bam_index.c

/*  bam_index.c -- index and idxstats subcommands.

    Copyright (C) 2008-2011, 2013-2016, 2018, 2019, 2023-2024  Genome Research Ltd.
    Portions copyright (C) 2010 Broad Institute.
    Portions copyright (C) 2013 Peter Cock, The James Hutton 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 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 <htslib/hts.h>
#include <htslib/sam.h>
#include <htslib/hfile.h>
#include <htslib/khash.h>
#include <stdlib.h>
#include <stdio.h>
#include <inttypes.h>
#include <unistd.h>
#include <getopt.h>

#include "samtools.h"
#include "sam_opts.h"

#define BAM_LIDX_SHIFT    14

static void index_usage(FILE *fp)
{
    fprintf(fp,
"Usage: samtools index -M [-bc] [-m INT] <in1.bam> <in2.bam>...\n"
"   or: samtools index [-bc] [-m INT] <in.bam> [out.index]\n"
"Options:\n"
"  -b, --bai            Generate BAI-format index for BAM files [default]\n"
"  -c, --csi            Generate CSI-format index for BAM files\n"
"  -m, --min-shift INT  Set minimum interval size for CSI indices to 2^INT [%d]\n"
"  -M                   Interpret all filename arguments as files to be indexed\n"
"  -o, --output FILE    Write index to FILE [alternative to <out.index> in args]\n"
"  -@, --threads INT    Sets the number of threads [none]\n", BAM_LIDX_SHIFT);
}

// Returns 1 if the file does not exist or can be positively
// identified as an index file.
static int nonexistent_or_index(const char *fn)
{
    int ret1, ret2;
    htsFormat fmt;
    hFILE *fp = hopen(fn, "r");
    if (fp == NULL) return 1;

    ret1 = hts_detect_format2(fp, fn, &fmt);
    ret2 = hclose(fp);
    if (ret1 < 0 || ret2 < 0) return 0;

    return fmt.category == index_file;
}

int bam_index(int argc, char *argv[])
{
    int csi = 0;
    int min_shift = BAM_LIDX_SHIFT;
    int multiple = 0;
    int n_threads = 0;
    int n_files, c, i, ret;
    const char *fn_idx = NULL;

    static const struct option lopts[] = {
        SAM_OPT_GLOBAL_OPTIONS('-', '-', '-', '-', '-', '@'),
        {"output",    required_argument, NULL, 'o'},
        {"bai",       no_argument,       NULL, 'b'},
        {"csi",       no_argument,       NULL, 'c'},
        {"min-shift", required_argument, NULL, 'm'},
        { NULL, 0, NULL, 0 }
    };

    while ((c = getopt_long(argc, argv, "bcm:Mo:@:", lopts, NULL)) >= 0)
        switch (c) {
        case 'b': csi = 0; break;
        case 'c': csi = 1; break;
        case 'm': csi = 1; min_shift = atoi(optarg); break;
        case 'M': multiple = 1; break;
        case 'o': fn_idx = optarg; break;
        case '@': n_threads = atoi(optarg); break;
        default:
            index_usage(stderr);
            return 1;
        }

    n_files = argc - optind;

    if (n_files == 0) {
        index_usage(stdout);
        return 0;
    }

    // Handle legacy synopsis
    if (n_files == 2 && !fn_idx && nonexistent_or_index(argv[optind+1])) {
        n_files = 1;
        fn_idx = argv[optind+1];
    }

    if (n_files > 1 && !multiple) {
        print_error("index", "use -M to enable indexing more than one alignment file");
        return EXIT_FAILURE;
    }

    if (fn_idx && n_files > 1) {
        // TODO In future we may allow %* placeholders or similar
        print_error("index", "can't use -o with multiple input alignment files");
        return EXIT_FAILURE;
    }

    for (i = optind; i < optind + n_files; i++) {
        ret = sam_index_build3(argv[i], fn_idx, csi? min_shift : 0, n_threads);
        if (ret < 0) {
            if (ret == -2)
                print_error_errno("index", "failed to open \"%s\"", argv[i]);
            else if (ret == -3)
                print_error("index", "\"%s\" is in a format that cannot be usefully indexed", argv[i]);
            else if (ret == -4 && fn_idx)
                print_error("index", "failed to create or write index \"%s\"", fn_idx);
            else if (ret == -4)
                print_error("index", "failed to create or write index");
            else
                print_error_errno("index", "failed to create index for \"%s\"", argv[i]);
            return EXIT_FAILURE;
        }
    }

    return EXIT_SUCCESS;
}

/*
 * Cram indices do not contain mapped/unmapped record counts, so we have to
 * decode each record and count.  However we can speed this up as much as
 * possible by using the required fields parameter.
 *
 * This prints the stats to stdout in the same manner than the BAM function
 * does.
 *
 * Returns 0 on success,
 *        -1 on failure.
 */
int slow_idxstats(samFile *fp, sam_hdr_t *header) {
    int ret, last_tid = -2;
    bam1_t *b = bam_init1();

    if (hts_set_opt(fp, CRAM_OPT_REQUIRED_FIELDS, SAM_RNAME | SAM_FLAG))
        return -1;

    uint64_t (*count0)[2] = calloc(sam_hdr_nref(header)+1, sizeof(*count0));
    uint64_t (*counts)[2] = count0+1;
    if (!count0)
        return -1;

    while ((ret = sam_read1(fp, header, b)) >= 0) {
        if (b->core.tid >= sam_hdr_nref(header) || b->core.tid < -1) {
            free(count0);
            return -1;
        }

        if (b->core.tid != last_tid) {
            if (last_tid >= -1) {
                if (counts[b->core.tid][0] + counts[b->core.tid][1]) {
                    print_error("idxstats", "file is not position sorted");
                    free(count0);
                    return -1;
                }
            }
            last_tid = b->core.tid;
        }

        counts[b->core.tid][(b->core.flag & BAM_FUNMAP) ? 1 : 0]++;
    }

    if (ret == -1) {
        int i;
        for (i = 0; i < sam_hdr_nref(header); i++) {
            printf("%s\t%"PRId64"\t%"PRIu64"\t%"PRIu64"\n",
                   sam_hdr_tid2name(header, i),
                   (int64_t) sam_hdr_tid2len(header, i),
                   counts[i][0], counts[i][1]);
        }
        printf("*\t0\t%"PRIu64"\t%"PRIu64"\n", counts[-1][0], counts[-1][1]);
    }

    free(count0);

    bam_destroy1(b);

    return (ret == -1) ? 0 : -1;
}

static void usage_exit(FILE *fp, int exit_status)
{
    fprintf(fp, "Usage: samtools idxstats [options] <in.bam>\n"
                "  -X           Include customized index file\n");
    sam_global_opt_help(fp, "-.---@-.");
    exit(exit_status);
}

int bam_idxstats(int argc, char *argv[])
{
    hts_idx_t* idx;
    sam_hdr_t* header;
    samFile* fp;
    int c, has_index_file = 0, file_names = 1;
    char *index_name = NULL;

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

    while ((c = getopt_long(argc, argv, "@:X", lopts, NULL)) >= 0) {
        switch (c) {
            case 'X': has_index_file=1; break;
            default:  if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
                /* else fall-through */
            case '?':
                usage_exit(stderr, EXIT_FAILURE);
        }
    }

    if (has_index_file) {
        file_names = 2;
        index_name = argv[optind + 1];
    }

    if (argc != optind + file_names) {
        if (argc == optind) usage_exit(stdout, EXIT_SUCCESS);
        else usage_exit(stderr, EXIT_FAILURE);
    }

    fp = sam_open_format(argv[optind], "r", &ga.in);
    if (fp == NULL) {
        print_error_errno("idxstats", "failed to open \"%s\"", argv[optind]);
        return 1;
    }
    header = sam_hdr_read(fp);
    if (header == NULL) {
        print_error("idxstats", "failed to read header for \"%s\"", argv[optind]);
        return 1;
    }

    if (hts_get_format(fp)->format != bam) {
    slow_method:
        if (ga.nthreads)
            hts_set_threads(fp, ga.nthreads);

        if (slow_idxstats(fp, header) < 0) {
            print_error("idxstats", "failed to process \"%s\"", argv[optind]);
            return 1;
        }
    } else {
        idx = sam_index_load2(fp, argv[optind], index_name);
        if (idx == NULL) {
            print_error("idxstats", "fail to load index for \"%s\", "
                        "reverting to slow method", argv[optind]);
            goto slow_method;
        }

        int i;
        for (i = 0; i < sam_hdr_nref(header); ++i) {
            // Print out contig name and length
            printf("%s\t%"PRId64, sam_hdr_tid2name(header, i), (int64_t) sam_hdr_tid2len(header, i));
            // Now fetch info about it from the meta bin
            uint64_t u, v;
            hts_idx_get_stat(idx, i, &u, &v);
            printf("\t%" PRIu64 "\t%" PRIu64 "\n", u, v);
        }
        // Dump information about unmapped reads
        printf("*\t0\t0\t%" PRIu64 "\n", hts_idx_get_n_no_coor(idx));
        hts_idx_destroy(idx);
    }

    sam_hdr_destroy(header);
    sam_close(fp);
    return 0;
}