bam_split.c

/*  bam_split.c -- split subcommand.

    Copyright (C) 2013-2016,2018 Genome Research Ltd.

    Author: Martin Pollard <mp15@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 <htslib/sam.h>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <stdbool.h>
#include <limits.h>
#include <unistd.h>
#include <regex.h>
#include <assert.h>
#include <htslib/khash.h>
#include <htslib/kstring.h>
#include <htslib/cram.h>
#include "htslib/thread_pool.h"
#include "sam_opts.h"
#include "samtools.h"


KHASH_MAP_INIT_STR(c2i, int)

struct parsed_opts {
    const char *merged_input_name;
    const char *unaccounted_header_name;
    const char *unaccounted_name;
    const char *output_format_string;
    bool verbose;
    sam_global_args ga;
};

typedef struct parsed_opts parsed_opts_t;

struct state {
    samFile* merged_input_file;
    bam_hdr_t* merged_input_header;
    samFile* unaccounted_file;
    bam_hdr_t* unaccounted_header;
    size_t output_count;
    char** rg_id;
    char **rg_output_file_name;
    samFile** rg_output_file;
    bam_hdr_t** rg_output_header;
    kh_c2i_t* rg_hash;
    htsThreadPool p;
};

typedef struct state state_t;

static int cleanup_state(state_t* status, bool check_close);
static void cleanup_opts(parsed_opts_t* opts);

static void usage(FILE *write_to)
{
    fprintf(write_to,
"Usage: samtools split [-u <unaccounted.bam>] [-h <unaccounted_header.sam>]\n"
"                      [-f <format_string>] [-v] <merged.bam>\n"
"Options:\n"
"  -f STRING       output filename format string [\"%%*_%%#.%%.\"]\n"
"  -u FILE1        put reads with no RG tag or an unrecognised RG tag in FILE1\n"
"  -h FILE2        ... and override the header with FILE2 (-u file only)\n"
"  -v              verbose output\n");
    sam_global_opt_help(write_to, "-....@");
    fprintf(write_to,
"\n"
"Format string expansions:\n"
"  %%%%     %%\n"
"  %%*     basename\n"
"  %%#     @RG index\n"
"  %%!     @RG ID\n"
"  %%.     filename extension for output format\n"
      );
}

// Takes the command line options and turns them into something we can understand
static parsed_opts_t* parse_args(int argc, char** argv)
{
    if (argc == 1) { usage(stdout); return NULL; }

    const char *optstring = "vf:h:u:@:";

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

    parsed_opts_t* retval = calloc(sizeof(parsed_opts_t), 1);
    if (! retval ) { perror("cannot allocate option parsing memory"); return NULL; }

    sam_global_args_init(&retval->ga);

    int opt;
    while ((opt = getopt_long(argc, argv, optstring, lopts, NULL)) != -1) {
        switch (opt) {
        case 'f':
            retval->output_format_string = optarg;
            break;
        case 'h':
            retval->unaccounted_header_name = optarg;
            break;
        case 'v':
            retval->verbose = true;
            break;
        case 'u':
            retval->unaccounted_name = optarg;
            break;
        default:
            if (parse_sam_global_opt(opt, optarg, lopts, &retval->ga) == 0) break;
            /* else fall-through */
        case '?':
            usage(stdout);
            free(retval);
            return NULL;
        }
    }

    if (retval->output_format_string == NULL) retval->output_format_string = "%*_%#.%.";

    argc -= optind;
    argv += optind;

    if (argc != 1) {
        print_error("split", "Invalid number of arguments: %d", argc);
        usage(stderr);
        free(retval);
        return NULL;
    }

    retval->merged_input_name = argv[0];

    return retval;
}

// Expands a output filename format string
static char* expand_format_string(const char* format_string, const char* basename, const char* rg_id, const int rg_idx, const htsFormat *format)
{
    kstring_t str = { 0, 0, NULL };
    const char* pointer = format_string;
    const char* next;
    while ((next = strchr(pointer, '%')) != NULL) {
        if (kputsn(pointer, next-pointer, &str) < 0) goto memfail;
        ++next;
        switch (*next) {
            case '%':
                if (kputc('%', &str) < 0) goto memfail;
                break;
            case '*':
                if (kputs(basename, &str) < 0) goto memfail;
                break;
            case '#':
                if (kputl(rg_idx, &str) < 0) goto memfail;
                break;
            case '!':
                if (kputs(rg_id, &str) < 0) goto memfail;
                break;
            case '.':
                // Only really need to cope with sam, bam, cram
                if (format->format != unknown_format) {
                    if (kputs(hts_format_file_extension(format), &str) < 0)
                        goto memfail;
                } else {
                    if (kputs("bam", &str) < 0) goto memfail;
                }
                break;
            case '\0':
                print_error("split", "Trailing %% in filename format string");
                goto fail;
            default:
                // Error is: fprintf(stderr, "bad format string, unknown format specifier\n");
                print_error("split", "Unknown specifier %%%c in filename format string", *next);
                goto fail;
        }
        pointer = next + 1;
    }
    if (kputs(pointer, &str) < 0) goto memfail;
    return ks_release(&str);

 memfail:
    print_error_errno("split", "Couldn't build output filename");
 fail:
    free(str.s);
    return NULL;
}

// Parse the header, count the number of RG tags and return a list of their names
static bool count_RG(bam_hdr_t* hdr, size_t* count, char*** output_name)
{
    char **names = NULL;

    if (hdr->l_text < 3 ) {
        *count = 0;
        *output_name = NULL;
        return true;
    }

    //////////////////////////////////////////
    // First stage count number of @RG tags //
    //////////////////////////////////////////
    const char *pointer = hdr->text;
    size_t n_rg = 0;
    // Guard against rare case where @RG is first header line
    // This shouldn't happen but could where @HD is omitted
    if (pointer[0] == '@' && pointer[1] == 'R' && pointer[2] == 'G' ) {
        ++n_rg;
        pointer += 3;
    }
    const char *line;
    while ((line = strstr(pointer, "\n@RG")) != NULL) {
        ++n_rg;
        pointer = line + 1;
    }

    //////////////////////////////////
    // Second stage locate @RG ID's //
    //////////////////////////////////
    regex_t rg_finder;
    int error;
    memset(&rg_finder, 0, sizeof(rg_finder));
    if ((error = regcomp(&rg_finder, "^@RG.*\tID:([!-)+-<>-~][ !-~]*)(\t.*$|$)", REG_EXTENDED|REG_NEWLINE)) != 0) {
        goto regfail;
    }
    regmatch_t matches[2] = {{0, 0}, {0, 0}};
    const char *begin = hdr->text;

    names = calloc(n_rg, sizeof(names[0]));
    if (!names) goto memfail;
    size_t n_rg_id = 0;

    while ((error = regexec(&rg_finder, begin, 2, matches, 0)) == 0) {
        kstring_t str = { 0, 0, NULL };
        if (kputsn(begin+matches[1].rm_so, matches[1].rm_eo-matches[1].rm_so, &str) < 0)
            goto memfail;
        assert(n_rg_id < n_rg);
        names[n_rg_id++] = ks_release(&str);
        begin += matches[0].rm_eo;
    }

    if (error != REG_NOMATCH)
        goto regfail;

    // return results
    *count = n_rg_id;
    *output_name = names;
    regfree(&rg_finder);
    return true;

 memfail:
    print_error_errno("split", "Failed to get @RG IDs");
    *count = 0;
    *output_name = NULL;
    regfree(&rg_finder);
    free(names);
    return false;

 regfail: {
        char msg[256];
        regerror(error, &rg_finder, msg, sizeof(msg));
        print_error("split", "Failed to parse @RG IDs : %s", msg);
        *count = 0;
        *output_name = NULL;
        regfree(&rg_finder);
        free(names);
        return false;
    }
}

// Filters a header of @RG lines where ID != id_keep
// TODO: strip @PG's descended from other RGs and their descendants
static bool filter_header_rg(bam_hdr_t* hdr, const char* id_keep, const char *arg_list)
{
    kstring_t str = {0, 0, NULL};
    size_t len_id_keep = strlen(id_keep);
    SAM_hdr *sh = NULL;
    regex_t rg_finder;
    int error;
    memset(&rg_finder, 0, sizeof(rg_finder));

    if ((error = regcomp(&rg_finder, "^@RG.*\tID:([!-)+-<>-~][ !-~]*)(\t.*$|$)", REG_EXTENDED|REG_NEWLINE)) != 0) {
        goto regfail;
    }

    // regex vars
    char* header = hdr->text;
    regmatch_t matches[2] = {{0, 0}, {0, 0}};

    // We're removing lines so new header must be shorter than old
    if (ks_resize(&str, hdr->l_text + 1) < 0)
        goto memfail;

    while ((error = regexec(&rg_finder, header, 2, matches, 0)) == 0) {
        kputsn(header, matches[0].rm_so, &str); // copy header up until the found RG line

        // if ID matches keep keep it, else we can just ignore it
        if (matches[1].rm_eo-matches[1].rm_so == len_id_keep &&
            memcmp(header+matches[1].rm_so, id_keep, len_id_keep) == 0) {
            kputsn(header+matches[0].rm_so, (matches[0].rm_eo+1)-matches[0].rm_so, &str);
        }
        // move pointer forward
        header += matches[0].rm_eo+1;
    }
    // cleanup
    // Did we leave loop because of an error?
    if (error != REG_NOMATCH)
        goto regfail;

    // Write remainder of string
    kputs(header, &str);

    // Modify header
    hdr->l_text = ks_len(&str);
    free(hdr->text);
    hdr->text = ks_release(&str);

    // Add the PG line
    sh = sam_hdr_parse_(hdr->text, hdr->l_text);
    if (!sh) {
        print_error("split", "Couldn't parse SAM header");
        goto fail;
    }
    if (sam_hdr_add_PG(sh, "samtools",
                           "VN", samtools_version(),
                           arg_list ? "CL": NULL,
                           arg_list ? arg_list : NULL,
                           NULL) != 0)
        goto fail;

    free(hdr->text);
    char *new_text = strdup(sam_hdr_str(sh));
    if (!new_text)
        goto memfail;
    hdr->l_text = sam_hdr_length(sh);
    hdr->text = new_text;
    sam_hdr_free(sh);
    regfree(&rg_finder);

    return true;

 regfail: {
        char msg[256];
        regerror(error, &rg_finder, msg, sizeof(msg));
        print_error("split", "Failed to parse @RG IDs : %s", msg);
        goto fail;
    }

 memfail:
    print_error_errno("split", "Couldn't make new SAM header");
 fail:
    regfree(&rg_finder);
    free(ks_release(&str));
    if (sh) sam_hdr_free(sh);
    return false;
}

static int header_compatible(bam_hdr_t *hdr1, bam_hdr_t *hdr2)
{
    size_t n;
    if (hdr1->n_targets != hdr2->n_targets) {
        print_error("split",
                    "Unaccounted header contains wrong number of references");
        return -1;
    }
    for (n = 0; n < hdr1->n_targets; n++) {
        if (hdr1->target_len[n] != hdr2->target_len[n]) {
            print_error("split",
                        "Unaccounted header reference %zu \"%s\" is not the same length as in the input file",
                        n + 1, hdr2->target_name[n]);
            return -1;
        }
    }
    return 0;
}

// Set the initial state
static state_t* init(parsed_opts_t* opts, const char *arg_list)
{
    state_t* retval = calloc(sizeof(state_t), 1);
    if (!retval) {
        print_error_errno("split", "Initialisation failed");
        return NULL;
    }

    if (opts->ga.nthreads > 0) {
        if (!(retval->p.pool = hts_tpool_init(opts->ga.nthreads))) {
            fprintf(stderr, "Error creating thread pool\n");
            cleanup_state(retval, false);
            return NULL;
        }
    }

    retval->merged_input_file = sam_open_format(opts->merged_input_name, "rb", &opts->ga.in);
    if (!retval->merged_input_file) {
        print_error_errno("split", "Could not open \"%s\"", opts->merged_input_name);
        cleanup_state(retval, false);
        return NULL;
    }
    if (retval->p.pool)
        hts_set_opt(retval->merged_input_file, HTS_OPT_THREAD_POOL, &retval->p);
    retval->merged_input_header = sam_hdr_read(retval->merged_input_file);
    if (retval->merged_input_header == NULL) {
        print_error("split", "Could not read header from \"%s\"", opts->merged_input_name);
        cleanup_state(retval, false);
        return NULL;
    }

    if (opts->unaccounted_name) {
        if (opts->unaccounted_header_name) {
            samFile* hdr_load = sam_open_format(opts->unaccounted_header_name, "r", &opts->ga.in);
            if (!hdr_load) {
                print_error_errno("split", "Could not open unaccounted header file \"%s\"", opts->unaccounted_header_name);
                cleanup_state(retval, false);
                return NULL;
            }
            retval->unaccounted_header = sam_hdr_read(hdr_load);
            if (retval->unaccounted_header == NULL) {
                print_error("split", "Could not read header from \"%s\"", opts->unaccounted_header_name);
                cleanup_state(retval, false);
                sam_close(hdr_load);
                return NULL;
            }
            sam_close(hdr_load);
            if (header_compatible(retval->merged_input_header,
                                  retval->unaccounted_header) != 0) {
                cleanup_state(retval, false);
                return NULL;
            }
        } else {
            retval->unaccounted_header = bam_hdr_dup(retval->merged_input_header);
        }

        retval->unaccounted_file = sam_open_format(opts->unaccounted_name, "wb", &opts->ga.out);
        if (retval->unaccounted_file == NULL) {
            print_error_errno("split", "Could not open unaccounted output file \"%s\"", opts->unaccounted_name);
            cleanup_state(retval, false);
            return NULL;
        }
        if (retval->p.pool)
            hts_set_opt(retval->unaccounted_file, HTS_OPT_THREAD_POOL, &retval->p);
    }

    // Open output files for RGs
    if (!count_RG(retval->merged_input_header, &retval->output_count, &retval->rg_id)) return NULL;
    if (opts->verbose) fprintf(stderr, "@RG's found %zu\n",retval->output_count);

    retval->rg_output_file_name = (char **)calloc(retval->output_count, sizeof(char *));
    retval->rg_output_file = (samFile**)calloc(retval->output_count, sizeof(samFile*));
    retval->rg_output_header = (bam_hdr_t**)calloc(retval->output_count, sizeof(bam_hdr_t*));
    retval->rg_hash = kh_init_c2i();
    if (!retval->rg_output_file_name || !retval->rg_output_file || !retval->rg_output_header || !retval->rg_hash) {
        print_error_errno("split", "Could not initialise output file array");
        cleanup_state(retval, false);
        return NULL;
    }

    char* dirsep = strrchr(opts->merged_input_name, '/');
    char* input_base_name = strdup(dirsep? dirsep+1 : opts->merged_input_name);
    if (!input_base_name) {
        print_error_errno("split", "Filename manipulation failed");
        cleanup_state(retval, false);
        return NULL;
    }
    char* extension = strrchr(input_base_name, '.');
    if (extension) *extension = '\0';

    size_t i;
    for (i = 0; i < retval->output_count; i++) {
        char* output_filename = NULL;

        output_filename = expand_format_string(opts->output_format_string,
                                               input_base_name,
                                               retval->rg_id[i], i,
                                               &opts->ga.out);

        if ( output_filename == NULL ) {
            cleanup_state(retval, false);
            free(input_base_name);
            return NULL;
        }

        retval->rg_output_file_name[i] = output_filename;
        retval->rg_output_file[i] = sam_open_format(output_filename, "wb", &opts->ga.out);
        if (retval->rg_output_file[i] == NULL) {
            print_error_errno("split", "Could not open \"%s\"", output_filename);
            cleanup_state(retval, false);
            free(input_base_name);
            return NULL;
        }
        if (retval->p.pool)
            hts_set_opt(retval->rg_output_file[i], HTS_OPT_THREAD_POOL, &retval->p);

        // Record index in hash
        int ret;
        khiter_t iter = kh_put_c2i(retval->rg_hash, retval->rg_id[i], &ret);
        if (ret < 0) {
            print_error_errno("split", "Couldn't add @RG ID to look-up table");
            cleanup_state(retval, false);
            free(input_base_name);
            return NULL;
        }
        kh_val(retval->rg_hash,iter) = i;

        // Set and edit header
        retval->rg_output_header[i] = bam_hdr_dup(retval->merged_input_header);
        if ( !filter_header_rg(retval->rg_output_header[i], retval->rg_id[i], arg_list) ) {
            print_error("split", "Could not rewrite header for \"%s\"", output_filename);
            cleanup_state(retval, false);
            free(input_base_name);
            return NULL;
        }
    }

    free(input_base_name);

    return retval;
}

static bool split(state_t* state)
{
    if (state->unaccounted_file && sam_hdr_write(state->unaccounted_file, state->unaccounted_header) != 0) {
        print_error_errno("split", "Could not write output file header");
        return false;
    }
    size_t i;
    for (i = 0; i < state->output_count; i++) {
        if (sam_hdr_write(state->rg_output_file[i], state->rg_output_header[i]) != 0) {
            print_error_errno("split", "Could not write file header to \"%s\"", state->rg_output_file_name[i]);
            return false;
        }
    }

    bam1_t* file_read = bam_init1();
    // Read the first record
    int r;
    if ((r=sam_read1(state->merged_input_file, state->merged_input_header, file_read)) < 0) {
        // Nothing more to read?  Ignore this file
        bam_destroy1(file_read);
        file_read = NULL;
        if (r < -1) {
            print_error("split", "Could not read first input record");
            return false;
        }
    }

    while (file_read != NULL) {
        // Get RG tag from read and look it up in hash to find file to output it to
        uint8_t* tag = bam_aux_get(file_read, "RG");
        khiter_t iter;
        if ( tag != NULL ) {
            char* rg = bam_aux2Z(tag);
            iter = kh_get_c2i(state->rg_hash, rg);
        } else {
            iter = kh_end(state->rg_hash);
        }

        // Write the read out to correct file
        if (iter != kh_end(state->rg_hash)) {
            // if found write to the appropriate untangled bam
            int i = kh_val(state->rg_hash,iter);
            if (sam_write1(state->rg_output_file[i], state->rg_output_header[i], file_read) < 0) {
                print_error_errno("split", "Could not write to \"%s\"", state->rg_output_file_name[i]);
                bam_destroy1(file_read);
                return false;
            }
        } else {
            // otherwise write to the unaccounted bam if there is one or fail
            if (state->unaccounted_file == NULL) {
                if (tag) {
                    fprintf(stderr, "Read \"%s\" with unaccounted for tag \"%s\".\n", bam_get_qname(file_read), bam_aux2Z(tag));
                } else {
                    fprintf(stderr, "Read \"%s\" has no RG tag.\n", bam_get_qname(file_read));
                }
                bam_destroy1(file_read);
                return false;
            } else {
                if (sam_write1(state->unaccounted_file, state->unaccounted_header, file_read) < 0) {
                    print_error_errno("split", "Could not write to unaccounted output file");
                    bam_destroy1(file_read);
                    return false;
                }
            }
        }

        // Replace written read with the next one to process
        if ((r=sam_read1(state->merged_input_file, state->merged_input_header, file_read)) < 0) {
            // Nothing more to read?  Ignore this file in future
            bam_destroy1(file_read);
            file_read = NULL;
            if (r < -1) {
                print_error("split", "Could not read input record");
                return false;
            }
        }
    }

    return true;
}

static int cleanup_state(state_t* status, bool check_close)
{
    int ret = 0;

    if (!status) return 0;
    if (status->unaccounted_header) bam_hdr_destroy(status->unaccounted_header);
    if (status->unaccounted_file) {
        if (sam_close(status->unaccounted_file) < 0 && check_close) {
            print_error("split", "Error on closing unaccounted file");
            ret = -1;
        }
    }
    sam_close(status->merged_input_file);
    size_t i;
    for (i = 0; i < status->output_count; i++) {
        if (status->rg_output_header && status->rg_output_header[i])
            bam_hdr_destroy(status->rg_output_header[i]);
        if (status->rg_output_file && status->rg_output_file[i]) {
            if (sam_close(status->rg_output_file[i]) < 0 && check_close) {
                print_error("split", "Error on closing output file \"%s\"", status->rg_output_file_name[i]);
                ret = -1;
            }
        }
        if (status->rg_id) free(status->rg_id[i]);
        if (status->rg_output_file_name) free(status->rg_output_file_name[i]);
    }
    if (status->merged_input_header)
        bam_hdr_destroy(status->merged_input_header);
    free(status->rg_output_header);
    free(status->rg_output_file);
    free(status->rg_output_file_name);
    kh_destroy_c2i(status->rg_hash);
    free(status->rg_id);
    if (status->p.pool)
        hts_tpool_destroy(status->p.pool);
    free(status);

    return ret;
}

static void cleanup_opts(parsed_opts_t* opts)
{
    if (!opts) return;
    sam_global_args_free(&opts->ga);
    free(opts);
}

int main_split(int argc, char** argv)
{
    int ret = 1;
    char *arg_list = stringify_argv(argc+1, argv-1);
    parsed_opts_t* opts = parse_args(argc, argv);
    if (!opts) goto cleanup_opts;
    state_t* status = init(opts, arg_list);
    if (!status) goto cleanup_opts;

    if (!split(status)) {
        cleanup_state(status, false);
        goto cleanup_opts;
    }

    ret = cleanup_state(status, true);

cleanup_opts:
    cleanup_opts(opts);
    free(arg_list);

    return ret;
}