bam_plcmd.c

/*  bam_plcmd.c -- mpileup subcommand.

    Copyright (C) 2008-2015, 2019-2021 Genome Research Ltd.
    Portions copyright (C) 2009-2012 Broad Institute.

    Author: Heng Li <lh3@sanger.ac.uk>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.  */

#include <config.h>

#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <ctype.h>
#include <string.h>
#include <strings.h>
#include <limits.h>
#include <errno.h>
#include <sys/stat.h>
#include <getopt.h>
#include <inttypes.h>
#include <htslib/sam.h>
#include <htslib/faidx.h>
#include <htslib/kstring.h>
#include <htslib/klist.h>
#include <htslib/khash_str2int.h>
#include "samtools.h"
#include "bedidx.h"
#include "sam_opts.h"

#define dummy_free(p)
KLIST_INIT(auxlist, char *, dummy_free)

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 int pileup_seq(FILE *fp, const bam_pileup1_t *p, hts_pos_t pos,
                              hts_pos_t ref_len, const char *ref, kstring_t *ks,
                              int rev_del)
{
    int j;
    if (p->is_head) {
        putc('^', fp);
        putc(p->b->core.qual > 93? 126 : p->b->core.qual + 33, fp);
    }
    if (!p->is_del) {
        int c = p->qpos < p->b->core.l_qseq
            ? seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos)]
            : 'N';
        if (ref) {
            int rb = pos < ref_len? ref[pos] : 'N';
            if (c == '=' || seq_nt16_table[c] == seq_nt16_table[rb]) c = bam_is_rev(p->b)? ',' : '.';
            else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
        } else {
            if (c == '=') c = bam_is_rev(p->b)? ',' : '.';
            else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
        }
        putc(c, fp);
    } else putc(p->is_refskip? (bam_is_rev(p->b)? '<' : '>') : ((bam_is_rev(p->b) && rev_del) ? '#' : '*'), fp);
    int del_len = -p->indel;
    if (p->indel > 0) {
        int len = bam_plp_insertion(p, ks, &del_len);
        if (len < 0) {
            print_error("mpileup", "bam_plp_insertion() failed");
            return -1;
        }
        putc('+', fp); printw(len, fp);
        if (bam_is_rev(p->b)) {
            char pad = rev_del ? '#' : '*';
            for (j = 0; j < len; j++)
                putc(ks->s[j] != '*' ? tolower(ks->s[j]) : pad, fp);
        } else {
            for (j = 0; j < len; j++)
                putc(toupper(ks->s[j]), fp);
        }
    }
    if (del_len > 0) {
        printw(-del_len, fp);
        for (j = 1; j <= del_len; ++j) {
            int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
            putc(bam_is_rev(p->b)? tolower(c) : toupper(c), fp);
        }
    }
    if (p->is_tail) putc('$', fp);
    return 0;
}

#include <assert.h>
#include "bam2bcf.h"
#include "sample.h"

#define MPLP_BCF        1
#define MPLP_VCF        (1<<1)
#define MPLP_NO_COMP    (1<<2)
#define MPLP_NO_ORPHAN  (1<<3)
#define MPLP_REALN      (1<<4)
#define MPLP_NO_INDEL   (1<<5)
#define MPLP_REDO_BAQ   (1<<6)
#define MPLP_ILLUMINA13 (1<<7)
#define MPLP_IGNORE_RG  (1<<8)
#define MPLP_PER_SAMPLE (1<<9)
#define MPLP_SMART_OVERLAPS (1<<10)

#define MPLP_PRINT_MAPQ_CHAR (1<<11)
#define MPLP_PRINT_QPOS  (1<<12)
#define MPLP_PRINT_QNAME (1<<13)
#define MPLP_PRINT_FLAG  (1<<14)
#define MPLP_PRINT_RNAME (1<<15)
#define MPLP_PRINT_POS   (1<<16)
#define MPLP_PRINT_MAPQ  (1<<17)
#define MPLP_PRINT_CIGAR (1<<18)
#define MPLP_PRINT_RNEXT (1<<19)
#define MPLP_PRINT_PNEXT (1<<20)
#define MPLP_PRINT_TLEN  (1<<21)
#define MPLP_PRINT_SEQ   (1<<22)
#define MPLP_PRINT_QUAL  (1<<23)

#define MPLP_MAX_DEPTH 8000
#define MPLP_MAX_INDEL_DEPTH 250

typedef struct {
    int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag, all, rev_del;
    int rflag_require, rflag_filter;
    int openQ, extQ, tandemQ, min_support; // for indels
    double min_frac; // for indels
    char *reg, *pl_list, *fai_fname, *output_fname;
    faidx_t *fai;
    void *bed, *rghash, *auxlist;
    int argc;
    char **argv;
    char sep, empty;
    sam_global_args ga;
} mplp_conf_t;

typedef struct {
    char *ref[2];
    int ref_id[2];
    hts_pos_t ref_len[2];
} mplp_ref_t;

#define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}}

typedef struct {
    samFile *fp;
    hts_itr_t *iter;
    sam_hdr_t *h;
    mplp_ref_t *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 build_auxlist(mplp_conf_t *conf, char *optstring) {
    if (!optstring)
        return 0;

    void *colhash = khash_str2int_init();
    if (!colhash)
        return 1;

    struct active_cols {
        char *name;
        int supported;
    };

    const struct active_cols colnames[11] = {
            {"QNAME", 1}, {"FLAG", 1}, {"RNAME", 1}, {"POS", 1}, {"MAPQ", 1}, {"CIGAR", 0}, {"RNEXT", 1}, {"PNEXT", 1}, {"TLEN", 0}, {"SEQ", 0}, {"QUAL", 0}
    };

    int i, f = MPLP_PRINT_QNAME, colno = 11;
    for (i = 0; i < colno; i++, f <<= 1)
        if (colnames[i].supported)
            khash_str2int_set(colhash, colnames[i].name, f);

    conf->auxlist = kl_init(auxlist);
    if (!conf->auxlist)
        return 1;

    char *save_p;
    char *tag = strtok_r(optstring, ",", &save_p);
    while (tag) {
        if (khash_str2int_get(colhash, tag, &f) == 0) {
            conf->flag |= f;
        } else {
            if (strlen(tag) != 2) {
                fprintf(stderr, "[%s] tag '%s' has more than two characters or not supported\n", __func__, tag);
            } else {
                char **tag_p = kl_pushp(auxlist, conf->auxlist);
                *tag_p = tag;
            }
        }
        tag = strtok_r(NULL, ",", &save_p);
    }

    khash_str2int_destroy(colhash);

    return 0;
}

static int mplp_get_ref(mplp_aux_t *ma, int tid, char **ref, hts_pos_t *ref_len) {
    mplp_ref_t *r = ma->ref;

    //printf("get ref %d {%d/%p, %d/%p}\n", tid, r->ref_id[0], r->ref[0], r->ref_id[1], r->ref[1]);

    if (!r || !ma->conf->fai) {
        *ref = NULL;
        return 0;
    }

    // Do we need to reference count this so multiple mplp_aux_t can
    // track which references are in use?
    // For now we just cache the last two. Sufficient?
    if (tid == r->ref_id[0]) {
        *ref = r->ref[0];
        *ref_len = r->ref_len[0];
        return 1;
    }
    if (tid == r->ref_id[1]) {
        // Last, swap over
        int tmp_id;
        hts_pos_t tmp_len;
        tmp_id  = r->ref_id[0];  r->ref_id[0]  = r->ref_id[1];  r->ref_id[1]  = tmp_id;
        tmp_len = r->ref_len[0]; r->ref_len[0] = r->ref_len[1]; r->ref_len[1] = tmp_len;

        char *tc;
        tc = r->ref[0]; r->ref[0] = r->ref[1]; r->ref[1] = tc;
        *ref = r->ref[0];
        *ref_len = r->ref_len[0];
        return 1;
    }

    // New, so migrate to old and load new
    free(r->ref[1]);
    r->ref[1]     = r->ref[0];
    r->ref_id[1]  = r->ref_id[0];
    r->ref_len[1] = r->ref_len[0];

    r->ref_id[0] = tid;
    r->ref[0] = faidx_fetch_seq64(ma->conf->fai,
                                sam_hdr_tid2name(ma->h, r->ref_id[0]),
                                0,
                                HTS_POS_MAX,
                                &r->ref_len[0]);

    if (!r->ref[0]) {
        r->ref[0] = NULL;
        r->ref_id[0] = -1;
        r->ref_len[0] = 0;
        *ref = NULL;
        return 0;
    }

    *ref = r->ref[0];
    *ref_len = r->ref_len[0];
    return 1;
}

static void
print_empty_pileup(FILE *fp, const mplp_conf_t *conf, const char *tname,
                   hts_pos_t pos, int n, const char *ref, hts_pos_t ref_len)
{
    int i;
    fprintf(fp, "%s\t%"PRIhts_pos"\t%c", tname, pos+1, (ref && pos < ref_len)? ref[pos] : 'N');
    for (i = 0; i < n; ++i) {
        fputs("\t0\t*\t*", fp);
        int flag_value = MPLP_PRINT_MAPQ_CHAR;
        while(flag_value < MPLP_PRINT_QUAL + 1) {
            if (conf->flag & flag_value)
                fputs("\t*", fp);
            flag_value <<= 1;
        }
        if (conf->auxlist) {
            int t = 0;
            while(t++ < ((klist_t(auxlist) *)conf->auxlist)->size)
                fputs("\t*", fp);
        }
    }
    putc('\n', fp);
}

static int mplp_func(void *data, bam1_t *b)
{
    char *ref;
    mplp_aux_t *ma = (mplp_aux_t*)data;
    int ret, skip = 0;
    hts_pos_t ref_len;

    do {
        int has_ref;
        ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b);
        if (ret < 0) break;
        // The 'B' cigar operation is not part of the specification, considering as obsolete.
        //  bam_remove_B(b);
        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 && ma->conf->all == 0) { // test overlap
            skip = !bed_overlap(ma->conf->bed, sam_hdr_tid2name(ma->h, b->core.tid), b->core.pos, bam_endpos(b));
            if (skip) continue;
        }
        if (ma->conf->rghash) { // exclude read groups
            uint8_t *rg = bam_aux_get(b, "RG");
            skip = (rg && khash_str2int_get(ma->conf->rghash, (const char*)(rg+1), NULL)==0);
            if (skip) continue;
        }
        if (ma->conf->flag & MPLP_ILLUMINA13) {
            int i;
            uint8_t *qual = bam_get_qual(b);
            for (i = 0; i < b->core.l_qseq; ++i)
                qual[i] = qual[i] > 31? qual[i] - 31 : 0;
        }

        if (ma->conf->fai && b->core.tid >= 0) {
            has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len);
            if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence
                fprintf(stderr,"[%s] Skipping because %"PRIhts_pos" is outside of %"PRIhts_pos" [ref:%d]\n",
                        __func__, (int64_t) b->core.pos, ref_len, b->core.tid);
                skip = 1;
                continue;
            }
        } else {
            has_ref = 0;
        }

        skip = 0;
        if (has_ref && (ma->conf->flag&MPLP_REALN)) sam_prob_realn(b, ref, ref_len, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
        if (has_ref && ma->conf->capQ_thres > 10) {
            int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres);
            if (q < 0) skip = 1;
            else if (b->core.qual > q) b->core.qual = q;
        }
        if (b->core.qual < ma->conf->min_mq) skip = 1;
        else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) 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? NULL : 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(EXIT_FAILURE);
            }
            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;
        }
    }
}

/*
 * Performs pileup
 * @param conf configuration for this pileup
 * @param n number of files specified in fn
 * @param fn filenames
 * @param fn_idx index filenames
 */
static int mpileup(mplp_conf_t *conf, int n, char **fn, char **fn_idx)
{
    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, *n_plp, tid0 = 0, max_depth, max_indel_depth;
    hts_pos_t pos, beg0 = 0, end0 = HTS_POS_MAX, ref_len;
    const bam_pileup1_t **plp;
    mplp_ref_t mp_ref = MPLP_REF_INIT;
    bam_mplp_t iter;
    sam_hdr_t *h = NULL; /* header of first file in input list */
    char *ref;
    void *rghash = NULL;
    FILE *pileup_fp = NULL;

    bcf_callaux_t *bca = NULL;
    bcf_callret1_t *bcr = NULL;
    bcf_call_t bc;
    htsFile *bcf_fp = NULL;
    bcf_hdr_t *bcf_hdr = NULL;

    bam_sample_t *sm = NULL;
    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(mplp_aux_t*));
    plp = calloc(n, sizeof(bam_pileup1_t*));
    n_plp = calloc(n, sizeof(int));
    sm = bam_smpl_init();

    if (n == 0) {
        fprintf(stderr,"[%s] no input file/data given\n", __func__);
        exit(EXIT_FAILURE);
    }

    // read the header of each file in the list and initialize data
    for (i = 0; i < n; ++i) {
        sam_hdr_t *h_tmp;
        data[i] = calloc(1, sizeof(mplp_aux_t));
        data[i]->fp = sam_open_format(fn[i], "rb", &conf->ga.in);
        if ( !data[i]->fp )
        {
            fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno));
            exit(EXIT_FAILURE);
        }
        if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) {
            fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
            exit(EXIT_FAILURE);
        }
        if (conf->fai_fname && hts_set_fai_filename(data[i]->fp, conf->fai_fname) != 0) {
            fprintf(stderr, "[%s] failed to process %s: %s\n",
                    __func__, conf->fai_fname, strerror(errno));
            exit(EXIT_FAILURE);
        }
        data[i]->conf = conf;
        data[i]->ref = &mp_ref;
        h_tmp = sam_hdr_read(data[i]->fp);
        if ( !h_tmp ) {
            fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
            exit(EXIT_FAILURE);
        }
        bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : sam_hdr_str(h_tmp));
        if (conf->flag & MPLP_BCF) {
            // Collect read group IDs with PL (platform) listed in pl_list (note: fragile, strstr search)
            rghash = bcf_call_add_rg(rghash, sam_hdr_str(h_tmp), conf->pl_list);
        }
        if (conf->reg) {
            hts_idx_t *idx = NULL;
            // If index filename has not been specfied, look in BAM folder
            if (fn_idx != NULL)  {
                idx = sam_index_load2(data[i]->fp, fn[i], fn_idx[i]);
            } else {
                idx = sam_index_load(data[i]->fp, fn[i]);
            }

            if (idx == NULL) {
                fprintf(stderr, "[%s] fail to load index for %s\n", __func__, fn[i]);
                exit(EXIT_FAILURE);
            }
            if ( (data[i]->iter=sam_itr_querys(idx, h_tmp, conf->reg)) == 0) {
                fprintf(stderr, "[E::%s] fail to parse region '%s' with %s\n", __func__, conf->reg, fn[i]);
                exit(EXIT_FAILURE);
            }
            if (i == 0) beg0 = data[i]->iter->beg, end0 = data[i]->iter->end, tid0 = data[i]->iter->tid;
            hts_idx_destroy(idx);
        }
        else
            data[i]->iter = NULL;

        if (i == 0) h = data[i]->h = h_tmp; // save the header of the first file
        else {
            // FIXME: check consistency between h and h_tmp
            sam_hdr_destroy(h_tmp);

            // we store only the first file's header; it's (alleged to be)
            // compatible with the i-th file's target_name lookup needs
            data[i]->h = h;
        }
    }
    fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
    if (conf->flag & MPLP_BCF)
    {
        const char *mode;
        // allocate data storage proportionate to number of samples being studied sm->n
        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(bam_pileup1_t*));

        // write the VCF header

        if ( conf->flag & MPLP_VCF )
            mode = (conf->flag&MPLP_NO_COMP)? "wu" : "wz";   // uncompressed VCF or compressed VCF
        else
            mode = (conf->flag&MPLP_NO_COMP)? "wub" : "wb";  // uncompressed BCF or compressed BCF

        bcf_fp = bcf_open(conf->output_fname? conf->output_fname : "-", mode);
        if (bcf_fp == NULL) {
            fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno));
            exit(EXIT_FAILURE);
        }

        // BCF header creation
        bcf_hdr = bcf_hdr_init("w");
        kstring_t str = {0,0,NULL};

        ksprintf(&str, "##samtoolsVersion=%s+htslib-%s\n",samtools_version(),hts_version());
        bcf_hdr_append(bcf_hdr, str.s);

        str.l = 0;
        ksprintf(&str, "##samtoolsCommand=samtools mpileup");
        for (i=1; i<conf->argc; i++) ksprintf(&str, " %s", conf->argv[i]);
        kputc('\n', &str);
        bcf_hdr_append(bcf_hdr, str.s);

        if (conf->fai_fname)
        {
            str.l = 0;
            ksprintf(&str, "##reference=file://%s\n", conf->fai_fname);
            bcf_hdr_append(bcf_hdr, str.s);
        }

        // Translate BAM @SQ tags to BCF ##contig tags
        // todo: use/write new BAM header manipulation routines, fill also UR, M5
        for (i=0; i < sam_hdr_nref(h); i++)
        {
            str.l = 0;
            ksprintf(&str, "##contig=<ID=%s,length=%"PRId64">", sam_hdr_tid2name(h, i), (int64_t) sam_hdr_tid2len(h, i));
            bcf_hdr_append(bcf_hdr, str.s);
        }
        free(str.s);
        bcf_hdr_append(bcf_hdr,"##ALT=<ID=*,Description=\"Represents allele(s) other than observed.\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of reads supporting an indel\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of reads supporting an indel\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">");
#if CDF_MWU_TESTS
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias [CDF] (bigger is better)\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias [CDF] (bigger is better)\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias [CDF] (bigger is better)\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias [CDF] (bigger is better)\">");
#endif
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">");
        bcf_hdr_append(bcf_hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">");
        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">");
        if ( conf->fmt_flag&B2B_FMT_DP )
            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-quality bases\">");
        if ( conf->fmt_flag&B2B_FMT_DV )
            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-quality non-reference bases\">");
        if ( conf->fmt_flag&B2B_FMT_DPR )
            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
        if ( conf->fmt_flag&B2B_INFO_DPR )
            bcf_hdr_append(bcf_hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
        if ( conf->fmt_flag&B2B_FMT_DP4 )
            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases\">");
        if ( conf->fmt_flag&B2B_FMT_SP )
            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">");
        if ( conf->fmt_flag&B2B_FMT_AD )
            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths\">");
        if ( conf->fmt_flag&B2B_FMT_ADF )
            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADF,Number=R,Type=Integer,Description=\"Allelic depths on the forward strand\">");
        if ( conf->fmt_flag&B2B_FMT_ADR )
            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADR,Number=R,Type=Integer,Description=\"Allelic depths on the reverse strand\">");
        if ( conf->fmt_flag&B2B_INFO_AD )
            bcf_hdr_append(bcf_hdr,"##INFO=<ID=AD,Number=R,Type=Integer,Description=\"Total allelic depths\">");
        if ( conf->fmt_flag&B2B_INFO_ADF )
            bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADF,Number=R,Type=Integer,Description=\"Total allelic depths on the forward strand\">");
        if ( conf->fmt_flag&B2B_INFO_ADR )
            bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADR,Number=R,Type=Integer,Description=\"Total allelic depths on the reverse strand\">");

        for (i=0; i<sm->n; i++)
            bcf_hdr_add_sample(bcf_hdr, sm->smpl[i]);
        bcf_hdr_add_sample(bcf_hdr, NULL);
        if (bcf_hdr_write(bcf_fp, bcf_hdr) != 0) {
            print_error_errno("mpileup", "Failed to write VCF/BCF header to \"%s\"",
                              conf->output_fname? conf->output_fname : "standard output");
            exit(EXIT_FAILURE);
        }
        // End of BCF header creation

        // Initialise the calling algorithm
        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;

        bc.bcf_hdr = bcf_hdr;
        bc.n = sm->n;
        bc.PL = malloc(15 * sm->n * sizeof(*bc.PL));
        if (conf->fmt_flag)
        {
            assert( sizeof(float)==sizeof(int32_t) );
            bc.DP4 = malloc(sm->n * sizeof(int32_t) * 4);
            bc.fmt_arr = malloc(sm->n * sizeof(float)); // all fmt_flag fields
            if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR|B2B_INFO_AD|B2B_INFO_ADF|B2B_INFO_ADR|B2B_FMT_AD|B2B_FMT_ADF|B2B_FMT_ADR) )
            {
                // first B2B_MAX_ALLELES fields for total numbers, the rest per-sample
                bc.ADR = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
                bc.ADF = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
                for (i=0; i<sm->n; i++)
                {
                    bcr[i].ADR = bc.ADR + (i+1)*B2B_MAX_ALLELES;
                    bcr[i].ADF = bc.ADF + (i+1)*B2B_MAX_ALLELES;
                }
            }
        }
    }
    else {
        pileup_fp = conf->output_fname? fopen(conf->output_fname, "w") : stdout;

        if (pileup_fp == NULL) {
            fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname, strerror(errno));
            exit(EXIT_FAILURE);
        }
    }

    // init pileup
    iter = bam_mplp_init(n, mplp_func, (void**)data);
    if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(iter);
    if ( !conf->max_depth ) {
        max_depth = INT_MAX;
        fprintf(stderr, "[%s] Max depth set to maximum value (%d)\n", __func__, INT_MAX);
    } else {
        max_depth = conf->max_depth;
        if ( max_depth * n > 1<<20 )
            fprintf(stderr, "[%s] Combined max depth is above 1M. Potential memory hog!\n", __func__);
    }

    // Only used when writing BCF
    max_indel_depth = conf->max_indel_depth * sm->n;
    bam_mplp_set_maxcnt(iter, max_depth);
    bcf1_t *bcf_rec = bcf_init1();
    int ret;
    int last_tid = -1;
    hts_pos_t last_pos = -1;

    // begin pileup
    while ( (ret=bam_mplp64_auto(iter, &tid, &pos, n_plp, plp)) > 0) {
        if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
        mplp_get_ref(data[0], tid, &ref, &ref_len);
        //printf("tid=%d len=%d ref=%p/%s\n", tid, ref_len, ref, ref);
        if (conf->flag & MPLP_BCF) {
            int total_depth, _ref0, ref16;
            if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), pos, pos+1)) continue;
            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 = seq_nt16_table[_ref0];
            bcf_callaux_clean(bca, &bc);
            for (i = 0; i < gplp.n; ++i)
                bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
            bc.tid = tid; bc.pos = pos;
            bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
            bcf_clear1(bcf_rec);
            bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0);
            if (bcf_write1(bcf_fp, bcf_hdr, bcf_rec) != 0) {
                print_error_errno("mpileup", "Failed to write VCF/BCF record to \"%s\"",
                                  conf->output_fname?conf->output_fname:"standard output");
                exit(EXIT_FAILURE);
            }
            // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
            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)
            {
                bcf_callaux_clean(bca, &bc);
                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) {
                    bcf_clear1(bcf_rec);
                    bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, bca, ref);
                    if (bcf_write1(bcf_fp, bcf_hdr, bcf_rec) != 0) {
                        print_error_errno("mpileup", "Failed to write VCF/BCF record to \"%s\"",
                                          conf->output_fname?conf->output_fname:"standard output");
                        exit(EXIT_FAILURE);
                    }
                }
            }
        } else {
            if (conf->all) {
                // Deal with missing portions of previous tids
                while (tid > last_tid) {
                    if (last_tid >= 0 && !conf->reg) {
                        while (++last_pos < sam_hdr_tid2len(h, last_tid)) {
                            if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, last_tid), last_pos, last_pos + 1) == 0)
                                continue;
                            print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, last_tid), last_pos, n, ref, ref_len);
                        }
                    }
                    last_tid++;
                    last_pos = -1;
                    if (conf->all < 2)
                        break;
                }
            }
            if (conf->all) {
                // Deal with missing portion of current tid
                while (++last_pos < pos) {
                    if (conf->reg && last_pos < beg0) continue; // out of range; skip
                    if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), last_pos, last_pos + 1) == 0)
                        continue;
                    print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, tid), last_pos, n, ref, ref_len);
                }
                last_tid = tid;
                last_pos = pos;
            }
            if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), pos, pos+1)) continue;

            fprintf(pileup_fp, "%s\t%"PRIhts_pos"\t%c", sam_hdr_tid2name(h, 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;
                    int c = p->qpos < p->b->core.l_qseq
                             ? bam_get_qual(p->b)[p->qpos]
                             : 0;
                    if (c >= conf->min_baseQ) ++cnt;
                }
                fprintf(pileup_fp, "\t%d\t", cnt);
                if (n_plp[i] == 0) {
                    fputs("*\t*", pileup_fp);
                    int flag_value = MPLP_PRINT_MAPQ_CHAR;
                    while(flag_value < MPLP_PRINT_QUAL + 1) {
                        if (conf->flag & flag_value)
                            fputs("\t*", pileup_fp);
                        flag_value <<= 1;
                    }
                    if (conf->auxlist) {
                        int t = 0;
                        while(t++ < ((klist_t(auxlist) *)conf->auxlist)->size)
                            fputs("\t*", pileup_fp);
                    }
                } else {
                    int n = 0;
                    kstring_t ks = KS_INITIALIZE;
                    for (j = 0; j < n_plp[i]; ++j) {
                        const bam_pileup1_t *p = plp[i] + j;
                        int c = p->qpos < p->b->core.l_qseq
                            ? bam_get_qual(p->b)[p->qpos]
                            : 0;
                        if (c >= conf->min_baseQ) {
                            n++;
                            if (pileup_seq(pileup_fp, plp[i] + j, pos, ref_len, ref, &ks, conf->rev_del) < 0) {
                                ret = 1;
                                goto fail;
                            }
                        }
                    }
                    if (!n) putc('*', pileup_fp);

                    /* Print base qualities */
                    n = 0;
                    ks_free(&ks);
                    putc('\t', pileup_fp);
                    for (j = 0; j < n_plp[i]; ++j) {
                        const bam_pileup1_t *p = plp[i] + j;
                        int c = p->qpos < p->b->core.l_qseq
                            ? bam_get_qual(p->b)[p->qpos]
                            : 0;
                        if (c >= conf->min_baseQ) {
                            c = c + 33 < 126? c + 33 : 126;
                            putc(c, pileup_fp);
                            n++;
                        }
                    }
                    if (!n) putc('*', pileup_fp);

                    /* Print selected columns */
                    int flag_value = MPLP_PRINT_MAPQ_CHAR;
                    while(flag_value < MPLP_PRINT_QUAL + 1) {
                        if (conf->flag & flag_value) {
                            n = 0;
                            putc('\t', pileup_fp);
                            for (j = 0; j < n_plp[i]; ++j) {
                                const bam_pileup1_t *p = &plp[i][j];
                                int c = p->qpos < p->b->core.l_qseq
                                    ? bam_get_qual(p->b)[p->qpos]
                                    : 0;
                                if ( c < conf->min_baseQ ) continue;
                                if (n > 0 && flag_value != MPLP_PRINT_MAPQ_CHAR) putc(',', pileup_fp);
                                n++;

                                switch (flag_value) {
                                case MPLP_PRINT_MAPQ_CHAR:
                                    c = p->b->core.qual + 33;
                                    if (c > 126) c = 126;
                                    putc(c, pileup_fp);
                                    break;
                                case MPLP_PRINT_QPOS:
                                    fprintf(pileup_fp, "%d", p->qpos + 1);
                                    break;
                                case MPLP_PRINT_QNAME:
                                    fputs(bam_get_qname(p->b), pileup_fp);
                                    break;
                                case MPLP_PRINT_FLAG:
                                    fprintf(pileup_fp, "%d", p->b->core.flag);
                                    break;
                                case MPLP_PRINT_RNAME:
                                    if (p->b->core.tid >= 0)
                                        fputs(sam_hdr_tid2name(h, p->b->core.tid), pileup_fp);
                                    else
                                        putc('*', pileup_fp);
                                    break;
                                case MPLP_PRINT_POS:
                                    fprintf(pileup_fp, "%"PRId64, (int64_t) p->b->core.pos + 1);
                                    break;
                                case MPLP_PRINT_MAPQ:
                                    fprintf(pileup_fp, "%d", p->b->core.qual);
                                    break;
                                case MPLP_PRINT_RNEXT:
                                    if (p->b->core.mtid >= 0)
                                        fputs(sam_hdr_tid2name(h, p->b->core.mtid), pileup_fp);
                                    else
                                        putc('*', pileup_fp);
                                    break;
                                case MPLP_PRINT_PNEXT:
                                    fprintf(pileup_fp, "%"PRId64, (int64_t) p->b->core.mpos + 1);
                                    break;
                                }
                            }
                            if (!n) putc('*', pileup_fp);
                        }
                        flag_value <<= 1;
                    }

                    /* Print selected tags */
                    klist_t(auxlist) *auxlist_p = ((klist_t(auxlist) *)conf->auxlist);
                    if (auxlist_p && auxlist_p->size) {
                        kliter_t(auxlist) *aux;
                        for (aux = kl_begin(auxlist_p); aux != kl_end(auxlist_p); aux = kl_next(aux)) {
                            n = 0;
                            putc('\t', pileup_fp);
                            for (j = 0; j < n_plp[i]; ++j) {
                                const bam_pileup1_t *p = &plp[i][j];
                                int c = p->qpos < p->b->core.l_qseq
                                    ? bam_get_qual(p->b)[p->qpos]
                                    : 0;
                                if ( c < conf->min_baseQ ) continue;

                                if (n > 0) putc(conf->sep, pileup_fp);
                                n++;
                                uint8_t* tag_u = bam_aux_get(p->b, kl_val(aux));
                                if (!tag_u) {
                                    putc(conf->empty , pileup_fp);
                                    continue;
                                }

                                /* Tag value is string */
                                if (*tag_u == 'Z' || *tag_u == 'H') {
                                    char *tag_s = bam_aux2Z(tag_u);
                                    if (!tag_s) continue;
                                    fputs(tag_s, pileup_fp);
                                }

                                /* Tag value is integer */
                                if (*tag_u == 'I' || *tag_u == 'i' || *tag_u == 'C' || *tag_u == 'c' || *tag_u == 'S' || *tag_u == 's') {
                                    int64_t tag_i = bam_aux2i(tag_u);
                                    fprintf(pileup_fp, "%" PRId64 "", tag_i);
                                }

                                /* Tag value is float */
                                if (*tag_u == 'd' || *tag_u == 'f') {
                                    double tag_f = bam_aux2f(tag_u);
                                    fprintf(pileup_fp, "%lf", tag_f);
                                }

                                /* Tag value is character */
                                if (*tag_u == 'A') {
                                    char tag_c = bam_aux2A(tag_u);
                                    putc(tag_c, pileup_fp);
                                }
                            }
                            if (!n) putc('*', pileup_fp);
                        }
                    }
                }
            }
            putc('\n', pileup_fp);
        }
    }

    if (ret < 0) {
        print_error("mpileup", "error reading from input file");
        ret = EXIT_FAILURE;
        goto fail;
    }

    if (conf->all && !(conf->flag & MPLP_BCF)) {
        // Handle terminating region
        if (last_tid < 0 && conf->reg && conf->all > 1) {
            last_tid = tid0;
            last_pos = beg0-1;
            mplp_get_ref(data[0], tid0, &ref, &ref_len);
        }
       while (last_tid >= 0 && last_tid < sam_hdr_nref(h)) {
            while (++last_pos < sam_hdr_tid2len(h, last_tid)) {
                if (last_pos >= end0) break;
                if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, last_tid), last_pos, last_pos + 1) == 0)
                    continue;
                print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, last_tid), last_pos, n, ref, ref_len);
            }
            last_tid++;
            last_pos = -1;
            if (conf->all < 2 || conf->reg)
                break;
        }
    }

fail:
    // clean up
    free(bc.tmp.s);
    bcf_destroy1(bcf_rec);
    if (bcf_fp)
    {
        hts_close(bcf_fp);
        bcf_hdr_destroy(bcf_hdr);
        bcf_call_destroy(bca);
        free(bc.PL);
        free(bc.DP4);
        free(bc.ADR);
        free(bc.ADF);
        free(bc.fmt_arr);
        free(bcr);
    }
    if (pileup_fp && conf->output_fname) fclose(pileup_fp);
    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);
    bam_mplp_destroy(iter);
    sam_hdr_destroy(h);
    for (i = 0; i < n; ++i) {
        sam_close(data[i]->fp);
        if (data[i]->iter) hts_itr_destroy(data[i]->iter);
        free(data[i]);
    }
    free(data); free(plp); free(n_plp);
    free(mp_ref.ref[0]);
    free(mp_ref.ref[1]);
    return ret;
}

static int is_url(const char *s)
{
    static const char uri_scheme_chars[] =
        "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+.-";
    return s[strspn(s, uri_scheme_chars)] == ':';
}

#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 (! (is_url(buf) || 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 parse_format_flag(const char *str)
{
    int i, flag = 0, n_tags;
    char **tags = hts_readlist(str, 0, &n_tags);
    for(i=0; i<n_tags; i++)
    {
        if ( !strcasecmp(tags[i],"DP") ) flag |= B2B_FMT_DP;
        else if ( !strcasecmp(tags[i],"DV") ) { flag |= B2B_FMT_DV; fprintf(stderr, "[warning] tag DV functional, but deprecated. Please switch to `AD` in future.\n"); }
        else if ( !strcasecmp(tags[i],"SP") ) flag |= B2B_FMT_SP;
        else if ( !strcasecmp(tags[i],"DP4") ) { flag |= B2B_FMT_DP4; fprintf(stderr, "[warning] tag DP4 functional, but deprecated. Please switch to `ADF` and `ADR` in future.\n"); }
        else if ( !strcasecmp(tags[i],"DPR") ) { flag |= B2B_FMT_DPR; fprintf(stderr, "[warning] tag DPR functional, but deprecated. Please switch to `AD` in future.\n"); }
        else if ( !strcasecmp(tags[i],"INFO/DPR") ) { flag |= B2B_INFO_DPR; fprintf(stderr, "[warning] tag INFO/DPR functional, but deprecated. Please switch to `INFO/AD` in future.\n"); }
        else if ( !strcasecmp(tags[i],"AD") ) flag |= B2B_FMT_AD;
        else if ( !strcasecmp(tags[i],"ADF") ) flag |= B2B_FMT_ADF;
        else if ( !strcasecmp(tags[i],"ADR") ) flag |= B2B_FMT_ADR;
        else if ( !strcasecmp(tags[i],"INFO/AD") ) flag |= B2B_INFO_AD;
        else if ( !strcasecmp(tags[i],"INFO/ADF") ) flag |= B2B_INFO_ADF;
        else if ( !strcasecmp(tags[i],"INFO/ADR") ) flag |= B2B_INFO_ADR;
        else
        {
            fprintf(stderr,"Could not parse tag \"%s\" in \"%s\"\n", tags[i], str);
            exit(EXIT_FAILURE);
        }
        free(tags[i]);
    }
    if (n_tags) free(tags);
    return flag;
}

static void print_usage(FILE *fp, const mplp_conf_t *mplp)
{
    char *tmp_require = bam_flag2str(mplp->rflag_require);
    char *tmp_filter  = bam_flag2str(mplp->rflag_filter);

    // Display usage information, formatted for the standard 80 columns.
    // (The unusual string formatting here aids the readability of this
    // source code in 80 columns, to the extent that's possible.)

    fprintf(fp,
"\n"
"Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n"
"\n"
"Input options:\n"
"  -6, --illumina1.3+      quality is in the Illumina-1.3+ encoding\n"
"  -A, --count-orphans     do not discard anomalous read pairs\n"
"  -b, --bam-list FILE     list of input BAM filenames, one per line\n"
"  -B, --no-BAQ            disable BAQ (per-Base Alignment Quality)\n"
"  -C, --adjust-MQ INT     adjust mapping quality; recommended:50, disable:0 [0]\n"
"  -d, --max-depth INT     max per-file depth; avoids excessive memory usage [%d]\n", mplp->max_depth);
    fprintf(fp,
"  -E, --redo-BAQ          recalculate BAQ on the fly, ignore existing BQs\n"
"  -f, --fasta-ref FILE    faidx indexed reference sequence file\n"
"  -G, --exclude-RG FILE   exclude read groups listed in FILE\n"
"  -l, --positions FILE    skip unlisted positions (chr pos) or regions (BED)\n"
"  -q, --min-MQ INT        skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq);
    fprintf(fp,
"  -Q, --min-BQ INT        skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ);
    fprintf(fp,
"  -r, --region REG        region in which pileup is generated\n"
"  -R, --ignore-RG         ignore RG tags (one BAM = one sample)\n"
"  --rf, --incl-flags STR|INT  required flags: include reads with any of the mask bits set [%s]\n", tmp_require);
    fprintf(fp,
"  --ff, --excl-flags STR|INT  filter flags: skip reads with any of the mask bits set\n"
"                                            [%s]\n", tmp_filter);
    fprintf(fp,
"  -x, --ignore-overlaps   disable read-pair overlap detection\n"
"  -X, --customized-index  use customized index files\n" // -X flag for index filename
"\n"
"Output options:\n"
"  -o, --output FILE       write output to FILE [standard output]\n"
"  -O, --output-BP         output base positions on reads\n"
"  -s, --output-MQ         output mapping quality\n"
"      --output-QNAME      output read names\n"
"      --output-extra STR  output extra read fields and read tag values\n"
"      --output-sep CHAR   set the separator character for tag lists [,]\n"
"      --output-empty CHAR set the no value character for tag lists [*]\n"
"      --reverse-del       use '#' character for deletions on the reverse strand\n"
"  -a                      output all positions (including zero depth)\n"
"  -a -a (or -aa)          output absolutely all positions, including unused ref. sequences\n"
"\n"
"Generic options:\n");
    sam_global_opt_help(fp, "-.--.--.");

    fprintf(fp, "\n"
"Note that using \"samtools mpileup\" to generate BCF or VCF files is now\n"
"deprecated.  To output these formats, please use \"bcftools mpileup\" instead.\n");

    free(tmp_require);
    free(tmp_filter);
}

static void deprecated(char opt) {
    fprintf(stderr, "[warning] samtools mpileup option `%c` is functional, "
            "but deprecated. Please switch to using bcftools mpileup in future.\n", opt);
}

int bam_mpileup(int argc, char *argv[])
{
    int c;
    const char *file_list = NULL;
    char **fn = NULL;
    int nfiles = 0, use_orphan = 0, has_index_file = 0;
    mplp_conf_t mplp;
    memset(&mplp, 0, sizeof(mplp_conf_t));
    mplp.min_baseQ = 13;
    mplp.capQ_thres = 0;
    mplp.max_depth = MPLP_MAX_DEPTH;
    mplp.max_indel_depth = MPLP_MAX_INDEL_DEPTH;
    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 | MPLP_SMART_OVERLAPS;
    mplp.argc = argc; mplp.argv = argv;
    mplp.rflag_filter = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP;
    mplp.output_fname = NULL;
    mplp.all = 0;
    mplp.rev_del = 0;
    mplp.sep = ',';
    mplp.empty = '*';
    sam_global_args_init(&mplp.ga);

    static const struct option lopts[] =
    {
        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'),
        {"rf", required_argument, NULL, 1},   // require flag
        {"ff", required_argument, NULL, 2},   // filter flag
        {"incl-flags", required_argument, NULL, 1},
        {"excl-flags", required_argument, NULL, 2},
        {"output", required_argument, NULL, 3},
        {"open-prob", required_argument, NULL, 4},
        {"output-QNAME", no_argument, NULL, 5},
        {"output-qname", no_argument, NULL, 5},
        {"illumina1.3+", no_argument, NULL, '6'},
        {"count-orphans", no_argument, NULL, 'A'},
        {"bam-list", required_argument, NULL, 'b'},
        {"no-BAQ", no_argument, NULL, 'B'},
        {"no-baq", no_argument, NULL, 'B'},
        {"adjust-MQ", required_argument, NULL, 'C'},
        {"adjust-mq", required_argument, NULL, 'C'},
        {"max-depth", required_argument, NULL, 'd'},
        {"redo-BAQ", no_argument, NULL, 'E'},
        {"redo-baq", no_argument, NULL, 'E'},
        {"fasta-ref", required_argument, NULL, 'f'},
        {"exclude-RG", required_argument, NULL, 'G'},
        {"exclude-rg", required_argument, NULL, 'G'},
        {"positions", required_argument, NULL, 'l'},
        {"region", required_argument, NULL, 'r'},
        {"ignore-RG", no_argument, NULL, 'R'},
        {"ignore-rg", no_argument, NULL, 'R'},
        {"min-MQ", required_argument, NULL, 'q'},
        {"min-mq", required_argument, NULL, 'q'},
        {"min-BQ", required_argument, NULL, 'Q'},
        {"min-bq", required_argument, NULL, 'Q'},
        {"ignore-overlaps", no_argument, NULL, 'x'},
        {"BCF", no_argument, NULL, 'g'},
        {"bcf", no_argument, NULL, 'g'},
        {"VCF", no_argument, NULL, 'v'},
        {"vcf", no_argument, NULL, 'v'},
        {"output-BP", no_argument, NULL, 'O'},
        {"output-bp", no_argument, NULL, 'O'},
        {"output-MQ", no_argument, NULL, 's'},
        {"output-mq", no_argument, NULL, 's'},
        {"output-tags", required_argument, NULL, 't'},
        {"uncompressed", no_argument, NULL, 'u'},
        {"ext-prob", required_argument, NULL, 'e'},
        {"gap-frac", required_argument, NULL, 'F'},
        {"tandem-qual", required_argument, NULL, 'h'},
        {"skip-indels", no_argument, NULL, 'I'},
        {"max-idepth", required_argument, NULL, 'L'},
        {"min-ireads ", required_argument, NULL, 'm'},
        {"per-sample-mF", no_argument, NULL, 'p'},
        {"per-sample-mf", no_argument, NULL, 'p'},
        {"platforms", required_argument, NULL, 'P'},
        {"customized-index", no_argument, NULL, 'X'},
        {"reverse-del", no_argument, NULL, 6},
        {"output-extra", required_argument, NULL, 7},
        {"output-sep", required_argument, NULL, 8},
        {"output-empty", required_argument, NULL, 9},
        {NULL, 0, NULL, 0}
    };

    while ((c = getopt_long(argc, argv, "Agf:r:l:q:Q:uRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsVvxXt:a",lopts,NULL)) >= 0) {
        switch (c) {
        case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
        case  1 :
            mplp.rflag_require = bam_str2flag(optarg);
            if ( mplp.rflag_require<0 ) { fprintf(stderr,"Could not parse --rf %s\n", optarg); return 1; }
            break;
        case  2 :
            mplp.rflag_filter = bam_str2flag(optarg);
            if ( mplp.rflag_filter<0 ) { fprintf(stderr,"Could not parse --ff %s\n", optarg); return 1; }
            break;
        case  3 : mplp.output_fname = optarg; break;
        case  4 : mplp.openQ = atoi(optarg); break;
        case  5 : mplp.flag |= MPLP_PRINT_QNAME; break;
        case  6 : mplp.rev_del = 1; break;
        case  7 :
            if (build_auxlist(&mplp, optarg) != 0) {
                fprintf(stderr,"Could not build aux list using '%s'\n", optarg);
                return 1;
            }
            break;
        case 8: mplp.sep = optarg[0]; break;
        case 9: mplp.empty = optarg[0]; break;
        case 'f':
            mplp.fai = fai_load(optarg);
            if (mplp.fai == NULL) return 1;
            mplp.fai_fname = optarg;
            break;
        case 'd': mplp.max_depth = atoi(optarg); break;
        case 'r': mplp.reg = strdup(optarg); break;
        case 'l':
                  // In the original version the whole BAM was streamed which is inefficient
                  //  with few BED intervals and big BAMs. Todo: devise a heuristic to determine
                  //  best strategy, that is streaming or jumping.
                  mplp.bed = bed_read(optarg);
                  if (!mplp.bed) { print_error_errno("mpileup", "Could not read file \"%s\"", optarg); return 1; }
                  break;
        case 'P': mplp.pl_list = strdup(optarg); deprecated(c); break;
        case 'p': mplp.flag |= MPLP_PER_SAMPLE; deprecated(c); break;
        case 'g': mplp.flag |= MPLP_BCF; deprecated(c); break;
        case 'v': mplp.flag |= MPLP_BCF | MPLP_VCF; deprecated(c); break;
        case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_BCF; deprecated(c); break;
        case 'B': mplp.flag &= ~MPLP_REALN; break;
        case 'X': has_index_file = 1; break;
        case 'D': mplp.fmt_flag |= B2B_FMT_DP; deprecated(c); break;
        case 'S': mplp.fmt_flag |= B2B_FMT_SP; deprecated(c); break;
        case 'V': mplp.fmt_flag |= B2B_FMT_DV; deprecated(c); break;
        case 'I': mplp.flag |= MPLP_NO_INDEL; deprecated(c); 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_CHAR; break;
        case 'O': mplp.flag |= MPLP_PRINT_QPOS; break;
        case 'C': mplp.capQ_thres = 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': {
                char *end;
                long value = strtol(optarg, &end, 10);
                // Distinguish between -o INT and -o FILE (a bit of a hack!)
                if (*end == '\0') {
                    mplp.openQ = value;
                    fprintf(stderr, "[warning] samtools mpileup option "
                            "'--open-prob INT' is functional, but deprecated. "
                            "Please switch to using bcftools mpileup in future.\n");
                } else {
                    mplp.output_fname = optarg;
                }
            }
            break;
        case 'e': mplp.extQ = atoi(optarg); deprecated(c); break;
        case 'h': mplp.tandemQ = atoi(optarg); deprecated(c); break;
        case 'A': use_orphan = 1; break;
        case 'F': mplp.min_frac = atof(optarg); deprecated(c); break;
        case 'm': mplp.min_support = atoi(optarg); deprecated(c); break;
        case 'L': mplp.max_indel_depth = atoi(optarg); deprecated(c); break;
        case 'G': {
                FILE *fp_rg;
                char buf[1024];
                mplp.rghash = khash_str2int_init();
                if ((fp_rg = fopen(optarg, "r")) == NULL)
                    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...
                    khash_str2int_inc(mplp.rghash, strdup(buf));
                fclose(fp_rg);
            }
            break;
        case 't': mplp.fmt_flag |= parse_format_flag(optarg); deprecated(c); break;
        case 'a': mplp.all++; break;
        default:
            if (parse_sam_global_opt(c, optarg, lopts, &mplp.ga) == 0) break;
            /* else fall-through */
        case '?':
            print_usage(stderr, &mplp);
            return 1;
        }
    }
    if (!mplp.fai && mplp.ga.reference) {
        mplp.fai_fname = mplp.ga.reference;
        mplp.fai = fai_load(mplp.fai_fname);
        if (mplp.fai == NULL) return 1;
    }

    if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ )
    {
        fprintf(stderr,"Error: The -B option cannot be combined with -E\n");
        return 1;
    }
    if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
    if (argc == 1)
    {
        print_usage(stderr, &mplp);
        return 1;
    }
    int ret;
    if (file_list) {
        if (has_index_file) {
            fprintf(stderr,"Error: The -b option cannot be combined with -X\n"); // No customize index loc in file list mode
            return 1;
        }
        if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
        ret = mpileup(&mplp,nfiles,fn,NULL);
        for (c=0; c<nfiles; c++) free(fn[c]);
        free(fn);
    }
    else {
        if (has_index_file) {
            if ((argc - optind)%2 !=0) { // Calculate # of input BAM files
                fprintf(stderr, "Odd number of filenames detected! Each BAM file should have an index file\n");
                return 1;
            }
            nfiles = (argc - optind)/2;
            ret = mpileup(&mplp, nfiles, argv + optind, argv + nfiles + optind);
        } else {
            nfiles = argc - optind;
            ret = mpileup(&mplp, nfiles, argv + optind, NULL);
        }
    }
    if (mplp.rghash) khash_str2int_destroy_free(mplp.rghash);
    free(mplp.reg); free(mplp.pl_list);
    if (mplp.fai) fai_destroy(mplp.fai);
    if (mplp.bed) bed_destroy(mplp.bed);
    if (mplp.auxlist) kl_destroy(auxlist, (klist_t(auxlist) *)mplp.auxlist);
    return ret;
}