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sam_view.c
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sam_view.c
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/* sam_view.c -- SAM<->BAM<->CRAM conversion.
Copyright (C) 2009-2023 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 <getopt.h>
#include "htslib/sam.h"
#include "htslib/faidx.h"
#include "htslib/khash.h"
#include "htslib/kstring.h"
#include "htslib/thread_pool.h"
#include "htslib/hts_expr.h"
#include "samtools.h"
#include "sam_opts.h"
#include "bam.h" // for bam_get_library and bam_remove_B
#include "bedidx.h"
#include "sam_utils.h"
KHASH_SET_INIT_STR(str)
typedef khash_t(str) *strhash_t;
// This structure contains the settings for a samview run
typedef struct samview_settings {
strhash_t rghash;
strhash_t rnhash;
strhash_t tvhash;
int min_mapQ;
int rghash_discard; // 0 keep, 1 discard
int rnhash_discard; // 0 keep, 1 discard
// Described here in the same terms as the usage statement.
// The code however always negates to "reject if" keep if:
int flag_on; // keep if (FLAG & N) == N (all on)
int flag_off; // keep if (FLAG & N) == 0 (all off)
int flag_anyon; // keep if (FLAG & N) != 0 (any on)
int flag_alloff; // reject if (FLAG & N) == N (any off)
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;
char* tag;
hts_filter_t *filter;
int remove_flag;
int add_flag;
int unmap;
auxhash_t remove_tag;
auxhash_t keep_tag;
hts_idx_t *hts_idx;
sam_hdr_t *header;
samFile *in, *out, *un_out;
int64_t count;
int is_count;
char *fn_in, *fn_idx_in, *fn_out, *fn_fai, *fn_un_out, *fn_out_idx, *fn_un_out_idx;
int fetch_pairs, nreglist;
hts_reglist_t *reglist;
int sanitize;
int count_rf; // CRAM_OPT_REQUIRED_FIELDS for view -c
} samview_settings_t;
// Copied from htslib/sam.c.
// TODO: we need a proper interface to find the length of an aux tag,
// or at the very make exportable versions of these in htslib.
static inline int aux_type2size(uint8_t type)
{
switch (type) {
case 'A': case 'c': case 'C':
return 1;
case 's': case 'S':
return 2;
case 'i': case 'I': case 'f':
return 4;
case 'd':
return 8;
case 'Z': case 'H': case 'B':
return type;
default:
return 0;
}
}
// Copied from htslib/sam.c.
static inline uint8_t *skip_aux(uint8_t *s, uint8_t *end)
{
int size;
uint32_t n;
if (s >= end) return end;
size = aux_type2size(*s); ++s; // skip type
switch (size) {
case 'Z':
case 'H':
while (s < end && *s) ++s;
return s < end ? s + 1 : end;
case 'B':
if (end - s < 5) return NULL;
size = aux_type2size(*s); ++s;
n = le_to_u32(s);
s += 4;
if (size == 0 || end - s < size * n) return NULL;
return s + size * n;
case 0:
return NULL;
default:
if (end - s < size) return NULL;
return s + size;
}
}
// Returns 0 to indicate read should be output 1 otherwise,
// and -1 on error.
static int process_aln(const sam_hdr_t *h, bam1_t *b, samview_settings_t* settings)
{
if (settings->filter) {
int r = sam_passes_filter(h, b, settings->filter);
if (r < 0) // err
return -1;
if (r == 0) // filter-out
return 1;
}
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->flag_anyon && ((b->core.flag & settings->flag_anyon) == 0))
return 1;
if (!settings->multi_region && settings->bed && (b->core.tid < 0 || !bed_overlap(settings->bed, sam_hdr_tid2name(h, 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(str, settings->rghash, (char*)(s + 1));
if ((k == kh_end(settings->rghash)) != settings->rghash_discard)
return 1;
}
}
if (settings->tag) {
uint8_t *s = bam_aux_get(b, settings->tag);
if (s) {
if (settings->tvhash) {
char t[32], *val;
if (*s == 'i' || *s == 'I' || *s == 's' || *s == 'S' || *s == 'c' || *s == 'C') {
int ret = snprintf(t, 32, "%"PRId64, bam_aux2i(s));
if (ret > 0) val = t;
else return 1;
} else if (*s == 'A') {
t[0] = *(s+1);
t[1] = 0;
val = t;
} else {
val = (char *)(s+1);
}
khint_t k = kh_get(str, settings->tvhash, val);
if (k == kh_end(settings->tvhash)) return 1;
}
} else {
return 1;
}
}
if (settings->rnhash) {
const char* rn = bam_get_qname(b);
strhash_t h = settings->rnhash;
if (!rn && !settings->rnhash_discard)
return 1;
if ((kh_get(str, h, rn) == kh_end(h)) != settings->rnhash_discard)
return 1;
}
if (settings->library) {
const char *p = bam_get_library((sam_hdr_t*)h, b);
if (!p || strcmp(p, settings->library) != 0) return 1;
}
return 0;
}
static int adjust_tags(const sam_hdr_t *h, bam1_t *b,
samview_settings_t* settings) {
if (settings->keep_tag) {
uint8_t *s_from, *s_to, *end = b->data + b->l_data;
auxhash_t h = settings->keep_tag;
s_from = s_to = bam_get_aux(b);
while (s_from < end) {
int x = (int)s_from[0]<<8 | s_from[1];
uint8_t *s = skip_aux(s_from+2, end);
if (s == NULL) {
print_error("view", "malformed aux data for record \"%s\"",
bam_get_qname(b));
return -1;
}
if (kh_get(aux_exists, h, x) != kh_end(h) ) {
if (s_to != s_from) memmove(s_to, s_from, s - s_from);
s_to += s - s_from;
}
s_from = s;
}
b->l_data = s_to - b->data;
} else if (settings->remove_tag) {
uint8_t *s_from, *s_to, *end = b->data + b->l_data;
auxhash_t h = settings->remove_tag;
s_from = s_to = bam_get_aux(b);
while (s_from < end) {
int x = (int)s_from[0]<<8 | s_from[1];
uint8_t *s = skip_aux(s_from+2, end);
if (s == NULL) {
print_error("view", "malformed aux data for record \"%s\"",
bam_get_qname(b));
return -1;
}
if (kh_get(aux_exists, h, x) == kh_end(h) ) {
if (s_to != s_from) memmove(s_to, s_from, s - s_from);
s_to += s - s_from;
}
s_from = s;
}
b->l_data = s_to - b->data;
}
return 0;
}
static int usage(FILE *fp, int exit_status, int is_long_help);
static int populate_lookup_from_file(const char *subcmd, strhash_t lookup, char *fn)
{
FILE *fp;
char buf[1024];
int ret = 0;
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(str, lookup, 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 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(str);
if (settings->rghash == NULL) goto err;
} else if (settings->rghash_discard == 1) {
print_error("view", "cannot mix include and exclude read-group files in the same command line");
free(d);
return -1;
}
settings->rghash_discard = 0;
kh_put(str, 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_names_file(const char *subcmd, samview_settings_t *settings, char *fn)
{
if (settings->rnhash == NULL) {
settings->rnhash = kh_init(str);
if (settings->rnhash == NULL) {
perror(NULL);
return -1;
}
} else if ((settings->rnhash_discard == 0 && *fn == '^') ||
(settings->rnhash_discard == 1 && *fn != '^')) {
print_error("view", "cannot mix include and exclude read-name files in the same command line");
return -1;
}
settings->rnhash_discard = (*fn == '^');
return populate_lookup_from_file(subcmd, settings->rnhash,
fn + (*fn == '^'));
}
static int add_read_groups_file(const char *subcmd, samview_settings_t *settings, char *fn)
{
if (settings->rghash == NULL) {
settings->rghash = kh_init(str);
if (settings->rghash == NULL) {
perror(NULL);
return -1;
}
} else if ((settings->rghash_discard == 0 && *fn == '^') ||
(settings->rghash_discard == 1 && *fn != '^')) {
print_error("view", "cannot mix include and exclude read-group files in the same command line");
return -1;
}
settings->rghash_discard = (*fn == '^');
return populate_lookup_from_file(subcmd, settings->rghash,
fn + (*fn == '^'));
}
static int add_tag_value_single(const char *subcmd, samview_settings_t *settings, char *name)
{
char *d = strdup(name);
int ret = 0;
if (d == NULL) goto err;
if (settings->tvhash == NULL) {
settings->tvhash = kh_init(str);
if (settings->tvhash == NULL) goto err;
}
kh_put(str, settings->tvhash, d, &ret);
if (ret == -1) goto err;
if (ret == 0) free(d); /* Duplicate */
return 0;
err:
print_error(subcmd, "Couldn't add \"%s\" to tag values list: memory exhausted?", name);
free(d);
return -1;
}
static int add_tag_values_file(const char *subcmd, samview_settings_t *settings, char *fn)
{
if (settings->tvhash == NULL) {
settings->tvhash = kh_init(str);
if (settings->tvhash == NULL) {
perror(NULL);
return -1;
}
}
return populate_lookup_from_file(subcmd, settings->tvhash, fn);
}
static inline int check_sam_write1(samFile *fp, const sam_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 inline void change_flag(bam1_t *b, samview_settings_t *settings)
{
if (settings->add_flag)
b->core.flag |= settings->add_flag;
if (settings->remove_flag)
b->core.flag &= ~settings->remove_flag;
}
static int cmp_reglist_intervals(const void *aptr, const void *bptr)
{
hts_pair_pos_t *a = (hts_pair_pos_t*)aptr;
hts_pair_pos_t *b = (hts_pair_pos_t*)bptr;
if ( a->beg < b->beg ) return -1;
if ( a->beg > b->beg ) return 1;
if ( a->end < b->end ) return -1;
if ( a->end > b->end ) return 1;
return 0;
}
static int cmp_reglist_tids(const void *aptr, const void *bptr)
{
hts_reglist_t *a = (hts_reglist_t*)aptr;
hts_reglist_t *b = (hts_reglist_t*)bptr;
if ( b->tid==HTS_IDX_NOCOOR || a->tid < b->tid ) return -1;
if ( a->tid==HTS_IDX_NOCOOR || a->tid > b->tid ) return 1;
return 0;
}
static hts_reglist_t *_reglist_dup(sam_hdr_t *hdr, hts_reglist_t *src, int nsrc)
{
int i,j;
hts_reglist_t *dst = (hts_reglist_t*)calloc(nsrc,sizeof(hts_reglist_t));
if ( !dst ) {
print_error_errno("view", "[%s:%d] could not allocate region list"
,__FILE__ ,__LINE__);
return NULL;
}
for (i=0; i<nsrc; i++)
{
// Assume tid is not set correctly, reg is informative but may not point to a long-lived memory
dst[i].tid = sam_hdr_name2tid(hdr,src[i].reg);
dst[i].min_beg = src[i].min_beg;
dst[i].max_end = src[i].max_end;
dst[i].count = src[i].count;
dst[i].intervals = (hts_pair_pos_t*)malloc(sizeof(hts_pair_pos_t)*dst[i].count);
if ( !dst[i].intervals ) {
print_error_errno("view", "[%s:%d] could not allocate region list",
__FILE__, __LINE__);
goto fail;
}
for (j=0; j<dst[i].count; j++)
dst[i].intervals[j] = src[i].intervals[j];
}
qsort(dst,nsrc,sizeof(*dst),cmp_reglist_tids);
return dst;
fail:
for (j = 0; j < i; j++)
free(dst[j].intervals);
free(dst);
return NULL;
}
static inline int _reglist_find_tid(hts_reglist_t *reg, int nreg, int tid) // binary search
{
int i = -1, imin = 0, imax = nreg - 1;
while ( imin <= imax )
{
i = (imin+imax)/2;
if ( tid==HTS_IDX_NOCOOR || reg[i].tid < tid ) imin = i + 1;
else if ( reg[i].tid==HTS_IDX_NOCOOR || reg[i].tid > tid ) imax = i - 1;
else break;
}
if ( i<0 || reg[i].tid < tid ) i++; // not found, i will be the index of the inserted element
return i;
}
static int _reglist_push(hts_reglist_t **_reg, int *_nreg, int tid, hts_pos_t beg, hts_pos_t end)
{
hts_reglist_t *reg = *_reg;
int nreg = *_nreg;
int i = _reglist_find_tid(reg,nreg,tid);
if ( i>=nreg || reg[i].tid!=tid ) {
nreg++;
reg = (hts_reglist_t*)realloc(reg,sizeof(hts_reglist_t)*nreg);
if ( !reg ) {
print_error_errno("view", "[%s:%d] could not extend region list",
__FILE__, __LINE__);
return -1;
}
if ( i+1 < nreg )
memmove(reg + i + 1, reg + i, sizeof(hts_reglist_t)*(nreg - i - 1));
reg[i].reg = NULL;
reg[i].tid = tid;
reg[i].min_beg = beg;
reg[i].max_end = end;
reg[i].intervals = NULL;
reg[i].count = 0;
}
*_reg = reg;
*_nreg = nreg;
if ( reg[i].count > 0
&& reg[i].intervals[reg[i].count - 1].beg==beg
&& reg[i].intervals[reg[i].count - 1].end==end ) {
return 0;
}
hts_pair_pos_t *new_intervals = realloc(reg[i].intervals, sizeof(hts_pair_pos_t)*(reg[i].count + 1));
if (!new_intervals) {
print_error_errno("view", "[%s:%d] could not extend region list",
__FILE__, __LINE__);
return -1;
}
reg[i].intervals = new_intervals;
reg[i].intervals[reg[i].count].beg = beg;
reg[i].intervals[reg[i].count].end = end;
reg[i].count++;
return 0;
}
static void _reglist_merge(hts_reglist_t *reg, int nreg)
{
int i,j;
for (i=0; i<nreg; i++)
{
qsort(reg[i].intervals,reg[i].count,sizeof(*reg[i].intervals),cmp_reglist_intervals);
int k = 1;
for (j=1; j<reg[i].count; j++)
{
if ( reg[i].intervals[k-1].end < reg[i].intervals[j].beg )
{
if ( k < j ) reg[i].intervals[k] = reg[i].intervals[j];
k++;
continue;
}
if ( reg[i].intervals[k-1].end < reg[i].intervals[j].end ) reg[i].intervals[k-1].end = reg[i].intervals[j].end;
}
reg[i].count = k;
reg[i].max_end = reg[i].intervals[k-1].end;
}
}
hts_itr_multi_t *multi_region_init(samview_settings_t *conf, char **regs, int nregs)
{
hts_itr_multi_t *iter = NULL;
int filter_state = ALL;
if ( nregs ) {
int filter_op = 0;
conf->bed = bed_hash_regions(conf->bed, regs, 0, nregs, &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(conf->bed);
if ( !conf->bed) { // index is unavailable or no regions have been specified
print_error("view", "No regions or BED file have been provided. Aborting.");
return NULL;
}
int regcount = 0;
hts_reglist_t *reglist = bed_reglist(conf->bed, filter_state, ®count);
if (!reglist) {
print_error("view", "Region list is empty or could not be created. Aborting.");
return NULL;
}
if ( conf->fetch_pairs ) {
conf->reglist = _reglist_dup(conf->header,reglist,regcount);
if (!conf->reglist)
return NULL;
conf->nreglist = regcount;
}
iter = sam_itr_regions(conf->hts_idx, conf->header, reglist, regcount);
if ( !iter ) {
print_error("view", "Iterator could not be created. Aborting.");
return NULL;
}
return iter;
}
KHASH_SET_INIT_STR(names)
static int fetch_pairs_collect_mates(samview_settings_t *conf, hts_itr_multi_t *iter)
{
khint_t k;
int nunmap = 0, r = 0, nmates = 0, write_error = 0, retval = EXIT_FAILURE;
kh_names_t *mate_names = kh_init(names);
bam1_t *rec = bam_init1();
if (!mate_names) {
print_error_errno("view", "could not allocate mate names table");
goto out;
}
if (!rec) {
print_error_errno("view", "could not allocate bam record");
goto out;
}
while ((r =sam_itr_multi_next(conf->in, iter, rec))>=0) {
if ( (rec->core.flag & BAM_FPAIRED) == 0 ) continue;
if ( rec->core.mtid>=0 && bed_overlap(conf->bed, sam_hdr_tid2name(conf->header,rec->core.mtid), rec->core.mpos, rec->core.mpos) ) continue;
int p = process_aln(conf->header, rec, conf);
if (p < 0) goto out;
if (p == 1) continue;
nmates++;
k = kh_get(names,mate_names,bam_get_qname(rec));
if ( k == kh_end(mate_names) ) {
int ret = 0;
char *name_copy = strdup(bam_get_qname(rec));
if (!name_copy) {
print_error_errno("view", "[%s:%d] could not store sample name, %d elements", __FILE__,__LINE__,nmates);
goto out;
}
kh_put(names, mate_names, name_copy, &ret);
if ( ret<0 ) {
print_error_errno("view", "[%s:%d] could not store sample name, %d elements",__FILE__,__LINE__,nmates);
free(name_copy);
goto out;
}
}
if ( rec->core.mtid < 0 || (rec->core.flag & BAM_FMUNMAP) ) nunmap = 1;
if ( rec->core.mtid >= 0 ) {
if (_reglist_push(&conf->reglist, &conf->nreglist, rec->core.mtid, rec->core.mpos,rec->core.mpos+1) != 0)
goto out;
}
}
if (r < -1) {
print_error_errno("view", "error reading file \"%s\"", conf->fn_in);
goto out;
}
_reglist_merge(conf->reglist, conf->nreglist);
if ( nunmap ) {
if (_reglist_push(&conf->reglist,&conf->nreglist,HTS_IDX_NOCOOR,0,HTS_POS_MAX) != 0)
goto out;
}
hts_itr_multi_destroy(iter);
iter = sam_itr_regions(conf->hts_idx, conf->header, conf->reglist, conf->nreglist);
if ( !iter ) {
print_error_errno("view", "[%s:%d] iterator could not be created",__FILE__,__LINE__);
goto out;
}
while ((r = sam_itr_multi_next(conf->in, iter, rec))>=0) {
int drop = 1;
if (rec->core.tid >=0 &&
bed_overlap(conf->bed, sam_hdr_tid2name(conf->header,rec->core.tid), rec->core.pos, bam_endpos(rec))) drop = 0;
if ( drop ) {
k = kh_get(names,mate_names,bam_get_qname(rec));
if ( k != kh_end(mate_names) ) drop = 0;
}
int p = 0;
if (!drop && (p=process_aln(conf->header, rec, conf))== 0) {
if (adjust_tags(conf->header, rec, conf) != 0)
goto out;
if (check_sam_write1(conf->out, conf->header, rec, conf->fn_out,
&write_error) < 0)
goto out;
}
if (p < 0)
goto out;
}
if (r < -1) {
print_error_errno("view", "error reading file \"%s\"", conf->fn_in);
goto out;
}
retval = EXIT_SUCCESS;
out:
hts_itr_multi_destroy(iter);
hts_idx_destroy(conf->hts_idx); // destroy the BAM index
conf->hts_idx = NULL;
if (mate_names) {
// free khash keys
for (k = 0; k < kh_end(mate_names); ++k)
if ( kh_exist(mate_names,k) ) free((char*)kh_key(mate_names, k));
kh_destroy(names,mate_names);
}
bam_destroy1(rec);
return retval;
}
// Common code for processing and writing a record
static inline int process_one_record(samview_settings_t *conf, bam1_t *b,
int *write_error) {
if (conf->sanitize)
if (bam_sanitize(conf->header, b, conf->sanitize) < 0)
return -1;
int p;
if ((p = process_aln(conf->header, b, conf)) < 0) {
// error
return -1;
} else if (p == 0) {
// emit read
if (!conf->is_count) {
change_flag(b, conf);
if (adjust_tags(conf->header, b, conf) != 0)
return -1;
if (check_sam_write1(conf->out, conf->header,
b, conf->fn_out, write_error) < 0) {
return -1;
}
}
conf->count++;
} else if (conf->unmap) {
b->core.flag |= BAM_FUNMAP;
b->core.qual = 0;
b->core.isize = 0;
// remove CIGAR
if (b->core.n_cigar) {
memmove(bam_get_cigar(b), bam_get_seq(b),
b->data + b->l_data - bam_get_seq(b));
b->l_data -= 4*b->core.n_cigar;
b->core.n_cigar = 0;
}
if (check_sam_write1(conf->out, conf->header,
b, conf->fn_out, write_error) < 0) {
return -1;
}
} else {
if (conf->un_out) {
if (check_sam_write1(conf->un_out, conf->header,
b, conf->fn_un_out, write_error) < 0) {
return -1;
}
}
}
return 0;
}
static int stream_view(samview_settings_t *conf) {
bam1_t *b = bam_init1();
int write_error = 0, r, p = 0;
if (!b) {
print_error_errno("view", "could not allocate bam record");
return 1;
}
errno = 0; // prevent false error messages.
while ((r = sam_read1(conf->in, conf->header, b)) >= 0) {
if ((p = process_one_record(conf, b, &write_error)) < 0) break;
}
bam_destroy1(b);
if (r < -1 || p < 0) {
print_error_errno("view", "error reading file \"%s\"", conf->fn_in);
return 1;
}
return write_error;
}
static int multi_region_view(samview_settings_t *conf, hts_itr_multi_t *iter)
{
bam1_t *b = bam_init1();
int write_error = 0, result;
if (!b) {
print_error_errno("view", "could not allocate bam record");
return 1;
}
// fetch alignments
while ((result = sam_itr_multi_next(conf->in, iter, b)) >= 0) {
if (process_one_record(conf, b, &write_error) < 0) break;
}
hts_itr_multi_destroy(iter);
bam_destroy1(b);
if (result < -1) {
print_error("view", "retrieval of region #%d failed", iter->curr_tid);
return 1;
}
return write_error;
}
// Make mnemonic distinct values for longoption-only options
#define LONGOPT(c) ((c) + 128)
// Check for ".sam" filenames as sam_open_mode cannot distinguish between
// foo.sam and foo.unknown, both getting mode "".
static int is_sam(const char *fn) {
if (!fn)
return 0;
size_t l = strlen(fn);
return (l >= 4 && strcasecmp(fn + l-4, ".sam") == 0);
}
static void aux_list_free(samview_settings_t *settings) {
if (settings->keep_tag)
kh_destroy(aux_exists, settings->keep_tag);
if (settings->remove_tag)
kh_destroy(aux_exists, settings->remove_tag);
}
int main_samview(int argc, char *argv[])
{
samview_settings_t settings;
int c, is_header = 0, is_header_only = 0, ret = 0, compress_level = -1, has_index_file = 0, no_pg = 0;
FILE *fp_out = NULL;
char out_mode[6] = {0}, out_un_mode[6] = {0};
char *out_format = "";
char *arg_list = NULL;
sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
htsThreadPool p = {NULL, 0};
memset(&settings,0,sizeof(settings));
settings.subsam_frac = -1.0;
settings.count_rf = SAM_FLAG; // don't want 0, and this is quick
static const struct option lopts[] = {
SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 'T', '@'),
{"add-flags", required_argument, NULL, LONGOPT('a')},
{"bam", no_argument, NULL, 'b'},
{"count", no_argument, NULL, 'c'},
{"cram", no_argument, NULL, 'C'},
{"customised-index", no_argument, NULL, 'X'},
{"customized-index", no_argument, NULL, 'X'},
{"excl-flags", required_argument, NULL, 'F'},
{"exclude-flags", required_argument, NULL, 'F'},
{"expr", required_argument, NULL, 'e'},
{"expression", required_argument, NULL, 'e'},
{"fai-reference", required_argument, NULL, 't'},
{"fast", no_argument, NULL, '1'},
{"fetch-pairs", no_argument, NULL, 'P'},
{"header-only", no_argument, NULL, 'H'},
{"help", no_argument, NULL, LONGOPT('?')},
{"incl-flags", required_argument, NULL, LONGOPT('g')},
{"include-flags", required_argument, NULL, LONGOPT('g')},
{"rf", required_argument, NULL, LONGOPT('g')}, // aka incl-flags
{"keep-tag", required_argument, NULL, LONGOPT('x') },
{"library", required_argument, NULL, 'l'},
{"min-mapq", required_argument, NULL, 'q'},
{"min-MQ", required_argument, NULL, 'q'},
{"min-mq", required_argument, NULL, 'q'},
{"min-qlen", required_argument, NULL, 'm'},
{"no-header", no_argument, NULL, LONGOPT('H')},
{"no-PG", no_argument, NULL, LONGOPT('P')},
{"output", required_argument, NULL, 'o'},
{"output-unselected", required_argument, NULL, 'U'},
{"QNAME-file", required_argument, NULL, 'N'},
{"qname-file", required_argument, NULL, 'N'},
{"read-group", required_argument, NULL, 'r'},
{"read-group-file", required_argument, NULL, 'R'},
{"readgroup", required_argument, NULL, 'r'},
{"readgroup-file", required_argument, NULL, 'R'},
{"region-file", required_argument, NULL, LONGOPT('L')},
{"regions-file", required_argument, NULL, LONGOPT('L')},
{"remove-B", no_argument, NULL, 'B'},
{"remove-flags", required_argument, NULL, LONGOPT('r')},
{"remove-tag", required_argument, NULL, 'x'},
{"require-flags", required_argument, NULL, 'f'},
{"subsample", required_argument, NULL, LONGOPT('s')},
{"subsample-seed", required_argument, NULL, LONGOPT('S')},
{"tag", required_argument, NULL, 'd'},
{"tag-file", required_argument, NULL, 'D'},
{"target-file", required_argument, NULL, 'L'},
{"targets-file", required_argument, NULL, 'L'},
{"uncompressed", no_argument, NULL, 'u'},
{"unmap", no_argument, NULL, 'p'},
{"unoutput", required_argument, NULL, 'U'},
{"use-index", no_argument, NULL, 'M'},
{"with-header", no_argument, NULL, 'h'},
{"sanitize", required_argument, NULL, 'z'},
};
/* 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;
char *tmp;
while ((c = getopt_long(argc, argv,
"SbBcCt:h1Ho:O:q:f:F:G:ul:r:T:R:N:d:D:L:s:@:m:x:U:MXe:pPz:",
lopts, NULL)) >= 0) {
switch (c) {
case 's':
settings.subsam_seed = strtol(optarg, &tmp, 10);
if (tmp && *tmp == '.') {
settings.subsam_frac = strtod(tmp, &tmp);
if (*tmp) ret = 1;
} else {
ret = 1;
}
if (ret == 1) {
print_error("view", "Incorrect sampling argument \"%s\"", optarg);
goto view_end;
}
settings.count_rf |= SAM_QNAME;
break;
case LONGOPT('s'):
settings.subsam_frac = strtod(optarg, &tmp);
if (*tmp || settings.subsam_frac < 0.0 || settings.subsam_frac > 1.0) {
print_error("view", "Incorrect sampling argument \"%s\"", optarg);
goto view_end;
}
settings.count_rf |= SAM_QNAME;
break;
case LONGOPT('S'): settings.subsam_seed = atoi(optarg); break;
case 'm':
settings.min_qlen = atoi(optarg);
settings.count_rf |= SAM_SEQ;
break;
case 'c': settings.is_count = 1; break;
case 'S': break;
case 'b': out_format = "b"; break;
case 'C': out_format = "c"; break;
case 't': settings.fn_fai = strdup(optarg); break;
case 'h': is_header = 1; break;
case 'H': is_header_only = 1; break;
case LONGOPT('H'): is_header = is_header_only = 0; break;
case 'o': settings.fn_out = strdup(optarg); break;
case 'U': settings.fn_un_out = strdup(optarg); break;
case 'X': has_index_file = 1; break;
case 'f':
settings.flag_on |= bam_str2flag(optarg);
settings.count_rf |= SAM_FLAG | SAM_RNEXT;
break;
case 'F':
settings.flag_off |= bam_str2flag(optarg);
settings.count_rf |= SAM_FLAG | SAM_RNEXT;
break;
case LONGOPT('g'):
settings.flag_anyon |= bam_str2flag(optarg);
settings.count_rf |= SAM_FLAG | SAM_RNEXT;
break;
case 'G':
settings.flag_alloff |= bam_str2flag(optarg);
settings.count_rf |= SAM_FLAG | SAM_RNEXT;
break;
case 'q':
settings.min_mapQ = atoi(optarg);
settings.count_rf |= SAM_MAPQ;
break;
case 'u': compress_level = 0; break;
case '1': compress_level = 1; break;
case 'l':
settings.library = strdup(optarg);
settings.count_rf |= SAM_RGAUX;
break;
case 'p': settings.unmap = 1; break;
case 'P': settings.fetch_pairs = 1; settings.multi_region = 1; break;
case 'z':
if ((settings.sanitize = bam_sanitize_options(optarg)) < 0) {
ret = 1;
goto view_end;
}
break;
case LONGOPT('L'):
settings.multi_region = 1;
// fall through
case 'L':
if ((settings.bed = bed_read(optarg)) == NULL) {
print_error_errno("view", "Could not read file \"%s\"", optarg);
ret = 1;
goto view_end;
}
settings.count_rf |= SAM_POS | SAM_RNAME | SAM_CIGAR;
break;
case 'r':
if (add_read_group_single("view", &settings, optarg) != 0) {
ret = 1;
goto view_end;
}
settings.count_rf |= SAM_RGAUX;
break;
case 'R':
if (add_read_groups_file("view", &settings, optarg) != 0) {
ret = 1;
goto view_end;
}
settings.count_rf |= SAM_RGAUX;
break;
case 'N':
if (add_read_names_file("view", &settings, optarg) != 0) {
ret = 1;
goto view_end;
}
settings.count_rf |= SAM_QNAME;