
+			data[i]->iter = bam_iter_query(idx, tid, beg, end);
+			bam_index_destroy(idx);
+		}
+		if (i == 0) h = h_tmp;
+		else {
+			// FIXME: to check consistency
+			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);
+	// write the VCF header
+	if (conf->flag & MPLP_GLF) {
+		kstring_t s;
+		bh = calloc(1, sizeof(bcf_hdr_t));
+		s.l = s.m = 0; s.s = 0;
+		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);
+		}
+		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);
+        s.l = 0;
+        ksprintf(&s, "##samtoolsVersion=%s\n", BAM_VERSION);
+        if (conf->fai_fname) ksprintf(&s, "##reference=file://%s\n", conf->fai_fname);
+        h->dict = sam_header_parse2(h->text);
+        int nseq;
+        const char *tags[] = {"SN","LN","UR","M5",NULL};
+        char **tbl = sam_header2tbl_n(h->dict, "SQ", tags, &nseq);
+        for (i=0; i<nseq; i++)
+        {
+            ksprintf(&s, "##contig=<ID=%s", tbl[4*i]);
+            if ( tbl[4*i+1] ) ksprintf(&s, ",length=%s", tbl[4*i+1]);
+            if ( tbl[4*i+2] ) ksprintf(&s, ",URL=%s", tbl[4*i+2]);
+            if ( tbl[4*i+3] ) ksprintf(&s, ",md5=%s", tbl[4*i+3]);
+            kputs(">\n", &s);
+        }
+        if (tbl) free(tbl);
+		bh->txt = s.s;
+		bh->l_txt = 1 + s.l;
+		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));
+		bca->rghash = rghash;
+		bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
+		bca->min_frac = conf->min_frac;
+		bca->min_support = conf->min_support;
+        bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
+	}
+	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-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 (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 = 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 total_depth, _ref0, ref16;
+			bcf1_t *b = calloc(1, sizeof(bcf1_t));
+			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)
+				bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
+			bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
+			bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, 0, 0);
+			bcf_write(bp, bh, b);
+			bcf_destroy(b);
+			// call indels
+			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, bca, -1, &bc) >= 0) {
+					b = calloc(1, sizeof(bcf1_t));
+					bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, bca, ref);
+					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) {
+				int j, cnt;
+				for (j = cnt = 0; j < n_plp[i]; ++j) {
+					const bam_pileup1_t *p = plp[i] + j;
+					if (bam1_qual(p->b)[p->qpos] >= conf->min_baseQ) ++cnt;
+				}
+				printf("\t%d\t", cnt);
+				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) {
+						const bam_pileup1_t *p = plp[i] + j;
+						if (bam1_qual(p->b)[p->qpos] >= conf->min_baseQ)
+							pileup_seq(plp[i] + j, pos, ref_len, ref);
+					}
+					putchar('\t');
+					for (j = 0; j < n_plp[i]; ++j) {
+						const bam_pileup1_t *p = plp[i] + j;
+						int c = bam1_qual(p->b)[p->qpos];
+						if (c >= conf->min_baseQ) {
+							c = c + 33 < 126? c + 33 : 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');
+		}
+	}
+
+	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);
+	bcf_call_del_rghash(rghash);
+	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) {
+		bam_close(data[i]->fp);
+		if (data[i]->iter) bam_iter_destroy(data[i]->iter);
+		free(data[i]);
+	}
+	free(data); free(plp); free(ref); free(n_plp);
+	return 0;
+}
+
+#define MAX_PATH_LEN 1024
+int read_file_list(const char *file_list,int *n,char **argv[])
+{
+    char buf[MAX_PATH_LEN];
+    int len, nfiles = 0;
+    char **files = NULL;
+    struct stat sb;
+
+    *n = 0;
+    *argv = NULL;
+
+    FILE *fh = fopen(file_list,"r");
+    if ( !fh )
+    {
+        fprintf(stderr,"%s: %s\n", file_list,strerror(errno));
+        return 1;
+    }
+
+    files = calloc(nfiles,sizeof(char*));
+    nfiles = 0;
+    while ( fgets(buf,MAX_PATH_LEN,fh) ) 
+    {
+        // allow empty lines and trailing spaces
+        len = strlen(buf);
+        while ( len>0 && isspace(buf[len-1]) ) len--;
+        if ( !len ) continue;
+
+        // check sanity of the file list
+        buf[len] = 0;
+        if (stat(buf, &sb) != 0)
+        {
+            // no such file, check if it is safe to print its name
+            int i, safe_to_print = 1;
+            for (i=0; i<len; i++)
+                if (!isprint(buf[i])) { safe_to_print = 0; break; } 
+            if ( safe_to_print )
+                fprintf(stderr,"The file list \"%s\" appears broken, could not locate: %s\n", file_list,buf);
+            else
+                fprintf(stderr,"Does the file \"%s\" really contain a list of files and do all exist?\n", file_list);
+            return 1;
+        }
+
+        nfiles++;
+        files = realloc(files,nfiles*sizeof(char*));
+        files[nfiles-1] = strdup(buf);
+    }
+    fclose(fh);
+    if ( !nfiles )
+    {
+        fprintf(stderr,"No files read from %s\n", file_list);
+        return 1;
+    }
+    *argv = files;
+    *n    = nfiles;
+    return 0;
+}
+#undef MAX_PATH_LEN
+
+int bam_mpileup(int argc, char *argv[])
+{
+	int c;
+    const char *file_list = NULL;
+    char **fn = NULL;
+    int nfiles = 0, use_orphan = 0;
+	mplp_conf_t mplp;
+	memset(&mplp, 0, sizeof(mplp_conf_t));
+	mplp.max_mq = 60;
+	mplp.min_baseQ = 13;
+	mplp.capQ_thres = 0;
+	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;
+    static struct option lopts[] = 
+    {
+        {"rf",1,0,1},   // require flag
+        {"ff",1,0,2},   // filter flag
+        {0,0,0,0}
+    };
+	while ((c = getopt_long(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsV1:2:",lopts,NULL)) >= 0) {
+		switch (c) {
+        case  1 : mplp.rflag_require = strtol(optarg,0,0); break;
+        case  2 : mplp.rflag_filter  = strtol(optarg,0,0); break;
+		case 'f':
+			mplp.fai = fai_load(optarg);
+			if (mplp.fai == 0) return 1;
+            mplp.fai_fname = optarg;
+			break;
+		case 'd': mplp.max_depth = atoi(optarg); break;
+		case 'r': mplp.reg = strdup(optarg); break;
+		case 'l': mplp.bed = bed_read(optarg); break;
+		case 'P': mplp.pl_list = strdup(optarg); break;
+		case 'p': mplp.flag |= MPLP_PER_SAMPLE; 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; break;
+		case 'D': mplp.fmt_flag |= B2B_FMT_DP; break;
+		case 'S': mplp.fmt_flag |= B2B_FMT_SP; break;
+		case 'V': mplp.fmt_flag |= B2B_FMT_DV; break;
+		case 'I': mplp.flag |= MPLP_NO_INDEL; break;
+		case 'E': mplp.flag |= MPLP_REDO_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;
+		case 'Q': mplp.min_baseQ = atoi(optarg); break;
+        case 'b': file_list = optarg; break;
+		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, "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 filenames, one per line [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           recalculate extended BAQ on the fly thus ignoring existing BQs\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, "       --rf INT     required flags: skip reads with mask bits unset []\n");
+		fprintf(stderr, "       --ff INT     filter flags: skip reads with mask bits set []\n");
+		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           apply -m and -F per-sample to increase sensitivity\n");
+		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;
+	}
+	bam_no_B = 1;
+    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);
+	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;
+}