cut_target.c

/*  cut_target.c -- targetcut subcommand.

    Copyright (C) 2011 Broad Institute.
    Copyright (C) 2012-2013, 2015, 2016, 2019 Genome Research Ltd.

    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 <unistd.h>
#include <stdlib.h>
#include <string.h>
#include "htslib/hts.h"
#include "htslib/sam.h"
#include "htslib/faidx.h"
#include "samtools.h"
#include "sam_opts.h"

#define ERR_DEP 0.83

typedef struct {
    int e[2][3], p[2][2];
} score_param_t;

/* Note that although the two matrics have 10 parameters in total, only 4
 * (probably 3) are free.  Changing the scoring matrices in a sort of symmetric
 * way will not change the result. */
static score_param_t g_param = { {{0,0,0},{-4,1,6}}, {{0,-14000}, {0,0}} };

typedef struct {
    int min_baseQ, tid, max_bases;
    uint16_t *bases;
    samFile *fp;
    sam_hdr_t *h;
    char *ref;
    hts_pos_t len;
    faidx_t *fai;
    errmod_t *em;
} ct_t;

static uint16_t gencns(ct_t *g, int n, const bam_pileup1_t *plp)
{
    int i, j, ret, tmp, k, sum[4], qual;
    float q[16];
    if (n > g->max_bases) { // enlarge g->bases
        g->max_bases = n;
        kroundup32(g->max_bases);
        g->bases = realloc(g->bases, (size_t) g->max_bases * 2);
    }
    for (i = k = 0; i < n; ++i) {
        const bam_pileup1_t *p = plp + i;
        uint8_t *seq;
        int q, baseQ, b;
        if (p->is_refskip || p->is_del) continue;
        baseQ = bam_get_qual(p->b)[p->qpos];
        if (baseQ < g->min_baseQ) continue;
        seq = bam_get_seq(p->b);
        b = seq_nt16_int[bam_seqi(seq, p->qpos)];
        if (b > 3) continue;
        q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
        if (q < 4) q = 4;
        if (q > 63) q = 63;
        g->bases[k++] = q<<5 | bam_is_rev(p->b)<<4 | b;
    }
    if (k == 0) return 0;
    errmod_cal(g->em, k, 4, g->bases, q);
    for (i = 0; i < 4; ++i) sum[i] = (int)(q[i<<2|i] + .499) << 2 | i;
    for (i = 1; i < 4; ++i) // insertion sort
        for (j = i; j > 0 && sum[j] < sum[j-1]; --j)
            tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp;
    qual = (sum[1]>>2) - (sum[0]>>2);
    k = k < 256? k : 255;
    ret = (qual < 63? qual : 63) << 2 | (sum[0]&3);
    return ret<<8|k;
}

static void process_cns(sam_hdr_t *h, int tid, hts_pos_t l, uint16_t *cns)
{
    int64_t i, s;
    int f[2][2], *prev, *curr, *swap_tmp;
    uint8_t *b; // backtrack array
    b = calloc(l, 1);
    f[0][0] = f[0][1] = 0;
    prev = f[0]; curr = f[1];
    // fill the backtrack matrix
    for (i = 0; i < l; ++i) {
        int c = (cns[i] == 0)? 0 : (cns[i]>>8 == 0)? 1 : 2;
        int tmp0, tmp1;
        // compute f[0]
        tmp0 = prev[0] + g_param.e[0][c] + g_param.p[0][0]; // (s[i+1],s[i])=(0,0)
        tmp1 = prev[1] + g_param.e[0][c] + g_param.p[1][0]; // (0,1)
        if (tmp0 > tmp1) curr[0] = tmp0, b[i] = 0;
        else curr[0] = tmp1, b[i] = 1;
        // compute f[1]
        tmp0 = prev[0] + g_param.e[1][c] + g_param.p[0][1]; // (s[i+1],s[i])=(1,0)
        tmp1 = prev[1] + g_param.e[1][c] + g_param.p[1][1]; // (1,1)
        if (tmp0 > tmp1) curr[1] = tmp0, b[i] |= 0<<1;
        else curr[1] = tmp1, b[i] |= 1<<1;
        // swap
        swap_tmp = prev; prev = curr; curr = swap_tmp;
    }
    // backtrack
    s = prev[0] > prev[1]? 0 : 1;
    for (i = l - 1; i > 0; --i) {
        b[i] |= s<<2;
        s = b[i]>>s&1;
    }
    // print
    for (i = 0, s = -1; i < INT64_MAX && i <= l; ++i) {
        if (i == l || ((b[i]>>2&3) == 0 && s >= 0)) {
            if (s >= 0) {
                int64_t j;
                printf("%s:%"PRId64"-%"PRId64"\t0\t%s\t%"PRId64"\t60\t%"PRId64"M\t*\t0\t0\t", sam_hdr_tid2name(h, tid), s+1, i, sam_hdr_tid2name(h, tid), s+1, i-s);
                for (j = s; j < i; ++j) {
                    int c = cns[j]>>8;
                    if (c == 0) putchar('N');
                    else putchar("ACGT"[c&3]);
                }
                putchar('\t');
                for (j = s; j < i; ++j)
                    putchar(33 + (cns[j]>>8>>2));
                putchar('\n');
            }
            //if (s >= 0) printf("%s\t%d\t%d\t%d\n", h->target_name[tid], s, i, i - s);
            s = -1;
        } else if ((b[i]>>2&3) && s < 0) s = i;
    }
    free(b);
}

static int read_aln(void *data, bam1_t *b)
{
    ct_t *g = (ct_t*)data;
    int ret;
    while (1)
    {
        ret = sam_read1(g->fp, g->h, b);
        if ( ret<0 ) break;
        if ( b->core.flag & (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) ) continue;
        if ( g->fai && b->core.tid >= 0 ) {
            if (b->core.tid != g->tid) { // then load the sequence
                free(g->ref);
                g->ref = fai_fetch64(g->fai, sam_hdr_tid2name(g->h, b->core.tid), &g->len);
                g->tid = b->core.tid;
            }
            sam_prob_realn(b, g->ref, g->len, 1<<1|1);
        }
        break;
    }
    return ret;
}

int main_cut_target(int argc, char *argv[])
{
    int c, tid, pos, n, lasttid = -1, usage = 0, status = EXIT_SUCCESS;
    hts_pos_t l, max_l;
    const bam_pileup1_t *p;
    bam_plp_t plp;
    uint16_t *cns;
    ct_t g;

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

    memset(&g, 0, sizeof(ct_t));
    g.min_baseQ = 13; g.tid = -1;
    while ((c = getopt_long(argc, argv, "f:Q:i:o:0:1:2:", lopts, NULL)) >= 0) {
        switch (c) {
            case 'Q': g.min_baseQ = atoi(optarg); break; // quality cutoff
            case 'i': g_param.p[0][1] = -atoi(optarg); break; // 0->1 transition (in) PENALTY
            case '0': g_param.e[1][0] = atoi(optarg); break; // emission SCORE
            case '1': g_param.e[1][1] = atoi(optarg); break;
            case '2': g_param.e[1][2] = atoi(optarg); break;
            default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
                      /* else fall-through */
            case '?': usage=1; break;
        }
    }
    if (ga.reference) {
        g.fai = fai_load(ga.reference);
        if (g.fai == 0) fprintf(stderr, "[%s] fail to load the fasta index.\n", __func__);
    }
    if (usage || argc == optind) {
        fprintf(stderr, "Usage: samtools targetcut [-Q minQ] [-i inPen] [-0 em0] [-1 em1] [-2 em2] <in.bam>\n");
        sam_global_opt_help(stderr, "-.--f--.");
        return 1;
    }
    l = max_l = 0; cns = 0;
    g.fp = sam_open_format(argv[optind], "r", &ga.in);
    if (g.fp == NULL) {
        print_error_errno("targetcut", "can't open \"%s\"", argv[optind]);
        return 1;
    }

    g.h = sam_hdr_read(g.fp);
    if (g.h == NULL) {
        print_error("targetcut", "couldn't read header for \"%s\"", argv[optind]);
        sam_close(g.fp);
        return 1;
    }
    g.em = errmod_init(1. - ERR_DEP);
    plp = bam_plp_init(read_aln, &g);
    while ((p = bam_plp_auto(plp, &tid, &pos, &n)) != 0) {
        if (tid < 0) break;
        if (tid != lasttid) { // change of chromosome
            if (cns) process_cns(g.h, lasttid, l, cns);
            if (max_l < sam_hdr_tid2len(g.h, tid)) {
                max_l = sam_hdr_tid2len(g.h, tid);
                kroundup32(max_l);
                cns = realloc(cns, max_l * 2);
            }
            l = sam_hdr_tid2len(g.h, tid);
            memset(cns, 0, max_l * 2);
            lasttid = tid;
        }
        cns[pos] = gencns(&g, n, p);
    }
    process_cns(g.h, lasttid, l, cns);

    if (n < 0) {
        print_error("targetcut", "error reading from \"%s\"", argv[optind]);
        status = EXIT_FAILURE;
    }

    free(cns);
    sam_hdr_destroy(g.h);
    bam_plp_destroy(plp);
    sam_close(g.fp);
    if (g.fai) {
        fai_destroy(g.fai); free(g.ref);
    }
    errmod_destroy(g.em);
    free(g.bases);
    sam_global_args_free(&ga);
    return status;
}