faidx.c

/*  faidx.c -- faidx subcommand.

    Copyright (C) 2008, 2009, 2013, 2016, 2018-2020 Genome Research Ltd.
    Portions copyright (C) 2011 Broad 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 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.

History:

  * 2016-01-12: Pierre Lindenbaum @yokofakun : added options -o -n

*/

#include <config.h>

#include <ctype.h>
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
#include <unistd.h>
#include <stdarg.h>
#include <errno.h>
#include <getopt.h>
#include <limits.h>
#include <htslib/faidx.h>
#include <htslib/hts.h>
#include <htslib/hfile.h>
#include <htslib/kstring.h>
#include "samtools.h"

#define DEFAULT_FASTA_LINE_LEN 60

static unsigned char comp_base[256] = {
  0,   1,   2,   3,   4,   5,   6,   7,   8,   9,  10,  11,  12,  13,  14,  15,
 16,  17,  18,  19,  20,  21,  22,  23,  24,  25,  26,  27,  28,  29,  30,  31,
 32, '!', '"', '#', '$', '%', '&', '\'','(', ')', '*', '+', ',', '-', '.', '/',
'0', '1', '2', '3', '4', '5', '6', '7', '8', '9', ':', ';', '<', '=', '>', '?',
'@', 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', '[', '\\',']', '^', '_',
'`', 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', '{', '|', '}', '~', 127,
128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,
144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,
176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191,
192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207,
208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,
224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239,
240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255,
};

static void reverse_complement(char *str, const hts_pos_t len) {
    char c;
    hts_pos_t i = 0, j = len - 1;

    while (i <= j) {
        c = str[i];
        str[i] = comp_base[(unsigned char)str[j]];
        str[j] = comp_base[(unsigned char)c];
        i++;
        j--;
    }
}

static void reverse(char *str, const hts_pos_t len) {
    char c;
    hts_pos_t i = 0, j = len - 1;

    while (i < j) {
        c = str[i];
        str[i] = str[j];
        str[j] = c;
        i++;
        j--;
    }
}


static int write_line(faidx_t *faid, FILE *file, const char *line, const char *name,
                      const int ignore, const int length, const hts_pos_t seq_len) {
    int id;
    hts_pos_t beg, end;

    if (seq_len < 0) {
        fprintf(stderr, "[faidx] Failed to fetch sequence in %s\n", name);

        if (ignore && seq_len == -2) {
            return EXIT_SUCCESS;
        } else {
            return EXIT_FAILURE;
        }
    } else if (seq_len == 0) {
        fprintf(stderr, "[faidx] Zero length sequence: %s\n", name);
    } else if (fai_parse_region(faid, name, &id, &beg, &end, 0)
               && (end < INT_MAX) && (seq_len != end - beg)) {
        fprintf(stderr, "[faidx] Truncated sequence: %s\n", name);
    }

    hts_pos_t i, seq_sz = seq_len;

    for (i = 0; i < seq_sz; i += length)
    {
        hts_pos_t len = i + length < seq_sz ? length : seq_sz - i;
        if (fwrite(line + i, 1, len, file) < len ||
            fputc('\n', file) == EOF) {
            print_error_errno("faidx", "failed to write output");
            return EXIT_FAILURE;
        }
    }

    return EXIT_SUCCESS;
}


static int write_output(faidx_t *faid, FILE *file, const char *name, const int ignore,
                        const int length, const int rev,
                        const char *pos_strand_name, const char *neg_strand_name,
                        enum fai_format_options format) {
    hts_pos_t seq_len;
    char *seq = fai_fetch64(faid, name, &seq_len);

    if (format == FAI_FASTA) {
        fprintf(file, ">%s%s\n", name, rev ? neg_strand_name : pos_strand_name);
    } else {
        fprintf(file, "@%s%s\n", name, rev ? neg_strand_name : pos_strand_name);
    }

    if (rev && seq_len > 0) {
        reverse_complement(seq, seq_len);
    }

    if (write_line(faid, file, seq, name, ignore, length, seq_len)
        == EXIT_FAILURE) {
        free(seq);
        return EXIT_FAILURE;
    }

    free(seq);

    if (format == FAI_FASTQ) {
        fprintf(file, "+\n");

        char *qual = fai_fetchqual64(faid, name, &seq_len);

        if (rev && seq_len > 0) {
            reverse(qual, seq_len);
        }

        if (write_line(faid, file, qual, name, ignore, length, seq_len)
            == EXIT_FAILURE) {
            free(qual);
            return EXIT_FAILURE;
        }

        free(qual);
    }

    return EXIT_SUCCESS;
}


static int read_regions_from_file(faidx_t *faid, hFILE *in_file, FILE *file, const int ignore,
                                  const int length, const int rev,
                                  const char *pos_strand_name,
                                  const char *neg_strand_name,
                                  enum fai_format_options format) {
    kstring_t line = {0, 0, NULL};
    int ret = EXIT_FAILURE;

    while (line.l = 0, kgetline(&line, (kgets_func *)hgets, in_file) >= 0) {
        if ((ret = write_output(faid, file, line.s, ignore, length, rev, pos_strand_name, neg_strand_name, format)) == EXIT_FAILURE) {
            break;
        }
    }

    free(line.s);

    return ret;
}

static int usage(FILE *fp, enum fai_format_options format, int exit_status)
{
    char *tool, *file_type, *index_name;

    if (format == FAI_FASTA) {
        tool = "faidx <file.fa|file.fa.gz>";
        file_type = "FASTA";
        index_name = "file.fa";
    } else {
        tool = "fqidx <file.fq|file.fq.gz>";
        file_type = "FASTQ";
        index_name = "file.fq";
    }

    fprintf(fp, "Usage: samtools %s [<reg> [...]]\n", tool);
    fprintf(fp, "Option: \n"
                " -o, --output FILE        Write %s to file.\n"
                " -n, --length INT         Length of %s sequence line. [60]\n"
                " -c, --continue           Continue after trying to retrieve missing region.\n"
                " -r, --region-file FILE   File of regions.  Format is chr:from-to. One per line.\n"
                " -i, --reverse-complement Reverse complement sequences.\n"
                "     --mark-strand TYPE   Add strand indicator to sequence name\n"
                "                          TYPE = rc   for /rc on negative strand (default)\n"
                "                                 no   for no strand indicator\n"
                "                                 sign for (+) / (-)\n"
                "                                 custom,<pos>,<neg> for custom indicator\n"
                "     --fai-idx      FILE  name of the index file (default %s.fai).\n"
                "     --gzi-idx      FILE  name of compressed file index (default %s.gz.gzi).\n",
                file_type, file_type, index_name, index_name);


    if (format == FAI_FASTA) {
       fprintf(fp, " -f, --fastq              File and index in FASTQ format.\n");
    }

    fprintf(fp, " -h, --help               This message.\n");

    return exit_status;
}

int faidx_core(int argc, char *argv[], enum fai_format_options format)
{
    int c, ignore_error = 0, rev = 0;
    int line_len = DEFAULT_FASTA_LINE_LEN ;/* fasta line len */
    char* output_file = NULL; /* output file (default is stdout ) */
    char *region_file = NULL; // list of regions from file, one per line
    char *pos_strand_name = ""; // Extension to add to name for +ve strand
    char *neg_strand_name = "/rc"; // Extension to add to name for -ve strand
    char *strand_names = NULL; // Used for custom strand annotation
    char *fai_name = NULL; // specified index name
    char *gzi_name = NULL; // specified compressed index name
    FILE* file_out = stdout;/* output stream */

    static const struct option lopts[] = {
        { "output", required_argument,       NULL, 'o' },
        { "help",   no_argument,             NULL, 'h' },
        { "length", required_argument,       NULL, 'n' },
        { "continue", no_argument,           NULL, 'c' },
        { "region-file", required_argument,  NULL, 'r' },
        { "fastq", no_argument,              NULL, 'f' },
        { "reverse-complement", no_argument, NULL, 'i' },
        { "mark-strand", required_argument, NULL, 1000 },
        { "fai-idx", required_argument,     NULL, 1001 },
        { "gzi-idx", required_argument,     NULL, 1002 },
        { NULL, 0, NULL, 0 }
    };

    while ((c = getopt_long(argc, argv, "ho:n:cr:fi", lopts, NULL)) >= 0) {
        switch (c) {
            case 'o': output_file = optarg; break;
            case 'n': line_len = atoi(optarg);
                      if(line_len<1) {
                        fprintf(stderr,"[faidx] bad line length '%s', using default:%d\n",optarg,DEFAULT_FASTA_LINE_LEN);
                        line_len= DEFAULT_FASTA_LINE_LEN ;
                        }
                      break;
            case 'c': ignore_error = 1; break;
            case 'r': region_file = optarg; break;
            case 'f': format = FAI_FASTQ; break;
            case 'i': rev = 1; break;
            case '?': return usage(stderr, format, EXIT_FAILURE);
            case 'h': return usage(stdout, format, EXIT_SUCCESS);
            case 1000:
                if (strcmp(optarg, "no") == 0) {
                    pos_strand_name = neg_strand_name = "";
                } else if (strcmp(optarg, "sign") == 0) {
                    pos_strand_name = "(+)";
                    neg_strand_name = "(-)";
                } else if (strcmp(optarg, "rc") == 0) {
                    pos_strand_name = "";
                    neg_strand_name = "/rc";
                } else if (strncmp(optarg, "custom,", 7) == 0) {
                    size_t len = strlen(optarg + 7);
                    size_t comma = strcspn(optarg + 7, ",");
                    free(strand_names);
                    strand_names = pos_strand_name = malloc(len + 2);
                    if (!strand_names) {
                        fprintf(stderr, "[faidx] Out of memory\n");
                        return EXIT_FAILURE;
                    }
                    neg_strand_name = pos_strand_name + comma + 1;
                    memcpy(pos_strand_name, optarg + 7, comma);
                    pos_strand_name[comma] = '\0';
                    if (comma < len)
                        memcpy(neg_strand_name, optarg + 7 + comma + 1,
                               len - comma);
                    neg_strand_name[len - comma] = '\0';
                } else {
                    fprintf(stderr, "[faidx] Unknown --mark-strand option \"%s\"\n", optarg);
                    return usage(stderr, format, EXIT_FAILURE);
                }
                break;
            case 1001: fai_name = optarg; break;
            case 1002: gzi_name = optarg; break;
            default:  break;
        }
    }

    if ( argc==optind )
        return usage(stdout, format, EXIT_SUCCESS);

    if (optind+1 == argc && !region_file) {
        if (output_file && !fai_name)
            fai_name = output_file;

        if (fai_build3(argv[optind], fai_name, gzi_name) != 0) {
            if (fai_name)
                fprintf(stderr, "[faidx] Could not build fai index %s", fai_name);
            else
                fprintf(stderr, "[faidx] Could not build fai index %s.fai", argv[optind]);

            if (gzi_name)
                fprintf(stderr, " or compressed index %s\n", gzi_name);
            else
                fprintf(stderr, "\n");

            return EXIT_FAILURE;
        }

        return 0;
    }

    faidx_t *fai = fai_load3_format(argv[optind], fai_name, gzi_name, FAI_CREATE, format);

    if (!fai) {
        if (fai_name)
            fprintf(stderr, "[faidx] Could not load fai index %s", fai_name);
        else
            fprintf(stderr, "[faidx] Could not build fai index %s.fai", argv[optind]);

        if (gzi_name)
            fprintf(stderr, " or compressed index %s\n", gzi_name);
        else
            fprintf(stderr, "\n");

        return EXIT_FAILURE;
    }

    /** output file provided by user */
    if( output_file != NULL ) {
        if( strcmp( output_file, argv[optind] ) == 0 ) {
            fprintf(stderr,"[faidx] Same input/output : %s\n", output_file);
            return EXIT_FAILURE;
        }

        file_out = fopen( output_file, "w" );

        if( file_out == NULL) {
            fprintf(stderr,"[faidx] Cannot open \"%s\" for writing :%s.\n", output_file, strerror(errno) );
            return EXIT_FAILURE;
        }
    }

    int exit_status = EXIT_SUCCESS;

    if (region_file) {
        hFILE *rf;

        if ((rf = hopen(region_file, "r"))) {
            exit_status = read_regions_from_file(fai, rf, file_out, ignore_error, line_len, rev, pos_strand_name, neg_strand_name, format);

            if (hclose(rf) != 0) {
                fprintf(stderr, "[faidx] Warning: failed to close %s", region_file);
            }
        } else {
            fprintf(stderr, "[faidx] Failed to open \"%s\" for reading.\n", region_file);
            exit_status = EXIT_FAILURE;
        }
    }

    while ( ++optind<argc && exit_status == EXIT_SUCCESS) {
        exit_status = write_output(fai, file_out, argv[optind], ignore_error, line_len, rev, pos_strand_name, neg_strand_name, format);
    }

    fai_destroy(fai);

    if (fflush(file_out) == EOF) {
        print_error_errno("faidx", "failed to flush output");
        exit_status = EXIT_FAILURE;
    }

    if( output_file != NULL) fclose(file_out);
    free(strand_names);

    return exit_status;
}


int faidx_main(int argc, char *argv[]) {
    return faidx_core(argc, argv, FAI_FASTA);
}


int fqidx_main(int argc, char *argv[]) {
    return faidx_core(argc, argv, FAI_FASTQ);
}