sam_opts.c

/*  sam_opts.c -- utilities to aid parsing common command line options.

    Copyright (C) 2015, 2019, 2025 Genome Research Ltd.

    Author: James Bonfield <jkb@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 <stdlib.h>
#include <string.h>
#include <limits.h>
#include <stdbool.h>
#include "sam_opts.h"
#include "samtools.h"

/*
 * Parse an integer from a value passed on the command-line. Return true on
 * success, false if the string was not a valid integer.
*/
bool parse_int_value(const char *optarg, int *value) {
    char *endptr;
    if (!optarg) return false;
    errno = 0;
    long result = strtol(optarg, &endptr, 10);
    if (endptr == optarg) return false; // No integer was parsed
    if (*endptr != '\0') return false; // Extra characters ("1hello")
    if (errno) return false; // Out of long range, result not valid
    if (result < INT_MIN || result > INT_MAX) return false; // result out of int range
    *value = result;
    return true;
}

/*
 * Parse an long int from a value passed on the command-line. Return true on
 * success, false if the string was not a valid long int.
*/
bool parse_long_value(const char *optarg, long *value, int base) {
    char *endptr;
    if (!optarg) return false;
    errno = 0;
    // Typically base is 10, or 0 to allow parsing strings like 0xff
    long result = strtol(optarg, &endptr, base);
    if (endptr == optarg) return false; // No integer was parsed
    if (*endptr != '\0') return false; // Extra characters ("1hello")
    if (errno) return false; // Out of long range, result not valid
    *value = result;
    return true;
}

/*
 * Processes a standard "global" samtools long option.
 *
 * The 'c' value is the return value from a getopt_long() call.  It is checked
 * against the lopt[] array to find the corresponding value as this may have
 * been reassigned by the individual subcommand.
 *
 * Having found the entry, the corresponding long form is used to apply the
 * option, storing the setting in sam_global_args *ga.
 *
 * Returns 0 on success,
 *        -1 on failure.
 */
int parse_sam_global_opt(int c, const char *optarg, const struct option *lopt,
                         sam_global_args *ga) {
    int r = 0;

    while (lopt->name) {
        if (c != lopt->val) {
            lopt++;
            continue;
        }

        if (strcmp(lopt->name, "input-fmt") == 0) {
            r = hts_parse_format(&ga->in, optarg);
            break;
        } else if (strcmp(lopt->name, "input-fmt-option") == 0) {
            r = hts_opt_add((hts_opt **)&ga->in.specific, optarg);
            break;
        } else if (strcmp(lopt->name, "output-fmt") == 0) {
            r = hts_parse_format(&ga->out, optarg);
            break;
        } else if (strcmp(lopt->name, "output-fmt-option") == 0) {
            r = hts_opt_add((hts_opt **)&ga->out.specific, optarg);
            break;
        } else if (strcmp(lopt->name, "reference") == 0) {
            char *ref = malloc(10 + strlen(optarg) + 1);

            if (!ref) {
                fprintf(stderr, "Unable to allocate memory in "
                                "parse_sam_global_opt.\n");

                return -1;
            }

            sprintf(ref, "reference=%s", optarg);

            if (!(ga->reference = strdup(optarg))) {
                fprintf(stderr, "Unable to allocate memory in "
                                "parse_sam_global_opt.\n");

                return -1;
            }

            r  = hts_opt_add((hts_opt **)&ga->in.specific, ref);
            r |= hts_opt_add((hts_opt **)&ga->out.specific, ref);
            free(ref);
            break;
        } else if (strcmp(lopt->name, "threads") == 0) {
            if (!parse_int_value(optarg, &ga->nthreads))
            {
                fprintf(stderr, "Invalid threads value.\n");
                return -1;
            }
            break;
        } else if (strcmp(lopt->name, "write-index") == 0) {
            ga->write_index = 1;
            break;
        } else if (strcmp(lopt->name, "verbosity") == 0) {
            if (!parse_int_value(optarg, &hts_verbose))
            {
                fprintf(stderr, "Invalid verbosity value.\n");
                return -1;
            }
            break;
        }
    }

    if (!lopt->name) {
        fprintf(stderr, "Unexpected global option.\n");
        return -1;
    }

    /*
     * SAM format with compression enabled implies SAM.bgzf
     */
    if (ga->out.format == sam) {
        hts_opt *opts = (hts_opt *)ga->out.specific;
        while (opts) {
            if (opts->opt == HTS_OPT_COMPRESSION_LEVEL)
                ga->out.compression = bgzf;
            opts = opts->next;
        }
    }

    return r;
}

/*
 * Report the usage for global options.
 *
 * This accepts a string with one character per SAM_OPT_GLOBAL_OPTIONS option
 * to determine which options need to be printed and how.
 * Each character should be one of:
 * '.'    No short option has been assigned. Use --long-opt only.
 * '-'    The long (and short) option has been disabled.
 * <c>    Otherwise the short option is character <c>.
 */
void sam_global_opt_help(FILE *fp, const char *shortopts) {
    int i = 0;

    static const struct option lopts[] = {
        SAM_OPT_GLOBAL_OPTIONS(0,0,0,0,0,0),
        { NULL, 0, NULL, 0 }
    };

    for (i = 0; shortopts && shortopts[i] && lopts[i].name; i++) {
        if (shortopts[i] == '-')
            continue;

        if (shortopts[i] == '.')
            fprintf(fp, "      --");
        else
            fprintf(fp, "  -%c, --", shortopts[i]);

        if (strcmp(lopts[i].name, "input-fmt") == 0)
            fprintf(fp,"input-fmt FORMAT[,OPT[=VAL]]...\n"
                    "               Specify input format (SAM, BAM, CRAM)\n");
        else if (strcmp(lopts[i].name, "input-fmt-option") == 0)
            fprintf(fp,"input-fmt-option OPT[=VAL]\n"
                    "               Specify a single input file format option in the form\n"
                    "               of OPTION or OPTION=VALUE\n");
        else if (strcmp(lopts[i].name, "output-fmt") == 0)
            fprintf(fp,"output-fmt FORMAT[,OPT[=VAL]]...\n"
                    "               Specify output format (SAM, BAM, CRAM)\n");
        else if (strcmp(lopts[i].name, "output-fmt-option") == 0)
            fprintf(fp,"output-fmt-option OPT[=VAL]\n"
                    "               Specify a single output file format option in the form\n"
                    "               of OPTION or OPTION=VALUE\n");
        else if (strcmp(lopts[i].name, "reference") == 0)
            fprintf(fp,"reference FILE\n"
                    "               Reference sequence FASTA FILE [null]\n");
        else if (strcmp(lopts[i].name, "threads") == 0)
            fprintf(fp,"threads INT\n"
                    "               Number of additional threads to use [0]\n");
        else if (strcmp(lopts[i].name, "write-index") == 0)
            fprintf(fp,"write-index\n"
                    "               Automatically index the output files [off]\n");
        else if (strcmp(lopts[i].name, "verbosity") == 0)
            fprintf(fp,"verbosity INT\n"
                    "               Set level of verbosity\n");
    }

    fprintf(fp, "\nSee https://www.htslib.org/doc/samtools.html#GLOBAL_COMMAND_OPTIONS\nfor more details.\n");
}

void sam_global_args_init(sam_global_args *ga) {
    if (!ga)
        return;

    memset(ga, 0, sizeof(*ga));
}

/*
 * Add the standard samtools @PG provenance line.  See samtools.h for details.
 */
int samtools_add_pg_line(sam_hdr_t *h, const char *arg_list, int no_pg) {
    if (no_pg)
        return 0;

    const char *sam_ver = samtools_version(), *hts_ver = hts_version();
    const char *version = sam_ver;
    char version_buf[256];
    int sam_maj, sam_min, hts_maj, hts_min;

    // SAMtools and HTSlib are released together and have matching major and
    // minor version numbers, so the HTSlib version can normally be deduced from
    // the SAMtools one.  Only record it when it cannot be, i.e. when the major
    // or minor numbers differ.
    if (!(sscanf(sam_ver, "%d.%d", &sam_maj, &sam_min) == 2 &&
          sscanf(hts_ver, "%d.%d", &hts_maj, &hts_min) == 2 &&
          sam_maj == hts_maj && sam_min == hts_min)) {
        snprintf(version_buf, sizeof(version_buf), "%s (with HTSlib %s)",
                 sam_ver, hts_ver);
        version = version_buf;
    }

    if (sam_hdr_add_pg(h, "samtools",
                       "VN", version,
                       arg_list ? "CL" : NULL,
                       arg_list ? arg_list : NULL,
                       NULL) == -1)
        return -1;

    return 0;
}

void sam_global_args_free(sam_global_args *ga) {
    if (ga->in.specific)
        hts_opt_free(ga->in.specific);

    if (ga->out.specific)
        hts_opt_free(ga->out.specific);

    if (ga->reference)
        free(ga->reference);
}