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sam_view.c
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/* sam_view.c -- SAM<->BAM<->CRAM conversion.
Copyright (C) 2009-2017 Genome Research Ltd.
Portions copyright (C) 2009, 2011, 2012 Broad Institute.
Author: Heng Li <[email protected]>
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 <stdlib.h>
#include <string.h>
#include <strings.h>
#include <stdio.h>
#include <unistd.h>
#include <math.h>
#include <inttypes.h>
#include <stdbool.h>
#include <assert.h>
#include <getopt.h>
#include <ctype.h>
#include "htslib/sam.h"
#include "htslib/faidx.h"
#include "htslib/kstring.h"
#include "htslib/khash.h"
#include "htslib/klist.h"
#include "htslib/thread_pool.h"
#include "htslib/bgzf.h"
#include "samtools.h"
#include "sam_opts.h"
#include "bedidx.h"
#define DEFAULT_BARCODE_TAG "BC"
#define DEFAULT_QUALITY_TAG "QT"
KHASH_SET_INIT_STR(rg)
#define taglist_free(p)
KLIST_INIT(ktaglist, char*, taglist_free)
typedef khash_t(rg) *rghash_t;
// This structure contains the settings for a samview run
typedef struct samview_settings {
rghash_t rghash;
int min_mapQ;
int flag_on;
int flag_off;
int flag_alloff;
int min_qlen;
int remove_B;
uint32_t subsam_seed;
double subsam_frac;
char* library;
void* bed;
size_t remove_aux_len;
char** remove_aux;
int multi_region;
} samview_settings_t;
// TODO Add declarations of these to a viable htslib or samtools header
extern const char *bam_get_library(bam_hdr_t *header, const bam1_t *b);
extern int bam_remove_B(bam1_t *b);
extern char *samfaipath(const char *fn_ref);
// Returns 0 to indicate read should be output 1 otherwise
static int process_aln(const bam_hdr_t *h, bam1_t *b, samview_settings_t* settings)
{
if (settings->remove_B) bam_remove_B(b);
if (settings->min_qlen > 0) {
int k, qlen = 0;
uint32_t *cigar = bam_get_cigar(b);
for (k = 0; k < b->core.n_cigar; ++k)
if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP)
qlen += bam_cigar_oplen(cigar[k]);
if (qlen < settings->min_qlen) return 1;
}
if (b->core.qual < settings->min_mapQ || ((b->core.flag & settings->flag_on) != settings->flag_on) || (b->core.flag & settings->flag_off))
return 1;
if (settings->flag_alloff && ((b->core.flag & settings->flag_alloff) == settings->flag_alloff))
return 1;
if (!settings->multi_region && settings->bed && (b->core.tid < 0 || !bed_overlap(settings->bed, h->target_name[b->core.tid], b->core.pos, bam_endpos(b))))
return 1;
if (settings->subsam_frac > 0.) {
uint32_t k = __ac_Wang_hash(__ac_X31_hash_string(bam_get_qname(b)) ^ settings->subsam_seed);
if ((double)(k&0xffffff) / 0x1000000 >= settings->subsam_frac) return 1;
}
if (settings->rghash) {
uint8_t *s = bam_aux_get(b, "RG");
if (s) {
khint_t k = kh_get(rg, settings->rghash, (char*)(s + 1));
if (k == kh_end(settings->rghash)) return 1;
}
}
if (settings->library) {
const char *p = bam_get_library((bam_hdr_t*)h, b);
if (!p || strcmp(p, settings->library) != 0) return 1;
}
if (settings->remove_aux_len) {
size_t i;
for (i = 0; i < settings->remove_aux_len; ++i) {
uint8_t *s = bam_aux_get(b, settings->remove_aux[i]);
if (s) {
bam_aux_del(b, s);
}
}
}
return 0;
}
static char *drop_rg(char *hdtxt, rghash_t h, int *len)
{
char *p = hdtxt, *q, *r, *s;
kstring_t str;
memset(&str, 0, sizeof(kstring_t));
while (1) {
int toprint = 0;
q = strchr(p, '\n');
if (q == 0) q = p + strlen(p);
if (q - p < 3) break; // the line is too short; then stop
if (strncmp(p, "@RG\t", 4) == 0) {
int c;
khint_t k;
if ((r = strstr(p, "\tID:")) != 0) {
r += 4;
for (s = r; *s != '\0' && *s != '\n' && *s != '\t'; ++s);
c = *s; *s = '\0';
k = kh_get(rg, h, r);
*s = c;
if (k != kh_end(h)) toprint = 1;
}
} else toprint = 1;
if (toprint) {
kputsn(p, q - p, &str); kputc('\n', &str);
}
p = q + 1;
}
*len = str.l;
return str.s;
}
static int usage(FILE *fp, int exit_status, int is_long_help);
static int add_read_group_single(const char *subcmd, samview_settings_t *settings, char *name)
{
char *d = strdup(name);
int ret = 0;
if (d == NULL) goto err;
if (settings->rghash == NULL) {
settings->rghash = kh_init(rg);
if (settings->rghash == NULL) goto err;
}
kh_put(rg, settings->rghash, d, &ret);
if (ret == -1) goto err;
if (ret == 0) free(d); /* Duplicate */
return 0;
err:
print_error(subcmd, "Couldn't add \"%s\" to read group list: memory exhausted?", name);
free(d);
return -1;
}
static int add_read_groups_file(const char *subcmd, samview_settings_t *settings, char *fn)
{
FILE *fp;
char buf[1024];
int ret = 0;
if (settings->rghash == NULL) {
settings->rghash = kh_init(rg);
if (settings->rghash == NULL) {
perror(NULL);
return -1;
}
}
fp = fopen(fn, "r");
if (fp == NULL) {
print_error_errno(subcmd, "failed to open \"%s\" for reading", fn);
return -1;
}
while (ret != -1 && !feof(fp) && fscanf(fp, "%1023s", buf) > 0) {
char *d = strdup(buf);
if (d != NULL) {
kh_put(rg, settings->rghash, d, &ret);
if (ret == 0) free(d); /* Duplicate */
} else {
ret = -1;
}
}
if (ferror(fp)) ret = -1;
if (ret == -1) {
print_error_errno(subcmd, "failed to read \"%s\"", fn);
}
fclose(fp);
return (ret != -1) ? 0 : -1;
}
static inline int check_sam_write1(samFile *fp, const bam_hdr_t *h, const bam1_t *b, const char *fname, int *retp)
{
int r = sam_write1(fp, h, b);
if (r >= 0) return r;
if (fname) print_error_errno("view", "writing to \"%s\" failed", fname);
else print_error_errno("view", "writing to standard output failed");
*retp = EXIT_FAILURE;
return r;
}
static void check_sam_close(const char *subcmd, samFile *fp, const char *fname, const char *null_fname, int *retp)
{
int r = sam_close(fp);
if (r >= 0) return;
// TODO Need error infrastructure so we can print a message instead of r
if (fname) print_error(subcmd, "error closing \"%s\": %d", fname, r);
else print_error(subcmd, "error closing %s: %d", null_fname, r);
*retp = EXIT_FAILURE;
}
int main_samview(int argc, char *argv[])
{
int c, is_header = 0, is_header_only = 0, ret = 0, compress_level = -1, is_count = 0;
int64_t count = 0;
samFile *in = 0, *out = 0, *un_out=0;
FILE *fp_out = NULL;
bam_hdr_t *header = NULL;
char out_mode[5], out_un_mode[5], *out_format = "";
char *fn_in = 0, *fn_out = 0, *fn_list = 0, *q, *fn_un_out = 0;
sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
htsThreadPool p = {NULL, 0};
int filter_state = ALL, filter_op = 0;
int result;
samview_settings_t settings = {
.rghash = NULL,
.min_mapQ = 0,
.flag_on = 0,
.flag_off = 0,
.flag_alloff = 0,
.min_qlen = 0,
.remove_B = 0,
.subsam_seed = 0,
.subsam_frac = -1.,
.library = NULL,
.bed = NULL,
.multi_region = 0
};
static const struct option lopts[] = {
SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 'T', '@'),
{ NULL, 0, NULL, 0 }
};
/* parse command-line options */
strcpy(out_mode, "w");
strcpy(out_un_mode, "w");
if (argc == 1 && isatty(STDIN_FILENO))
return usage(stdout, EXIT_SUCCESS, 0);
// Suppress complaints about '?' being an unrecognised option. Without
// this we have to put '?' in the options list, which makes it hard to
// tell a bad long option from the use of '-?' (both return '?' and
// set optopt to '\0').
opterr = 0;
while ((c = getopt_long(argc, argv,
"SbBcCt:h1Ho:O:q:f:F:G:ul:r:T:R:L:s:@:m:x:U:M",
lopts, NULL)) >= 0) {
switch (c) {
case 's':
if ((settings.subsam_seed = strtol(optarg, &q, 10)) != 0) {
// Convert likely user input 0,1,2,... to pseudo-random
// values with more entropy and more bits set
srand(settings.subsam_seed);
settings.subsam_seed = rand();
}
if (q && *q == '.') {
settings.subsam_frac = strtod(q, &q);
if (*q) ret = 1;
} else {
ret = 1;
}
if (ret == 1) {
print_error("view", "Incorrect sampling argument \"%s\"", optarg);
goto view_end;
}
break;
case 'm': settings.min_qlen = atoi(optarg); break;
case 'c': is_count = 1; break;
case 'S': break;
case 'b': out_format = "b"; break;
case 'C': out_format = "c"; break;
case 't': fn_list = strdup(optarg); break;
case 'h': is_header = 1; break;
case 'H': is_header_only = 1; break;
case 'o': fn_out = strdup(optarg); break;
case 'U': fn_un_out = strdup(optarg); break;
case 'f': settings.flag_on |= strtol(optarg, 0, 0); break;
case 'F': settings.flag_off |= strtol(optarg, 0, 0); break;
case 'G': settings.flag_alloff |= strtol(optarg, 0, 0); break;
case 'q': settings.min_mapQ = atoi(optarg); break;
case 'u': compress_level = 0; break;
case '1': compress_level = 1; break;
case 'l': settings.library = strdup(optarg); break;
case 'L':
if ((settings.bed = bed_read(optarg)) == NULL) {
print_error_errno("view", "Could not read file \"%s\"", optarg);
ret = 1;
goto view_end;
}
break;
case 'r':
if (add_read_group_single("view", &settings, optarg) != 0) {
ret = 1;
goto view_end;
}
break;
case 'R':
if (add_read_groups_file("view", &settings, optarg) != 0) {
ret = 1;
goto view_end;
}
break;
/* REMOVED as htslib doesn't support this
//case 'x': out_format = "x"; break;
//case 'X': out_format = "X"; break;
*/
case '?':
if (optopt == '?') { // '-?' appeared on command line
return usage(stdout, EXIT_SUCCESS, 1);
} else {
if (optopt) { // Bad short option
print_error("view", "invalid option -- '%c'", optopt);
} else { // Bad long option
// Do our best. There is no good solution to finding
// out what the bad option was.
// See, e.g. https://stackoverflow.com/questions/2723888/where-does-getopt-long-store-an-unrecognized-option
if (optind > 0 && strncmp(argv[optind - 1], "--", 2) == 0) {
print_error("view", "unrecognised option '%s'",
argv[optind - 1]);
}
}
return usage(stderr, EXIT_FAILURE, 0);
}
case 'B': settings.remove_B = 1; break;
case 'x':
{
if (strlen(optarg) != 2) {
fprintf(stderr, "main_samview: Error parsing -x auxiliary tags should be exactly two characters long.\n");
return usage(stderr, EXIT_FAILURE, 0);
}
settings.remove_aux = (char**)realloc(settings.remove_aux, sizeof(char*) * (++settings.remove_aux_len));
settings.remove_aux[settings.remove_aux_len-1] = optarg;
}
break;
case 'M': settings.multi_region = 1; break;
default:
if (parse_sam_global_opt(c, optarg, lopts, &ga) != 0)
return usage(stderr, EXIT_FAILURE, 0);
break;
}
}
if (compress_level >= 0 && !*out_format) out_format = "b";
if (is_header_only) is_header = 1;
// File format auto-detection first
if (fn_out) sam_open_mode(out_mode+1, fn_out, NULL);
if (fn_un_out) sam_open_mode(out_un_mode+1, fn_un_out, NULL);
// Overridden by manual -b, -C
if (*out_format)
out_mode[1] = out_un_mode[1] = *out_format;
out_mode[2] = out_un_mode[2] = '\0';
// out_(un_)mode now 1 or 2 bytes long, followed by nul.
if (compress_level >= 0) {
char tmp[2];
tmp[0] = compress_level + '0'; tmp[1] = '\0';
strcat(out_mode, tmp);
strcat(out_un_mode, tmp);
}
if (argc == optind && isatty(STDIN_FILENO)) {
print_error("view", "No input provided or missing option argument.");
return usage(stderr, EXIT_FAILURE, 0); // potential memory leak...
}
fn_in = (optind < argc)? argv[optind] : "-";
// generate the fn_list if necessary
if (fn_list == 0 && ga.reference) fn_list = samfaipath(ga.reference);
// open file handlers
if ((in = sam_open_format(fn_in, "r", &ga.in)) == 0) {
print_error_errno("view", "failed to open \"%s\" for reading", fn_in);
ret = 1;
goto view_end;
}
if (fn_list) {
if (hts_set_fai_filename(in, fn_list) != 0) {
fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", fn_list);
ret = 1;
goto view_end;
}
}
if ((header = sam_hdr_read(in)) == 0) {
fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", fn_in);
ret = 1;
goto view_end;
}
if (settings.rghash) { // FIXME: I do not know what "bam_header_t::n_text" is for...
char *tmp;
int l;
tmp = drop_rg(header->text, settings.rghash, &l);
free(header->text);
header->text = tmp;
header->l_text = l;
}
if (!is_count) {
if ((out = sam_open_format(fn_out? fn_out : "-", out_mode, &ga.out)) == 0) {
print_error_errno("view", "failed to open \"%s\" for writing", fn_out? fn_out : "standard output");
ret = 1;
goto view_end;
}
if (fn_list) {
if (hts_set_fai_filename(out, fn_list) != 0) {
fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", fn_list);
ret = 1;
goto view_end;
}
}
if (*out_format || is_header ||
out_mode[1] == 'b' || out_mode[1] == 'c' ||
(ga.out.format != sam && ga.out.format != unknown_format)) {
if (sam_hdr_write(out, header) != 0) {
fprintf(stderr, "[main_samview] failed to write the SAM header\n");
ret = 1;
goto view_end;
}
}
if (fn_un_out) {
if ((un_out = sam_open_format(fn_un_out, out_un_mode, &ga.out)) == 0) {
print_error_errno("view", "failed to open \"%s\" for writing", fn_un_out);
ret = 1;
goto view_end;
}
if (fn_list) {
if (hts_set_fai_filename(un_out, fn_list) != 0) {
fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", fn_list);
ret = 1;
goto view_end;
}
}
if (*out_format || is_header ||
out_un_mode[1] == 'b' || out_un_mode[1] == 'c' ||
(ga.out.format != sam && ga.out.format != unknown_format)) {
if (sam_hdr_write(un_out, header) != 0) {
fprintf(stderr, "[main_samview] failed to write the SAM header\n");
ret = 1;
goto view_end;
}
}
}
}
else {
if (fn_out) {
fp_out = fopen(fn_out, "w");
if (fp_out == NULL) {
print_error_errno("view", "can't create \"%s\"", fn_out);
ret = EXIT_FAILURE;
goto view_end;
}
}
}
if (ga.nthreads > 1) {
if (!(p.pool = hts_tpool_init(ga.nthreads))) {
fprintf(stderr, "Error creating thread pool\n");
ret = 1;
goto view_end;
}
hts_set_opt(in, HTS_OPT_THREAD_POOL, &p);
if (out) hts_set_opt(out, HTS_OPT_THREAD_POOL, &p);
}
if (is_header_only) goto view_end; // no need to print alignments
if (settings.multi_region) {
if (optind < argc - 1) { //regions have been specified in the command line
settings.bed = bed_hash_regions(settings.bed, argv, optind+1, argc, &filter_op); //insert(1) or filter out(0) the regions from the command line in the same hash table as the bed file
if (!filter_op)
filter_state = FILTERED;
} else {
bed_unify(settings.bed);
}
bam1_t *b = bam_init1();
if (settings.bed == NULL) { // index is unavailable or no regions have been specified
fprintf(stderr, "[main_samview] no regions or BED file have been provided. Aborting.\n");
} else {
hts_idx_t *idx = sam_index_load(in, fn_in); // load index
if (idx != NULL) {
int regcount = 0;
hts_reglist_t *reglist = bed_reglist(settings.bed, filter_state, ®count);
if(reglist) {
hts_itr_multi_t *iter = sam_itr_regions(idx, header, reglist, regcount);
if (iter) {
// fetch alignments
while ((result = sam_itr_multi_next(in, iter, b)) >= 0) {
if (!process_aln(header, b, &settings)) {
if (!is_count) { if (check_sam_write1(out, header, b, fn_out, &ret) < 0) break; }
count++;
} else {
if (un_out) { if (check_sam_write1(un_out, header, b, fn_un_out, &ret) < 0) break; }
}
}
if (result < -1) {
fprintf(stderr, "[main_samview] retrieval of region %d failed due to truncated file or corrupt BAM index file\n", iter->curr_tid);
ret = 1;
}
hts_itr_multi_destroy(iter);
} else {
fprintf(stderr, "[main_samview] iterator could not be created. Aborting.\n");
}
} else {
fprintf(stderr, "[main_samview] region list is empty or could not be created. Aborting.\n");
}
hts_idx_destroy(idx); // destroy the BAM index
} else {
fprintf(stderr, "[main_samview] random alignment retrieval only works for indexed BAM or CRAM files.\n");
}
}
bam_destroy1(b);
} else {
if (optind + 1 >= argc) { // convert/print the entire file
bam1_t *b = bam_init1();
int r;
while ((r = sam_read1(in, header, b)) >= 0) { // read one alignment from `in'
if (!process_aln(header, b, &settings)) {
if (!is_count) { if (check_sam_write1(out, header, b, fn_out, &ret) < 0) break; }
count++;
} else {
if (un_out) { if (check_sam_write1(un_out, header, b, fn_un_out, &ret) < 0) break; }
}
}
if (r < -1) {
fprintf(stderr, "[main_samview] truncated file.\n");
ret = 1;
}
bam_destroy1(b);
} else { // retrieve alignments in specified regions
int i;
bam1_t *b;
hts_idx_t *idx = sam_index_load(in, fn_in); // load index
if (idx == 0) { // index is unavailable
fprintf(stderr, "[main_samview] random alignment retrieval only works for indexed BAM or CRAM files.\n");
ret = 1;
goto view_end;
}
b = bam_init1();
for (i = optind + 1; i < argc; ++i) {
int result;
hts_itr_t *iter = sam_itr_querys(idx, header, argv[i]); // parse a region in the format like `chr2:100-200'
if (iter == NULL) { // region invalid or reference name not found
int beg, end;
if (hts_parse_reg(argv[i], &beg, &end))
fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);
else
fprintf(stderr, "[main_samview] region \"%s\" could not be parsed. Continue anyway.\n", argv[i]);
continue;
}
// fetch alignments
while ((result = sam_itr_next(in, iter, b)) >= 0) {
if (!process_aln(header, b, &settings)) {
if (!is_count) { if (check_sam_write1(out, header, b, fn_out, &ret) < 0) break; }
count++;
} else {
if (un_out) { if (check_sam_write1(un_out, header, b, fn_un_out, &ret) < 0) break; }
}
}
hts_itr_destroy(iter);
if (result < -1) {
fprintf(stderr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]);
ret = 1;
break;
}
}
bam_destroy1(b);
hts_idx_destroy(idx); // destroy the BAM index
}
}
view_end:
if (is_count && ret == 0) {
if (fprintf(fn_out? fp_out : stdout, "%" PRId64 "\n", count) < 0) {
if (fn_out) print_error_errno("view", "writing to \"%s\" failed", fn_out);
else print_error_errno("view", "writing to standard output failed");
ret = EXIT_FAILURE;
}
}
// close files, free and return
if (in) check_sam_close("view", in, fn_in, "standard input", &ret);
if (out) check_sam_close("view", out, fn_out, "standard output", &ret);
if (un_out) check_sam_close("view", un_out, fn_un_out, "file", &ret);
if (fp_out) fclose(fp_out);
free(fn_list); free(fn_out); free(settings.library); free(fn_un_out);
sam_global_args_free(&ga);
if ( header ) bam_hdr_destroy(header);
if (settings.bed) bed_destroy(settings.bed);
if (settings.rghash) {
khint_t k;
for (k = 0; k < kh_end(settings.rghash); ++k)
if (kh_exist(settings.rghash, k)) free((char*)kh_key(settings.rghash, k));
kh_destroy(rg, settings.rghash);
}
if (settings.remove_aux_len) {
free(settings.remove_aux);
}
if (p.pool)
hts_tpool_destroy(p.pool);
return ret;
}
static int usage(FILE *fp, int exit_status, int is_long_help)
{
fprintf(fp,
"\n"
"Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]\n"
"\n"
"Options:\n"
// output options
" -b output BAM\n"
" -C output CRAM (requires -T)\n"
" -1 use fast BAM compression (implies -b)\n"
" -u uncompressed BAM output (implies -b)\n"
" -h include header in SAM output\n"
" -H print SAM header only (no alignments)\n"
" -c print only the count of matching records\n"
" -o FILE output file name [stdout]\n"
" -U FILE output reads not selected by filters to FILE [null]\n"
// extra input
" -t FILE FILE listing reference names and lengths (see long help) [null]\n"
// read filters
" -L FILE only include reads overlapping this BED FILE [null]\n"
" -r STR only include reads in read group STR [null]\n"
" -R FILE only include reads with read group listed in FILE [null]\n"
" -q INT only include reads with mapping quality >= INT [0]\n"
" -l STR only include reads in library STR [null]\n"
" -m INT only include reads with number of CIGAR operations consuming\n"
" query sequence >= INT [0]\n"
" -f INT only include reads with all of the FLAGs in INT present [0]\n" // F&x == x
" -F INT only include reads with none of the FLAGS in INT present [0]\n" // F&x == 0
" -G INT only EXCLUDE reads with all of the FLAGs in INT present [0]\n" // !(F&x == x)
" -s FLOAT subsample reads (given INT.FRAC option value, 0.FRAC is the\n"
" fraction of templates/read pairs to keep; INT part sets seed)\n"
" -M use the multi-region iterator (increases the speed, removes\n"
" duplicates and outputs the reads as they are ordered in the file)\n"
// read processing
" -x STR read tag to strip (repeatable) [null]\n"
" -B collapse the backward CIGAR operation\n"
// general options
" -? print long help, including note about region specification\n"
" -S ignored (input format is auto-detected)\n");
sam_global_opt_help(fp, "-.O.T@");
fprintf(fp, "\n");
if (is_long_help)
fprintf(fp,
"Notes:\n"
"\n"
"1. This command now auto-detects the input format (BAM/CRAM/SAM).\n"
" Further control over the CRAM format can be specified by using the\n"
" --output-fmt-option, e.g. to specify the number of sequences per slice\n"
" and to use avoid reference based compression:\n"
"\n"
"\tsamtools view -C --output-fmt-option seqs_per_slice=5000 \\\n"
"\t --output-fmt-option no_ref -o out.cram in.bam\n"
"\n"
" Options can also be specified as a comma separated list within the\n"
" --output-fmt value too. For example this is equivalent to the above\n"
"\n"
"\tsamtools view --output-fmt cram,seqs_per_slice=5000,no_ref \\\n"
"\t -o out.cram in.bam\n"
"\n"
"2. The file supplied with `-t' is SPACE/TAB delimited with the first\n"
" two fields of each line consisting of the reference name and the\n"
" corresponding sequence length. The `.fai' file generated by \n"
" `samtools faidx' is suitable for use as this file. This may be an\n"
" empty file if reads are unaligned.\n"
"\n"
"3. SAM->BAM conversion: samtools view -bT ref.fa in.sam.gz\n"
"\n"
"4. BAM->SAM conversion: samtools view -h in.bam\n"
"\n"
"5. A region should be presented in one of the following formats:\n"
" `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n"
" specified, the input alignment file must be a sorted and indexed\n"
" alignment (BAM/CRAM) file.\n"
"\n"
"6. Option `-u' is preferred over `-b' when the output is piped to\n"
" another samtools command.\n"
"\n");
return exit_status;
}
int main_import(int argc, char *argv[])
{
int argc2, ret;
char **argv2;
if (argc != 4) {
fprintf(stderr, "Usage: samtools import <in.ref_list> <in.sam> <out.bam>\n");
return 1;
}
argc2 = 6;
argv2 = calloc(6, sizeof(char*));
argv2[0] = "import", argv2[1] = "-o", argv2[2] = argv[3], argv2[3] = "-bt", argv2[4] = argv[1], argv2[5] = argv[2];
ret = main_samview(argc2, argv2);
free(argv2);
return ret;
}
int8_t seq_comp_table[16] = { 0, 8, 4, 12, 2, 10, 6, 14, 1, 9, 5, 13, 3, 11, 7, 15 };
static const char *copied_tags[] = { "RG", "BC", "QT", NULL };
static void bam2fq_usage(FILE *to, const char *command)
{
int fq = strcasecmp("fastq", command) == 0 || strcasecmp("bam2fq", command) == 0;
fprintf(to,
"Usage: samtools %s [options...] <in.bam>\n", command);
fprintf(to,
"Options:\n"
" -0 FILE write reads designated READ_OTHER to FILE\n"
" -1 FILE write reads designated READ1 to FILE\n"
" -2 FILE write reads designated READ2 to FILE\n"
" note: if a singleton file is specified with -s, only\n"
" paired reads will be written to the -1 and -2 files.\n"
" -f INT only include reads with all of the FLAGs in INT present [0]\n" // F&x == x
" -F INT only include reads with none of the FLAGS in INT present [0]\n" // F&x == 0
" -G INT only EXCLUDE reads with all of the FLAGs in INT present [0]\n" // !(F&x == x)
" -n don't append /1 and /2 to the read name\n"
" -N always append /1 and /2 to the read name\n");
if (fq) fprintf(to,
" -O output quality in the OQ tag if present\n");
fprintf(to,
" -s FILE write singleton reads designated READ1 or READ2 to FILE\n"
" -t copy RG, BC and QT tags to the %s header line\n",
fq ? "FASTQ" : "FASTA");
fprintf(to,
" -T TAGLIST copy arbitrary tags to the %s header line\n",
fq ? "FASTQ" : "FASTA");
if (fq) fprintf(to,
" -v INT default quality score if not given in file [1]\n"
" -i add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)\n"
" -c compression level [0..9] to use when creating gz or bgzf fastq files [1]\n"
" --i1 FILE write first index reads to FILE\n"
" --i2 FILE write second index reads to FILE\n"
" --barcode-tag TAG Barcode tag [default: " DEFAULT_BARCODE_TAG "]\n"
" --quality-tag TAG Quality tag [default: " DEFAULT_QUALITY_TAG "]\n"
" --index-format STR How to parse barcode and quality tags\n\n");
sam_global_opt_help(to, "-.--.@");
fprintf(to,
"\n"
"Reads are designated READ1 if FLAG READ1 is set and READ2 is not set.\n"
"Reads are designated READ2 if FLAG READ1 is not set and READ2 is set.\n"
"Reads are designated READ_OTHER if FLAGs READ1 and READ2 are either both set\n"
"or both unset.\n"
"Run 'samtools flags' for more information on flag codes and meanings.\n");
fprintf(to,
"\n"
"The index-format string describes how to parse the barcode and quality tags, for example:\n"
" i14i8 the first 14 characters are index 1, the next 8 characters are index 2\n"
" n8i14 ignore the first 8 characters, and use the next 14 characters for index 1\n"
"If the tag contains a separator, then the numeric part can be replaced with '*' to mean\n"
"'read until the separator or end of tag', for example:\n"
" n*i* ignore the left part of the tag until the separator, then use the second part\n"
" of the tag as index 1\n");
fprintf(to,
"\n"
"Examples:\n"
" To get just the paired reads in separate files, use:\n"
" samtools %s -1 paired1.%s -2 paired2.%s -0 /dev/null -s /dev/null -n -F 0x900 in.bam\n"
"\n To get all non-supplementary/secondary reads in a single file, redirect the output:\n"
" samtools %s -F 0x900 in.bam > all_reads.%s\n",
command, fq ? "fq" : "fa", fq ? "fq" : "fa",
command, fq ? "fq" : "fa");
}
typedef enum { READ_UNKNOWN = 0, READ_1 = 1, READ_2 = 2 } readpart;
typedef enum { FASTA, FASTQ } fastfile;
typedef struct bam2fq_opts {
char *fnse;
char *fnr[3];
char *fn_input; // pointer to input filename in argv do not free
bool has12, has12always, use_oq, copy_tags, illumina_tag;
int flag_on, flag_off, flag_alloff;
sam_global_args ga;
fastfile filetype;
int def_qual;
char *barcode_tag;
char *quality_tag;
char *index_file[2];
char *index_format;
char *extra_tags;
char compression_level;
} bam2fq_opts_t;
typedef struct bam2fq_state {
samFile *fp;
BGZF *fpse;
BGZF *fpr[3];
BGZF *fpi[2];
BGZF *hstdout;
bam_hdr_t *h;
bool has12, use_oq, copy_tags, illumina_tag;
int flag_on, flag_off, flag_alloff;
fastfile filetype;
int def_qual;
klist_t(ktaglist) *taglist;
char *index_sequence;
char compression_level;
htsThreadPool p;
} bam2fq_state_t;
/*
* Get and decode the read from a BAM record.
*
* TODO: htslib really needs an interface for this. Consider this or perhaps
* bam_get_seq_str (current vs original orientation) and bam_get_qual_str
* functions as string formatted equivalents to bam_get_{seq,qual}?
*/
/*
* Reverse a string in place.
* From http://stackoverflow.com/questions/8534274/is-the-strrev-function-not-available-in-linux.
* Author Sumit-naik: http://stackoverflow.com/users/4590926/sumit-naik
*/
static char *reverse(char *str)
{
int i = strlen(str)-1,j=0;
char ch;
while (i>j) {
ch = str[i];
str[i]= str[j];
str[j] = ch;
i--;
j++;
}
return str;
}
/* return the read, reverse complemented if necessary */
static char *get_read(const bam1_t *rec)
{
int len = rec->core.l_qseq + 1;
char *read = calloc(1, len);
char *seq = (char *)bam_get_seq(rec);
int n;
if (!read) return NULL;
for (n=0; n < rec->core.l_qseq; n++) {
if (rec->core.flag & BAM_FREVERSE) read[n] = seq_nt16_str[seq_comp_table[bam_seqi(seq,n)]];
else read[n] = seq_nt16_str[bam_seqi(seq,n)];
}
if (rec->core.flag & BAM_FREVERSE) reverse(read);
return read;
}
/*
* get and decode the quality from a BAM record
*/
static int get_quality(const bam1_t *rec, char **qual_out)
{
char *quality = calloc(1, rec->core.l_qseq + 1);
char *q = (char *)bam_get_qual(rec);
int n;
if (!quality) return -1;
if (*q == '\xff') {
free(quality);
*qual_out = NULL;
return 0;
}
for (n=0; n < rec->core.l_qseq; n++) {
quality[n] = q[n]+33;
}
if (rec->core.flag & BAM_FREVERSE) reverse(quality);
*qual_out = quality;
return 0;
}
//
// End of htslib complaints
//
static readpart which_readpart(const bam1_t *b)
{
if ((b->core.flag & BAM_FREAD1) && !(b->core.flag & BAM_FREAD2)) {
return READ_1;
} else if ((b->core.flag & BAM_FREAD2) && !(b->core.flag & BAM_FREAD1)) {
return READ_2;
} else {
return READ_UNKNOWN;
}
}
/*
* parse the length part from the index-format string
*/
static int getLength(char **s)
{
int n = 0;
while (**s) {
if (**s == '*') { n=-1; (*s)++; break; }
if ( !isdigit(**s)) break;
n = n*10 + ((**s)-'0');
(*s)++;
}
return n;
}
static bool copy_tag(const char *tag, const bam1_t *rec, kstring_t *linebuf)
{
uint8_t *s = bam_aux_get(rec, tag);
if (s) {
char aux_type = *s;
switch (aux_type) {
case 'C':
case 'S': aux_type = 'I'; break;
case 'c':
case 's': aux_type = 'i'; break;
case 'd': aux_type = 'f'; break;
}
// Ensure space. Need 6 chars + length of tag. Max length of
// i is 16, A is 21, B currently 26, Z is unknown, so
// have to check that one later.
if (ks_resize(linebuf, ks_len(linebuf) + 64) < 0) return false;
kputc('\t', linebuf);
kputsn(tag, 2, linebuf);
kputc(':', linebuf);
kputc(aux_type=='I'? 'i': aux_type, linebuf);
kputc(':', linebuf);
switch (aux_type) {
case 'H':
case 'Z':
if (kputs(bam_aux2Z(s), linebuf) < 0) return false;
break;
case 'i': kputw(bam_aux2i(s), linebuf); break;
case 'I': kputuw(bam_aux2i(s), linebuf); break;
case 'A': kputc(bam_aux2A(s), linebuf); break;
case 'f': kputd(bam_aux2f(s), linebuf); break;
case 'B': kputs("*** Unhandled aux type ***", linebuf); return false;
default: kputs("*** Unknown aux type ***", linebuf); return false;
}
}
return true;
}
static int insert_index_sequence_into_linebuf(char *index_sequence, kstring_t *linebuf, bam1_t *rec)
{
if (!index_sequence) return 0;
kstring_t new = {0,0,NULL};
if (linebuf->s) {
char *s = strchr(linebuf->s, '\n');
if (s) {