rust-htslib 0.22.0

/*  test/test_view.c -- simple view tool, purely for use in a test harness.

    Copyright (C) 2012 Broad Institute.
    Copyright (C) 2013-2014 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 <stdio.h>
#include <unistd.h>
#include <stdlib.h>
#include <string.h>
#include <getopt.h>
#include <stdint.h>

#include "cram/cram.h"

#include "htslib/sam.h"

enum test_op {
    READ_COMPRESSED    = 1,
    WRITE_COMPRESSED   = 2,
    READ_CRAM          = 4,
    WRITE_CRAM         = 8,
    WRITE_UNCOMPRESSED = 16,
};

int main(int argc, char *argv[])
{
    samFile *in;
    char *fn_ref = 0;
    int flag = 0, c, clevel = -1, ignore_sam_err = 0;
    char moder[8];
    bam_hdr_t *h;
    bam1_t *b;
    htsFile *out;
    char modew[800];
    int r = 0, exit_code = 0;
    hts_opt *in_opts = NULL, *out_opts = NULL;
    int nreads = 0;
    int extra_hdr_nuls = 0;
    int benchmark = 0;
    int nthreads = 0; // shared pool
    int multi_reg = 0;

    while ((c = getopt(argc, argv, "DSIt:i:bCul:o:N:BZ:@:M")) >= 0) {
        switch (c) {
        case 'D': flag |= READ_CRAM; break;
        case 'S': flag |= READ_COMPRESSED; break;
        case 'I': ignore_sam_err = 1; break;
        case 't': fn_ref = optarg; break;
        case 'i': if (hts_opt_add(&in_opts, optarg)) return 1; break;
        case 'b': flag |= WRITE_COMPRESSED; break;
        case 'C': flag |= WRITE_CRAM; break;
        case 'u': flag |= WRITE_UNCOMPRESSED; break; // eg u-BAM not SAM
        case 'l': clevel = atoi(optarg); flag |= WRITE_COMPRESSED; break;
        case 'o': if (hts_opt_add(&out_opts, optarg)) return 1; break;
        case 'N': nreads = atoi(optarg); break;
        case 'B': benchmark = 1; break;
        case 'Z': extra_hdr_nuls = atoi(optarg); break;
        case 'M': multi_reg = 1; break;
        case '@': nthreads = atoi(optarg); break;
        }
    }
    if (argc == optind) {
        fprintf(stderr, "Usage: test_view [-DSI] [-t fn_ref] [-i option=value] [-bC] [-l level] [-o option=value] [-N num_reads] [-B] [-Z hdr_nuls] [-@ num_threads] <in.bam>|<in.sam>|<in.cram> [region]\n");
        fprintf(stderr, "\n");
        fprintf(stderr, "-D: read CRAM format (mode 'c')\n");
        fprintf(stderr, "-S: read compressed BCF, BAM, FAI (mode 'b')\n");
        fprintf(stderr, "-I: ignore SAM parsing errors\n");
        fprintf(stderr, "-t: fn_ref: load CRAM references from the specificed fasta file instead of @SQ headers when writing a CRAM file\n");
        fprintf(stderr, "-i: option=value: set an option for CRAM input\n");
        fprintf(stderr, "\n");
        fprintf(stderr, "-b: write compressed BCF, BAM, FAI (mode 'b')\n");
        fprintf(stderr, "-C: write CRAM format (mode 'c')\n");
        fprintf(stderr, "-l 0-9: set zlib compression level\n");
        fprintf(stderr, "-o option=value: set an option for CRAM output\n");
        fprintf(stderr, "-N: num_reads: limit the output to the first num_reads reads\n");
        fprintf(stderr, "\n");
        fprintf(stderr, "-B: enable benchmarking\n");
        fprintf(stderr, "-M: use hts_itr_multi iterator\n");
        fprintf(stderr, "-Z hdr_nuls: append specified number of null bytes to the SAM header\n");
        fprintf(stderr, "-@ num_threads: use thread pool with specified number of threads\n\n");
        fprintf(stderr, "The region list entries should be specified as 'reg:beg-end', with intervals of a region being disjunct and sorted by the starting coordinate.\n");
        return 1;
    }
    strcpy(moder, "r");
    if (flag & READ_CRAM) strcat(moder, "c");
    else if ((flag & READ_COMPRESSED) == 0) strcat(moder, "b");

    in = sam_open(argv[optind], moder);
    if (in == NULL) {
        fprintf(stderr, "Error opening \"%s\"\n", argv[optind]);
        return EXIT_FAILURE;
    }
    h = sam_hdr_read(in);
    if (h == NULL) {
        fprintf(stderr, "Couldn't read header for \"%s\"\n", argv[optind]);
        return EXIT_FAILURE;
    }
    h->ignore_sam_err = ignore_sam_err;
    if (extra_hdr_nuls) {
        char *new_text = realloc(h->text, h->l_text + extra_hdr_nuls);
        if (new_text == NULL) {
            fprintf(stderr, "Error reallocing header text\n");
            return EXIT_FAILURE;
        }
        h->text = new_text;
        memset(&h->text[h->l_text], 0, extra_hdr_nuls);
        h->l_text += extra_hdr_nuls;
    }

    b = bam_init1();

    strcpy(modew, "w");
    if (clevel >= 0 && clevel <= 9) sprintf(modew + 1, "%d", clevel);
    if (flag & WRITE_CRAM) strcat(modew, "c");
    else if (flag & WRITE_COMPRESSED) strcat(modew, "b");
    else if (flag & WRITE_UNCOMPRESSED) strcat(modew, "bu");
    out = hts_open("-", modew);
    if (out == NULL) {
        fprintf(stderr, "Error opening standard output\n");
        return EXIT_FAILURE;
    }

    /* CRAM output */
    if (flag & WRITE_CRAM) {
        int ret;

        // Parse input header and use for CRAM output
        out->fp.cram->header = sam_hdr_parse_(h->text, h->l_text);

        // Create CRAM references arrays
        if (fn_ref)
            ret = cram_set_option(out->fp.cram, CRAM_OPT_REFERENCE, fn_ref);
        else
            // Attempt to fill out a cram->refs[] array from @SQ headers
            ret = cram_set_option(out->fp.cram, CRAM_OPT_REFERENCE, NULL);

        if (ret != 0)
            return EXIT_FAILURE;
    }

    // Process any options; currently cram only.
    if (hts_opt_apply(in, in_opts))
        return EXIT_FAILURE;
    hts_opt_free(in_opts);

    if (hts_opt_apply(out, out_opts))
        return EXIT_FAILURE;
    hts_opt_free(out_opts);

    // Create and share the thread pool
    htsThreadPool p = {NULL, 0};
    if (nthreads > 0) {
        p.pool = hts_tpool_init(nthreads);
        if (!p.pool) {
            fprintf(stderr, "Error creating thread pool\n");
            exit_code = 1;
        } else {
            hts_set_opt(in,  HTS_OPT_THREAD_POOL, &p);
            hts_set_opt(out, HTS_OPT_THREAD_POOL, &p);
        }
    }

    if (!benchmark && sam_hdr_write(out, h) < 0) {
        fprintf(stderr, "Error writing output header.\n");
        exit_code = 1;
    }
    if (optind + 1 < argc && !(flag & READ_COMPRESSED)) { // BAM input and has a region
        int i;
        hts_idx_t *idx;
        if ((idx = sam_index_load(in, argv[optind])) == 0) {
            fprintf(stderr, "[E::%s] fail to load the BAM index\n", __func__);
            return 1;
        }
        if (multi_reg) {
            int reg_count = 0;
            hts_reglist_t *reg_list = calloc(argc-(optind+1), sizeof(*reg_list));
            if (!reg_list)
                return 1;

            // We need a public function somewhere to turn an array of region strings
            // into a region list, but for testing this will suffice for now.
            // Consider moving a derivation of this into htslib proper sometime.
            for (i = optind + 1; i < argc; ++i) {
                int j;
                uint32_t beg, end;
                char *cp = strrchr(argv[i], ':');
                if (cp) *cp = 0;

                for (j = 0; j < reg_count; j++)
                    if (strcmp(reg_list[j].reg, argv[i]) == 0)
                        break;
                if (j == reg_count) {
                    reg_list[reg_count++].reg = argv[i];
                    if (strcmp(".", argv[i]) == 0) {
                        reg_list[j].tid = HTS_IDX_START;

                    } else if (strcmp("*", argv[i]) == 0) {
                        reg_list[j].tid = HTS_IDX_NOCOOR;

                    } else {
                        int k; // need the header API here!
                        for (k = 0; k < h->n_targets; k++)
                            if (strcmp(h->target_name[k], argv[i]) == 0)
                                break;
                        if (k == h->n_targets)
                            return 1;
                        reg_list[j].tid = k;
                        reg_list[j].min_beg = h->target_len[k];
                        reg_list[j].max_end = 0;
                    }
                }

                hts_reglist_t *r = &reg_list[j];
                r->intervals = realloc(r->intervals, ++r->count * sizeof(*r->intervals));
                if (!r->intervals)
                    return 1;
                beg = 1;
                end = r->tid >= 0 ? h->target_len[r->tid] : 0;
                if (cp) {
                    *cp = 0;
                    // hts_parse_reg() is better, but awkward here
                    sscanf(cp+1, "%d-%d", &beg, &end);
                }
                r->intervals[r->count-1].beg = beg-1; // BED syntax
                r->intervals[r->count-1].end = end;

                if (r->min_beg > beg)
                    r->min_beg = beg;
                if (r->max_end < end)
                    r->max_end = end;
            }

            hts_itr_multi_t *iter = sam_itr_regions(idx, h, reg_list, reg_count);
            if (!iter)
                return 1;
            while ((r = sam_itr_multi_next(in, iter, b)) >= 0) {
                if (!benchmark && sam_write1(out, h, b) < 0) {
                    fprintf(stderr, "Error writing output.\n");
                    exit_code = 1;
                    break;
                }
                if (nreads && --nreads == 0)
                    break;
            }
            hts_itr_multi_destroy(iter);
        } else {
            for (i = optind + 1; i < argc; ++i) {
                hts_itr_t *iter;
                if ((iter = sam_itr_querys(idx, h, argv[i])) == 0) {
                    fprintf(stderr, "[E::%s] fail to parse region '%s'\n", __func__, argv[i]);
                    continue;
                }
                while ((r = sam_itr_next(in, iter, b)) >= 0) {
                    if (!benchmark && sam_write1(out, h, b) < 0) {
                        fprintf(stderr, "Error writing output.\n");
                        exit_code = 1;
                        break;
                    }
                    if (nreads && --nreads == 0)
                        break;
                }
                hts_itr_destroy(iter);
            }
        }
        hts_idx_destroy(idx);
    } else while ((r = sam_read1(in, h, b)) >= 0) {
        if (!benchmark && sam_write1(out, h, b) < 0) {
            fprintf(stderr, "Error writing output.\n");
            exit_code = 1;
            break;
        }
        if (nreads && --nreads == 0)
            break;
    }

    if (r < -1) {
        fprintf(stderr, "Error parsing input.\n");
        exit_code = 1;
    }

    r = sam_close(out);
    if (r < 0) {
        fprintf(stderr, "Error closing output.\n");
        exit_code = 1;
    }

    bam_destroy1(b);
    bam_hdr_destroy(h);

    r = sam_close(in);
    if (r < 0) {
        fprintf(stderr, "Error closing input.\n");
        exit_code = 1;
    }

    if (p.pool)
        hts_tpool_destroy(p.pool);

    return exit_code;
}