bam_tview.c

/*  bam_tview.c -- tview subcommand.

    Copyright (C) 2008-2016, 2019-2020 Genome Research Ltd.
    Portions copyright (C) 2013 Pierre Lindenbaum, Institut du Thorax, INSERM U1087, Université de Nantes.

    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 notices 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 <regex.h>
#include <assert.h>
#include "bam_tview.h"
#include <htslib/faidx.h>
#include <htslib/sam.h>
#include <htslib/bgzf.h>
#include "samtools.h"
#include "sam_opts.h"

// Threshold where spacing of numbers on the scale line changes from 10 to 20
// to stop them running into each other.
#define TEN_DIGITS 1000000000

static void destroy_rg_hash(khash_t(kh_rg)* rg_hash)
{
    khiter_t k;

    if (!rg_hash)
        return;

    for (k = 0; k < kh_end(rg_hash); k++) {
        if (kh_exist(rg_hash, k))
            free((char *) kh_key(rg_hash, k));
    }
    kh_destroy(kh_rg, rg_hash);
}

static
khash_t(kh_rg)* get_rg_sample(sam_hdr_t* header, const char* sample)
{
    int n_rg, i;
    kstring_t id_val = KS_INITIALIZE, sm_val = KS_INITIALIZE;
    khash_t(kh_rg)* rg_hash = kh_init(kh_rg);
    if (!rg_hash) return NULL;

    // There may be more than one @RG with a given SM:, so iterate through them
    n_rg = sam_hdr_count_lines(header, "RG");
    if (n_rg < 0) {
        print_error("tview", "couldn't parse header");
        goto fail;
    }

    for (i = 0; i < n_rg; i++) {
        // Try ID: first
        int r = sam_hdr_find_tag_pos(header, "RG", i, "ID", &id_val);
        if (r < -1) goto memfail;
        if (r == -1) continue;  // Shouldn't happen as ID is compulsory

        if (strcmp(sample, id_val.s) != 0) {
            // No match, try SM:
            r = sam_hdr_find_tag_pos(header, "RG", i, "SM", &sm_val);
            if (r < -1) goto memfail;
            if (r < 0 || strcmp(sample, sm_val.s) != 0)
                continue;
        }

        // Found a match, add ID to rg_hash
        kh_put(kh_rg, rg_hash, id_val.s, &r);
        if (r < 0) goto memfail;
        ks_release(&id_val); // Now owned by hash table
    }

    ks_free(&id_val);
    ks_free(&sm_val);
    return rg_hash;

 memfail:
    perror("tview");
 fail:
    ks_free(&id_val);
    ks_free(&sm_val);
    destroy_rg_hash(rg_hash);
    return NULL;
}

int base_tv_init(tview_t* tv, const char *fn, const char *fn_fa, const char *fn_idx,
                 const char *samples, const htsFormat *fmt)
{
    assert(tv!=NULL);
    assert(fn!=NULL);
    tv->mrow = 24; tv->mcol = 80;
    tv->color_for = TV_COLOR_MAPQ;
    tv->is_dot = 1;

    tv->fp = sam_open_format(fn, "r", fmt);
    if(tv->fp == NULL)
    {
        print_error_errno("tview", "can't open \"%s\"", fn);
        exit(EXIT_FAILURE);
    }
    // TODO bgzf_set_cache_size(tv->fp->fp.bgzf, 8 * 1024 *1024);
    assert(tv->fp);

    tv->header = sam_hdr_read(tv->fp);
    if(tv->header == NULL)
    {
        print_error("tview", "cannot read \"%s\"", fn);
        exit(EXIT_FAILURE);
    }
    // If index filename has not been specfied, look in BAM folder
    if (fn_idx != NULL) {
        tv->idx = sam_index_load2(tv->fp, fn, fn_idx);
    } else {
        tv->idx = sam_index_load(tv->fp, fn);
    }

    if (tv->idx == NULL)
    {
        print_error("tview", "cannot read index for \"%s\"", fn);
        exit(EXIT_FAILURE);
    }
    tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
    if (fn_fa) tv->fai = fai_load(fn_fa);
    tv->bca = bcf_call_init(0.83, 13);
    tv->ins = 1;

    // If the user has asked for specific samples find out create a list of readgroups make up these samples
    if ( samples )
    {
        tv->rg_hash = get_rg_sample(tv->header, samples); // Init the list of rg's
        if (kh_size(tv->rg_hash) == 0) {
            print_error("tview",
                        "The sample or read group \"%s\" not present.",
                        samples);
            exit(EXIT_FAILURE);
        }
    }

    return 0;
}


void base_tv_destroy(tview_t* tv)
{
    bam_lplbuf_destroy(tv->lplbuf);
    bcf_call_destroy(tv->bca);
    hts_idx_destroy(tv->idx);
    if (tv->fai) fai_destroy(tv->fai);
    free(tv->ref);
    sam_hdr_destroy(tv->header);
    destroy_rg_hash(tv->rg_hash);
    sam_close(tv->fp);
}


int tv_pl_func(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data)
{
    tview_t *tv = (tview_t*)data;
    hts_pos_t cp;
    int i, j, c, rb, attr, max_ins = 0, interval;
    uint32_t call = 0;
    kstring_t ks = KS_INITIALIZE;
    if (pos < tv->left_pos || tv->ccol > tv->mcol) return 0; // out of screen
    // print reference
    rb = (tv->ref && pos - tv->left_pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N';
    for (cp = tv->last_pos + 1; cp < pos; ++cp) {
        interval = cp < TEN_DIGITS ? 10 : 20;
        if (cp%interval == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-"PRIhts_pos, cp+1);
        c = tv->ref? tv->ref[cp - tv->left_pos] : 'N';
        tv->my_mvaddch(tv,1, tv->ccol++, c);
    }
    interval = pos < TEN_DIGITS ? 10 : 20;
    if (pos%interval == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-"PRIhts_pos, pos+1);
    { // call consensus
        bcf_callret1_t bcr;
        memset(&bcr, 0, sizeof bcr);
        int qsum[4], a1, a2, tmp;
        double p[3], prior = 30;
        bcf_call_glfgen(n, pl, seq_nt16_table[rb], tv->bca, &bcr);
        for (i = 0; i < 4; ++i) qsum[i] = ((int)bcr.qsum[i])<<2 | i;
        for (i = 1; i < 4; ++i) // insertion sort
            for (j = i; j > 0 && qsum[j] > qsum[j-1]; --j)
                tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
        a1 = qsum[0]&3; a2 = qsum[1]&3;
        p[0] = bcr.p[a1*5+a1]; p[1] = bcr.p[a1*5+a2] + prior; p[2] = bcr.p[a2*5+a2];
        if ("ACGT"[a1] != toupper(rb)) p[0] += prior + 3;
        if ("ACGT"[a2] != toupper(rb)) p[2] += prior + 3;
        if (p[0] < p[1] && p[0] < p[2]) call = (1<<a1)<<16 | (int)((p[1]<p[2]?p[1]:p[2]) - p[0] + .499);
        else if (p[2] < p[1] && p[2] < p[0]) call = (1<<a2)<<16 | (int)((p[0]<p[1]?p[0]:p[1]) - p[2] + .499);
        else call = (1<<a1|1<<a2)<<16 | (int)((p[0]<p[2]?p[0]:p[2]) - p[1] + .499);
    }
    attr = tv->my_underline(tv);
    c = ",ACMGRSVTWYHKDBN"[call>>16&0xf];
    i = (call&0xffff)/10+1;
    if (i > 4) i = 4;
    attr |= tv->my_colorpair(tv,i);
    if (c == toupper(rb)) c = '.';
    tv->my_attron(tv,attr);
    tv->my_mvaddch(tv,2, tv->ccol, c);
    tv->my_attroff(tv,attr);
    if(tv->ins) {
        // calculate maximum insert
        for (i = 0; i < n; ++i) {
            const bam_pileup1_t *p = pl + i;
            int len = bam_plp_insertion(p, &ks, NULL);
            if (len < 0) {
                print_error("tview", "Memory allocation failure.");
                exit(1);
            }
            if (max_ins < len) max_ins = len;
        }
    }
    // core loop
    for (j = 0; j <= max_ins; ++j) {
        for (i = 0; i < n; ++i) {
            const bam_pileup1_t *p = pl + i;
            int row = TV_MIN_ALNROW + p->level - tv->row_shift;
            if (j == 0) {
                if (!p->is_del) {
                    if (tv->base_for == TV_BASE_COLOR_SPACE &&
                            (c = bam_aux_getCSi(p->b, p->qpos))) {
                        // assume that if we found one color, we will be able to get the color error
                        if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos)) c = bam_is_rev(p->b)? ',' : '.';
                    } else {
                        if (tv->show_name) {
                            char *name = bam_get_qname(p->b);
                            c = (p->qpos + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos];
                        } else {
                            c = seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos)];
                            if (tv->is_dot && toupper(c) == toupper(rb)) c = bam_is_rev(p->b)? ',' : '.';
                        }
                    }
                } else c = p->is_refskip? (bam_is_rev(p->b)? '<' : '>') : '*';
            } else { // padding
                int len = bam_plp_insertion(p, &ks, NULL);
                if (len < 0) {
                    print_error("tview", "Memory allocation failure.");
                    exit(1);
                }

                if (j > len) c = '*';
                else { // insertion
                    if (tv->base_for ==  TV_BASE_NUCL) {
                        if (tv->show_name) {
                            char *name = bam_get_qname(p->b);
                            c = (p->qpos + j + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos + j];
                        } else {
                            c = ks.s[j-1];
                            if (j == 0 && tv->is_dot && toupper(c) == toupper(rb)) c = bam_is_rev(p->b)? ',' : '.';
                        }
                    } else {
                        c = bam_aux_getCSi(p->b, p->qpos + j);
                        if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos + j)) c = bam_is_rev(p->b)? ',' : '.';
                    }
                }
            }
            if (row > TV_MIN_ALNROW && row < tv->mrow) {
                int x;
                attr = 0;
                if (((p->b->core.flag&BAM_FPAIRED) && !(p->b->core.flag&BAM_FPROPER_PAIR))
                        || (p->b->core.flag & BAM_FSECONDARY)) attr |= tv->my_underline(tv);
                if (tv->color_for == TV_COLOR_BASEQ) {
                    x = bam_get_qual(p->b)[p->qpos]/10 + 1;
                    if (x > 4) x = 4;
                    attr |= tv->my_colorpair(tv,x);
                } else if (tv->color_for == TV_COLOR_MAPQ) {
                    x = p->b->core.qual/10 + 1;
                    if (x > 4) x = 4;
                    attr |= tv->my_colorpair(tv,x);
                } else if (tv->color_for == TV_COLOR_NUCL) {
                    x = seq_nt16_int[bam_seqi(bam_get_seq(p->b), p->qpos)] + 5;
                    attr |= tv->my_colorpair(tv,x);
                } else if(tv->color_for == TV_COLOR_COL) {
                    x = 0;
                    switch(bam_aux_getCSi(p->b, p->qpos)) {
                        case '0': x = 0; break;
                        case '1': x = 1; break;
                        case '2': x = 2; break;
                        case '3': x = 3; break;
                        case '4': x = 4; break;
                        default: x = seq_nt16_int[bam_seqi(bam_get_seq(p->b), p->qpos)]; break;
                    }
                    x+=5;
                    attr |= tv->my_colorpair(tv,x);
                } else if(tv->color_for == TV_COLOR_COLQ) {
                    x = bam_aux_getCQi(p->b, p->qpos);
                    if(0 == x) x = bam_get_qual(p->b)[p->qpos];
                    x = x/10 + 1;
                    if (x > 4) x = 4;
                    attr |= tv->my_colorpair(tv,x);
                }
                tv->my_attron(tv,attr);
                tv->my_mvaddch(tv,row, tv->ccol, bam_is_rev(p->b)? tolower(c) : toupper(c));
                tv->my_attroff(tv,attr);
            }
        }
        c = j? '*' : rb;
        if (c == '*') {
            attr = tv->my_colorpair(tv,8);
            tv->my_attron(tv,attr);
            tv->my_mvaddch(tv,1, tv->ccol++, c);
            tv->my_attroff(tv,attr);
        } else tv->my_mvaddch(tv,1, tv->ccol++, c);
    }
    tv->last_pos = pos;
    ks_free(&ks);
    return 0;
}




static int tv_push_aln(const bam1_t *b, tview_t *tv)
{
    /* If we are restricted to specific readgroups check RG is in the list */
    if ( tv->rg_hash )
    {
        const uint8_t *rg = bam_aux_get(b, "RG");
        if ( !rg ) return 0; // If we don't have an RG tag exclude read
        khiter_t k = kh_get(kh_rg, tv->rg_hash, (const char*)(rg + 1));
        if ( k == kh_end(tv->rg_hash) ) return 0; // if RG tag is not in list of allowed tags exclude read
    }
    if (tv->no_skip) {
        uint32_t *cigar = bam_get_cigar(b); // this is cheating...
        int i;
        for (i = 0; i <b->core.n_cigar; ++i) {
            if ((cigar[i]&0xf) == BAM_CREF_SKIP)
                cigar[i] = cigar[i]>>4<<4 | BAM_CDEL;
        }
    }
    bam_lplbuf_push(b, tv->lplbuf);
    return 0;
}

int base_draw_aln(tview_t *tv, int tid, hts_pos_t pos)
{
    int ret;
    assert(tv!=NULL);
    // reset
    tv->my_clear(tv);
    tv->curr_tid = tid; tv->left_pos = pos;
    tv->last_pos = tv->left_pos - 1;
    tv->ccol = 0;
    // print ref and consensus
    if (tv->fai) {
        char *str;
        if (tv->ref) free(tv->ref);
        assert(tv->curr_tid>=0);

        const char *ref_name = sam_hdr_tid2name(tv->header, tv->curr_tid);
        str = (char*)calloc(strlen(ref_name) + 30, 1);
        assert(str!=NULL);
        sprintf(str, "%s:%"PRIhts_pos"-%"PRIhts_pos, ref_name, tv->left_pos + 1, tv->left_pos + tv->mcol);
        tv->ref = fai_fetch64(tv->fai, str, &tv->l_ref);
        free(str);
        if ( !tv->ref )
        {
            fprintf(stderr,"Could not read the reference sequence. Is it seekable (plain text or compressed + .gzi indexed with bgzip)?\n");
            exit(1);
        }
    }
    // draw aln
    bam_lplbuf_reset(tv->lplbuf);
    hts_itr_t *iter = sam_itr_queryi(tv->idx, tv->curr_tid, tv->left_pos, tv->left_pos + tv->mcol);
    bam1_t *b = bam_init1();
    while ((ret = sam_itr_next(tv->fp, iter, b)) >= 0) tv_push_aln(b, tv);
    bam_destroy1(b);
    hts_itr_destroy(iter);
    if (ret < -1) {
        print_error("tview", "could not read from input file");
        exit(1);
    }

    bam_lplbuf_push(0, tv->lplbuf);

    while (tv->ccol < tv->mcol) {
        hts_pos_t pos = tv->last_pos + 1;
        int interval = pos < TEN_DIGITS ? 10 : 20;
        if (pos%interval == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-"PRIhts_pos, pos+1);
        tv->my_mvaddch(tv,1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
        ++tv->last_pos;
    }
    return 0;
}




static void error(const char *format, ...)
{
    if ( !format )
    {
        fprintf(stderr,
"Usage: samtools tview [options] <aln.bam> [ref.fasta]\n"
"Options:\n"
"   -d display      output as (H)tml or (C)urses or (T)ext \n"
"   -X              include customized index file\n"
"   -p chr:pos      go directly to this position\n"
"   -s STR          display only reads from this sample or group\n"
"   -w INT          display width (with -d T only)\n");
        sam_global_opt_help(stderr, "-.--.--.");
    }
    else
    {
        va_list ap;
        va_start(ap, format);
        vfprintf(stderr, format, ap);
        va_end(ap);
    }
    exit(-1);
}

enum dipsay_mode {display_ncurses,display_html,display_text};
extern tview_t* curses_tv_init(const char *fn, const char *fn_fa,
                               const char *samples, const htsFormat *fmt);
extern tview_t* html_tv_init(const char *fn, const char *fn_fa, const char *fn_idx,
                             const char *samples, const htsFormat *fmt);
extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *fn_idx,
                             const char *samples, const htsFormat *fmt);

int bam_tview_main(int argc, char *argv[])
{
    int view_mode=display_ncurses, display_width = 0;
    tview_t* tv=NULL;
    char *samples=NULL, *position=NULL, *ref, *fn_idx=NULL;
    int c, has_index_file = 0, ref_index = 0;

    sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
    static const struct option lopts[] = {
        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '-'),
        { NULL, 0, NULL, 0 }
    };

    char *tmp;
    while ((c = getopt_long(argc, argv, "s:p:d:Xw:", lopts, NULL)) >= 0) {
        switch (c) {
            case 'w':
                display_width = strtol(optarg,&tmp,10);
                if ( tmp==optarg || *tmp || display_width<1 ) error("Could not parse: -w %s\n",optarg);
                break;
            case 's': samples=optarg; break;
            case 'p': position=optarg; break;
            case 'X': has_index_file=1; break; // -X flag for index filename
            case 'd':
            {
                switch(optarg[0])
                {
                    case 'H': case 'h': view_mode=display_html;break;
                    case 'T': case 't': view_mode=display_text;break;
                    case 'C': case 'c': view_mode=display_ncurses;break;
                    default: view_mode=display_ncurses;break;
                }
                break;
            }
            default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
                      /* else fall-through */
            case '?': error(NULL);
        }
    }
    if (argc==optind) error(NULL);
    if (display_width && view_mode == display_ncurses)
        error("The -w option is currently supported only with -d T and -d H\n");

    ref = NULL;
    ref_index = optind;
    if (!has_index_file) {
        ref = (optind+1>=argc)? ga.reference : argv[optind+1];
    }
    else {
        ref = (optind+2>=argc)? ga.reference : argv[optind+2];
        if (optind+1 >= argc) {
            fprintf(stderr, "Incorrect number of arguments provided! Aborting...\n");
            return 1;
        }
        fn_idx = argv[optind+1];
        ref_index = optind+1;
    }

    switch(view_mode)
    {
        case display_ncurses:
            tv = curses_tv_init(argv[ref_index], ref, samples, &ga.in);
            break;

        case display_text:
            tv = text_tv_init(argv[ref_index], ref, fn_idx, samples, &ga.in);
            if ( display_width ) tv->mcol = display_width;
            break;

        case display_html:
            tv = html_tv_init(argv[ref_index], ref, fn_idx, samples, &ga.in);
            if ( display_width ) tv->mcol = display_width;
            break;
    }
    if (tv==NULL)
    {
        error("cannot create view");
        return EXIT_FAILURE;
    }

    if ( position )
    {
        int tid;
        hts_pos_t beg, end;
        if (!sam_parse_region(tv->header, position, &tid, &beg, &end, 0)) {
            tv->my_destroy(tv);
            fprintf(stderr, "Unknown reference or malformed region\n");
            exit(EXIT_FAILURE);
        }
        tv->curr_tid = tid;
        tv->left_pos = beg;
    }
    else if ( tv->fai )
    {
        // find the first sequence present in both BAM and the reference file
        int i;
        for (i=0; i < sam_hdr_nref(tv->header); i++)
        {
            if ( faidx_has_seq(tv->fai, sam_hdr_tid2name(tv->header, i)) ) break;
        }
        if ( i==sam_hdr_nref(tv->header) )
        {
            tv->my_destroy(tv);
            fprintf(stderr,"None of the BAM sequence names present in the fasta file\n");
            exit(EXIT_FAILURE);
        }
        tv->curr_tid = i;
    }
    tv->my_drawaln(tv, tv->curr_tid, tv->left_pos);
    tv->my_loop(tv);
    tv->my_destroy(tv);

    return EXIT_SUCCESS;
}