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bam_markdup.c
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bam_markdup.c
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/* bam_markdup.c -- Mark duplicates from a coord sorted file that has gone
through fixmates with the mate scoring option on.
Copyright (C) 2017-2023 Genome Research Ltd.
Author: Andrew Whitwham <[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 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
Estimate library size derived from Picard DuplicationMetrics.java
Copyright (c) 2009,2018 The Broad Institute. MIT license.
*/
#include <config.h>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <unistd.h>
#include <ctype.h>
#include <time.h>
#include <sys/stat.h>
#include <math.h>
#include <regex.h>
#include "htslib/thread_pool.h"
#include "htslib/sam.h"
#include "sam_opts.h"
#include "samtools.h"
#include "htslib/khash.h"
#include "htslib/klist.h"
#include "htslib/kstring.h"
#include "tmp_file.h"
#include "bam.h"
typedef struct {
samFile *in;
samFile *out;
char *prefix;
int remove_dups;
int32_t max_length;
int do_stats;
int supp;
int tag;
int opt_dist;
int no_pg;
int clear;
int mode;
int write_index;
int include_fails;
int check_chain;
char *stats_file;
char *arg_list;
char *out_fn;
regex_t *rgx;
int rgx_x;
int rgx_y;
int rgx_t;
char *barcode;
regex_t *bc_rgx;
int read_groups;
int json;
int dc;
} md_param_t;
typedef struct {
hts_pos_t this_coord;
hts_pos_t other_coord;
int32_t this_ref;
int32_t other_ref;
int32_t barcode;
int32_t read_group;
int8_t single;
int8_t leftmost;
int8_t orientation;
} key_data_t;
typedef struct read_queue_s {
key_data_t pair_key;
key_data_t single_key;
bam1_t *b;
struct read_queue_s *duplicate;
struct read_queue_s *original;
int dc;
hts_pos_t pos;
int dup_checked;
int read_group;
} read_queue_t;
typedef struct {
read_queue_t *p;
} in_hash_t;
typedef struct {
char *name;
char type;
int read_group;
} dup_map_t;
typedef struct {
bam1_t *b;
int64_t score;
int64_t mate_score;
long x;
long y;
int opt;
int beg;
int end;
int len;
} check_t;
typedef struct {
check_t *c;
size_t size;
size_t length;
} check_list_t;
typedef struct {
long reading;
long writing;
long excluded;
long duplicate;
long single;
long pair;
long single_dup;
long examined;
long optical;
long single_optical;
long np_duplicate;
long np_opt_duplicate;
} stats_block_t;
static khint32_t do_hash(unsigned char *key, khint32_t len);
static khint_t hash_key(key_data_t key) {
int i = 0;
khint_t hash;
if (key.single) {
unsigned char sig[21];
memcpy(sig + i, &key.this_ref, 4); i += 4;
memcpy(sig + i, &key.this_coord, 8); i += 8;
memcpy(sig + i, &key.orientation, 1); i += 1;
memcpy(sig + i, &key.barcode, 4); i += 4;
memcpy(sig + i, &key.read_group, 4); i += 4;
hash = do_hash(sig, i);
} else {
unsigned char sig[34];
memcpy(sig + i, &key.this_ref, 4); i += 4;
memcpy(sig + i, &key.this_coord, 8); i += 8;
memcpy(sig + i, &key.other_ref, 4); i += 4;
memcpy(sig + i, &key.other_coord, 8); i += 8;
memcpy(sig + i, &key.leftmost, 1); i += 1;
memcpy(sig + i, &key.orientation, 1); i += 1;
memcpy(sig + i, &key.barcode, 4); i += 4;
memcpy(sig + i, &key.read_group, 4); i += 4;
hash = do_hash(sig, i);
}
return hash;
}
static int key_equal(key_data_t a, key_data_t b) {
int match = 1;
if (a.this_coord != b.this_coord)
match = 0;
else if (a.orientation != b.orientation)
match = 0;
else if (a.this_ref != b.this_ref)
match = 0;
else if (a.single != b.single)
match = 0;
else if (a.barcode != b.barcode)
match = 0;
else if (a.read_group != b.read_group)
match = 0;
if (!a.single) {
if (a.other_coord != b.other_coord)
match = 0;
else if (a.leftmost != b.leftmost)
match = 0;
else if (a.other_ref != b.other_ref)
match = 0;
}
return match;
}
#define __free_queue_element(p)
// Orientations (prime numbers to feed to hashing algorithm)
#define O_FF 2
#define O_RR 3
#define O_FR 5
#define O_RF 7
// Left or rightmost
#define R_LE 11
#define R_RI 13
#define BMD_WARNING_MAX 10
#define MD_MIN_QUALITY 15
// Duplicate finding mode
#define MD_MODE_TEMPLATE 0
#define MD_MODE_SEQUENCE 1
KHASH_INIT(reads, key_data_t, in_hash_t, 1, hash_key, key_equal) // read map hash
KLIST_INIT(read_queue, read_queue_t, __free_queue_element) // the reads buffer
KHASH_MAP_INIT_STR(duplicates, dup_map_t) // map of duplicates for supplementary dup id
KHASH_MAP_INIT_STR(read_groups, int) // read group lookup
/* The Bob Jenkins one_at_a_time hash to reduce the key to a 32 bit value. */
static khint32_t do_hash(unsigned char *key, khint32_t len) {
khint32_t hash, i;
for (hash = 0, i = 0; i < len; ++i) {
hash += key[i];
hash += (hash << 10);
hash ^= (hash >> 6);
}
hash += (hash << 3);
hash ^= (hash >> 11);
hash += (hash << 15);
return hash;
}
/* Get mate score from tag. */
static int64_t get_mate_score(bam1_t *b) {
uint8_t *data;
int64_t score;
if ((data = bam_aux_get(b, "ms"))) {
score = bam_aux2i(data);
} else {
print_error("markdup", "error, no ms score tag. Please run samtools fixmate on file first.\n");
return -1;
}
return score;
}
/* Calc current score from quality. */
static int64_t calc_score(bam1_t *b)
{
int64_t score = 0;
uint8_t *qual = bam_get_qual(b);
int i;
for (i = 0; i < b->core.l_qseq; i++) {
if (qual[i] >= MD_MIN_QUALITY) score += qual[i];
}
return score;
}
/* Create a signature hash of the current read and its pair.
Uses the unclipped start (or end depending on orientation),
the reference id, orientation and whether the current
read is leftmost of the pair. */
static int make_pair_key(md_param_t *param, key_data_t *key, bam1_t *bam, int rg_num, long *warnings) {
hts_pos_t this_coord, this_end, other_coord, other_end, leftmost;
int32_t this_ref, other_ref, barcode = 0;
int8_t orientation, left_read;
uint8_t *data;
char *cig, *bar;
long incoming_warnings = *warnings;
this_ref = bam->core.tid + 1; // avoid a 0 being put into the hash
other_ref = bam->core.mtid + 1;
this_coord = unclipped_start(bam);
this_end = unclipped_end(bam);
if ((data = bam_aux_get(bam, "MC"))) {
if (!(cig = bam_aux2Z(data))) {
print_error("markdup", "error, MC tag wrong type. Please use the MC tag provided by samtools fixmate.\n");
return 1;
}
other_end = unclipped_other_end(bam->core.mpos, cig);
other_coord = unclipped_other_start(bam->core.mpos, cig);
} else {
print_error("markdup", "error, no MC tag. Please run samtools fixmate on file first.\n");
return 1;
}
// work out orientations
if (param->mode == MD_MODE_TEMPLATE) {
if (this_ref != other_ref) {
leftmost = this_ref < other_ref;
} else {
if (bam_is_rev(bam) == bam_is_mrev(bam)) {
if (!bam_is_rev(bam)) {
leftmost = this_coord <= other_coord;
} else {
leftmost = this_end <= other_end;
}
} else {
if (bam_is_rev(bam)) {
leftmost = this_end <= other_coord;
} else {
leftmost = this_coord <= other_end;
}
}
}
// pair orientation
if (leftmost) {
if (bam_is_rev(bam) == bam_is_mrev(bam)) {
other_coord = other_end;
if (!bam_is_rev(bam)) {
if (bam->core.flag & BAM_FREAD1) {
orientation = O_FF;
} else {
orientation = O_RR;
}
} else {
if (bam->core.flag & BAM_FREAD1) {
orientation = O_RR;
} else {
orientation = O_FF;
}
}
} else {
if (!bam_is_rev(bam)) {
orientation = O_FR;
other_coord = other_end;
} else {
orientation = O_RF;
this_coord = this_end;
}
}
} else {
if (bam_is_rev(bam) == bam_is_mrev(bam)) {
this_coord = this_end;
if (!bam_is_rev(bam)) {
if (bam->core.flag & BAM_FREAD1) {
orientation = O_RR;
} else {
orientation = O_FF;
}
} else {
if (bam->core.flag & BAM_FREAD1) {
orientation = O_FF;
} else {
orientation = O_RR;
}
}
} else {
if (!bam_is_rev(bam)) {
orientation = O_RF;
other_coord = other_end;
} else {
orientation = O_FR;
this_coord = this_end;
}
}
}
} else { // MD_MODE_SEQUENCE
if (this_ref != other_ref) {
leftmost = this_ref - other_ref;
} else {
if (bam_is_rev(bam) == bam_is_mrev(bam)) {
if (!bam_is_rev(bam)) {
leftmost = this_coord - other_coord;
} else {
leftmost = this_end - other_end;
}
} else {
if (bam_is_rev(bam)) {
leftmost = this_end - other_coord;
} else {
leftmost = this_coord - other_end;
}
}
}
if (leftmost < 0) {
leftmost = 1;
} else if (leftmost > 0) {
leftmost = 0;
} else {
// tie breaks
if (bam->core.pos == bam->core.mpos) {
if (bam->core.flag & BAM_FREAD1) {
leftmost = 1;
} else {
leftmost = 0;
}
} else if (bam->core.pos < bam->core.mpos) {
leftmost = 1;
} else {
leftmost = 0;
}
}
// pair orientation
if (leftmost) {
if (bam_is_rev(bam) == bam_is_mrev(bam)) {
if (!bam_is_rev(bam)) {
orientation = O_FF;
} else {
orientation = O_RR;
}
} else {
if (!bam_is_rev(bam)) {
orientation = O_FR;
} else {
orientation = O_RF;
}
}
} else {
if (bam_is_rev(bam) == bam_is_mrev(bam)) {
if (!bam_is_rev(bam)) {
orientation = O_RR;
} else {
orientation = O_FF;
}
} else {
if (!bam_is_rev(bam)) {
orientation = O_RF;
} else {
orientation = O_FR;
}
}
}
if (!bam_is_rev(bam)) {
this_coord = unclipped_start(bam);
} else {
this_coord = unclipped_end(bam);
}
if (!bam_is_mrev(bam)) {
other_coord = unclipped_other_start(bam->core.mpos, cig);
} else {
other_coord = unclipped_other_end(bam->core.mpos, cig);
}
}
if (!leftmost)
left_read = R_RI;
else
left_read = R_LE;
if (param->barcode) {
if ((data = bam_aux_get(bam, param->barcode))) {
if (!(bar = bam_aux2Z(data))) {
(*warnings)++;
if (*warnings <= BMD_WARNING_MAX) {
print_error("markdup", "warning, %s tag wrong type. Aux tag needs to be a string type.\n", param->barcode);
}
} else {
barcode = do_hash((unsigned char *)bar, strlen(bar));
}
}
} else if (param->bc_rgx) {
int result;
regmatch_t matches[3];
size_t max_matches = 2;
char *qname = bam_get_qname(bam);
if ((result = regexec(param->bc_rgx, qname, max_matches, matches, 0)) == 0) {
int bc_start, bc_end;
bc_start = matches[1].rm_so;
bc_end = matches[1].rm_eo;
if (bc_start != -1) {
barcode = do_hash((unsigned char *)qname + bc_start, bc_end - bc_start);
} else {
(*warnings)++;
if (*warnings <= BMD_WARNING_MAX) {
print_error("markdup", "warning, barcode regex unable to match substring on %s.\n", qname);
}
}
} else {
(*warnings)++;
if (*warnings <= BMD_WARNING_MAX) {
char warn_msg[256];
regerror(result, param->bc_rgx, warn_msg, 256);
print_error("markdup", "warning, barcode regex match error \"%s\" on %s.\n", warn_msg, qname);
}
}
}
if ((*warnings == BMD_WARNING_MAX) && (incoming_warnings != *warnings)) {
print_error("markdup", "warning, %ld barcode read warnings. New warnings will not be reported.\n",
*warnings);
}
key->single = 0;
key->this_ref = this_ref;
key->this_coord = this_coord;
key->other_ref = other_ref;
key->other_coord = other_coord;
key->leftmost = left_read;
key->orientation = orientation;
key->barcode = barcode;
key->read_group = rg_num;
return 0;
}
/* Create a signature hash of single read (or read with an unmatched pair).
Uses unclipped start (or end depending on orientation), reference id,
and orientation. */
static void make_single_key(md_param_t *param, key_data_t *key, bam1_t *bam, int rg_num, long *warnings) {
hts_pos_t this_coord;
int32_t this_ref, barcode = 0;
int8_t orientation;
uint8_t *data;
char *bar;
long incoming_warnings = *warnings;
this_ref = bam->core.tid + 1; // avoid a 0 being put into the hash
if (bam_is_rev(bam)) {
this_coord = unclipped_end(bam);
orientation = O_RR;
} else {
this_coord = unclipped_start(bam);
orientation = O_FF;
}
if (param->barcode) {
if ((data = bam_aux_get(bam, param->barcode))) {
if (!(bar = bam_aux2Z(data))) {
(*warnings)++;
if (*warnings <= BMD_WARNING_MAX) {
print_error("markdup", "warning, %s tag wrong type. Aux tag needs to be a string type.\n", param->barcode);
}
} else {
barcode = do_hash((unsigned char *)bar, strlen(bar));
}
}
} else if (param->bc_rgx) {
int result;
regmatch_t matches[3];
size_t max_matches = 2;
char *qname = bam_get_qname(bam);
if ((result = regexec(param->bc_rgx, qname, max_matches, matches, 0)) == 0) {
int bc_start, bc_end;
bc_start = matches[1].rm_so;
bc_end = matches[1].rm_eo;
if (bc_start != -1) {
barcode = do_hash((unsigned char *)qname + bc_start, bc_end - bc_start);
} else {
(*warnings)++;
if (*warnings <= BMD_WARNING_MAX) {
print_error("markdup", "warning, barcode regex unable to match substring on %s.\n", qname);
}
}
} else {
(*warnings)++;
if (*warnings <= BMD_WARNING_MAX) {
char warn_msg[256];
regerror(result, param->bc_rgx, warn_msg, 256);
print_error("markdup", "warning, barcode regex match error \"%s\" on %s.\n", warn_msg, qname);
}
}
}
if ((*warnings == BMD_WARNING_MAX) && (incoming_warnings != *warnings)) {
print_error("markdup", "warning, %ld barcode read warnings. New warnings will not be reported.\n",
*warnings);
}
key->single = 1;
key->this_ref = this_ref;
key->this_coord = this_coord;
key->orientation = orientation;
key->barcode = barcode;
key->read_group = rg_num;
}
/* Add the duplicate name to a hash if it does not exist. */
static int add_duplicate(khash_t(duplicates) *d_hash, bam1_t *dupe, char *orig_name, char type, int group) {
khiter_t d;
int ret;
d = kh_get(duplicates, d_hash, bam_get_qname(dupe));
if (d == kh_end(d_hash)) {
char *name = strdup(bam_get_qname(dupe));
if (name) {
d = kh_put(duplicates, d_hash, name, &ret);
} else {
ret = -1;
}
if (ret >= 0) {
if (orig_name) {
if (ret == 0) {
// replace old name
free(kh_value(d_hash, d).name);
free(name);
}
kh_value(d_hash, d).name = strdup(orig_name);
if (kh_value(d_hash, d).name == NULL) {
print_error("markdup", "error, unable to allocate memory for duplicate original name.\n");
return 1;
}
} else {
kh_value(d_hash, d).name = NULL;
}
kh_value(d_hash, d).type = type;
kh_value(d_hash, d).read_group = group;
} else {
print_error("markdup", "error, unable to store supplementary duplicates.\n");
free(name);
return 1;
}
}
return 0;
}
/* Get coordinates from the standard Illumina style read names.
Returned values are of the x and y coordinates and a section of
the read name to test (t) for string equality e.g. lane and tile part. */
static int get_coordinates_colons(md_param_t *param, const char *qname, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) {
int sep = 0;
int pos = 0;
int xpos = 0, ypos = 0;
char *end;
while (qname[pos]) {
if (qname[pos] == ':') {
sep++;
if (sep == 2) {
xpos = pos + 1;
} else if (sep == 3) {
ypos = pos + 1;
} else if (sep == 4) { // HiSeq style names
xpos = ypos;
ypos = pos + 1;
} else if (sep == 5) { // Newer Illumina format
xpos = pos + 1;
} else if (sep == 6) {
ypos = pos + 1;
}
}
pos++;
}
/* The most current Illumina read format at time of writing is:
@machine:run:flowcell:lane:tile:x:y:UMI or
@machine:run:flowcell:lane:tile:x:y
Counting the separating colons gives us a quick format check.
Older name formats have fewer elements.
*/
if (!(sep == 3 || sep == 4 || sep == 6 || sep == 7)) {
(*warnings)++;
if (*warnings <= BMD_WARNING_MAX) {
print_error("markdup", "warning, cannot decipher read name %s for optical duplicate marking.\n", qname);
}
return 1;
} else {
*x_coord = strtol(qname + xpos, &end, 10);
if ((qname + xpos) == end) {
(*warnings)++;
if (*warnings <= BMD_WARNING_MAX) {
print_error("markdup", "warning, cannot decipher x coordinate in %s .\n", qname);
}
return 1;
}
*y_coord = strtol(qname + ypos, &end, 10);
if ((qname + ypos) == end) {
(*warnings)++;
if (*warnings <= BMD_WARNING_MAX) {
print_error("markdup", "warning, cannot decipher y coordinate in %s .\n", qname);
}
return 1;
}
*t_beg = 0;
*t_end = xpos;
}
return 0;
}
/* Get the coordinates from the read name.
Returned values are of the x and y coordinates and an optional section of
the read name to test (t) for string equality e.g. lane and tile part. */
static inline int get_coordinates_regex(md_param_t *param, const char *qname, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) {
regmatch_t matches[5];
size_t max_matches = 5;
int xpos, ypos, xend, yend, xlen, ylen;
char coord[255];
char *end;
if (!param->rgx_t)
max_matches = 4;
if (regexec(param->rgx, qname, max_matches, matches, 0))
return -1;
xpos = matches[param->rgx_x].rm_so;
ypos = matches[param->rgx_y].rm_so;
if (param->rgx_t) {
*t_beg = matches[param->rgx_t].rm_so;
*t_end = matches[param->rgx_t].rm_eo;
} else {
*t_beg = *t_end = 0;
}
if (xpos == -1 || ypos == -1 || *t_beg == -1)
return -1;
xend = matches[param->rgx_x].rm_eo;
yend = matches[param->rgx_y].rm_eo;
if ((xlen = xend - xpos) > 254) {
(*warnings)++;
if (*warnings <= BMD_WARNING_MAX) {
print_error("markdup", "warning, x coordinate string longer than allowed qname length in %s (%d long).\n", qname, xlen);
}
return 1;
}
strncpy(coord, qname + xpos, xlen);
coord[xlen] = '\0';
*x_coord = strtol(coord, &end, 10);
if (coord == end) {
(*warnings)++;
if (*warnings <= BMD_WARNING_MAX) {
print_error("markdup", "warning, cannot decipher x coordinate in %s (%s).\n", qname, coord);
}
return 1;
}
if ((ylen = yend - ypos) > 254) {
(*warnings)++;
if (*warnings <= BMD_WARNING_MAX) {
print_error("markdup", "warning, y coordinate string longer than allowed qname length in %s (%d long).\n", qname, ylen);
}
return 1;
}
strncpy(coord, qname + ypos, ylen);
coord[ylen] = '\0';
*y_coord = strtol(coord, &end, 10);
if (coord == end) {
(*warnings)++;
if (*warnings <= BMD_WARNING_MAX) {
print_error("markdup", "warning, cannot decipher y coordinate in %s (%s).\n", qname, coord);
}
return 1;
}
return 0;
}
static int get_coordinates(md_param_t *param, const char *name, int *t_beg, int *t_end, long *x_coord, long *y_coord, long *warnings) {
int ret = 1;
if (param->rgx == NULL) {
ret = get_coordinates_colons(param, name, t_beg, t_end, x_coord, y_coord, warnings);
} else {
ret = get_coordinates_regex(param, name, t_beg, t_end, x_coord, y_coord, warnings);
}
return ret;
}
/* Using the coordinates from the read name, see whether the duplicated read is
close enough (set by max_dist) to the original to be counted as optical.*/
static int is_optical_duplicate(md_param_t *param, bam1_t *ori, bam1_t *dup, long max_dist, long *warnings) {
int ret = 0;
char *original, *duplicate;
long ox, oy, dx, dy;
int o_beg = 0, o_end = 0, d_beg = 0, d_end = 0;
original = bam_get_qname(ori);
duplicate = bam_get_qname(dup);
if (get_coordinates(param, original, &o_beg, &o_end, &ox, &oy, warnings)) {
return ret;
}
if (get_coordinates(param, duplicate, &d_beg, &d_end, &dx, &dy, warnings)) {
return ret;
}
int o_len = o_end - o_beg;
int d_len = d_end - d_beg;
if ((o_len == d_len) && memcmp(original + o_beg, duplicate + d_beg, o_len) == 0) {
long xdiff, ydiff;
if (ox > dx) {
xdiff = ox - dx;
} else {
xdiff = dx - ox;
}
if (xdiff <= max_dist) {
// still might be optical
if (oy > dy) {
ydiff = oy - dy;
} else {
ydiff = dy - oy;
}
if (ydiff <= max_dist) ret = 1;
}
}
return ret;
}
/* Using the coordinates from the Illumina read name, see whether the duplicated read is
close enough (set by max_dist) to the original to be counted as optical.
This function needs the values from the first read to be already calculated. */
static int optical_duplicate_partial(md_param_t *param, const char *name, const int o_beg, const int o_end, const long ox, const long oy, bam1_t *dup, check_t *c, long max_dist, long *warnings) {
int ret = 0;
char *duplicate;
int d_beg = 0, d_end = 0;
long dx, dy;
duplicate = bam_get_qname(dup);
if (get_coordinates(param, duplicate, &d_beg, &d_end, &dx, &dy, warnings)) {
return ret;
}
int o_len = o_end - o_beg;
int d_len = d_end - d_beg;
if ((o_len == d_len) && memcmp(name + o_beg, duplicate + d_beg, o_len) == 0) {
// the initial parts match, look at the numbers
long xdiff, ydiff;
if (ox > dx) {
xdiff = ox - dx;
} else {
xdiff = dx - ox;
}
if (xdiff <= max_dist) {
// still might be optical
if (oy > dy) {
ydiff = oy - dy;
} else {
ydiff = dy - oy;
}
if (ydiff <= max_dist) ret = 1;
}
}
c->x = dx;
c->y = dy;
c->beg = d_beg;
c->end = d_end;
c->len = d_end - d_beg;
return ret;
}
/* Mark the read as a duplicate and update the duplicate hash (if needed) */
static int mark_duplicates(md_param_t *param, khash_t(duplicates) *dup_hash, bam1_t *ori, bam1_t *dup,
int read_group, long *optical, long *warn) {
char dup_type = 0;
long incoming_warnings = *warn;
dup->core.flag |= BAM_FDUP;
if (param->tag) {
if (bam_aux_update_str(dup, "do", strlen(bam_get_qname(ori)) + 1, bam_get_qname(ori))) {
print_error("markdup", "error, unable to append 'do' tag.\n");
return -1;
}
}
if (param->opt_dist) { // mark optical duplicates
if (is_optical_duplicate(param, ori, dup, param->opt_dist, warn)) {
bam_aux_update_str(dup, "dt", 3, "SQ");
dup_type = 'O';
(*optical)++;
} else {
// not an optical duplicate
bam_aux_update_str(dup, "dt", 3, "LB");
}
}
if ((*warn == BMD_WARNING_MAX) && (incoming_warnings != *warn)) {
print_error("markdup", "warning, %ld decipher read name warnings. New warnings will not be reported.\n",
*warn);
}
if (param->supp) {
if (bam_aux_get(dup, "SA") || (dup->core.flag & BAM_FMUNMAP) || bam_aux_get(dup, "XA")) {
char *original = NULL;
if (param->tag) {
original = bam_get_qname(ori);
}
if (add_duplicate(dup_hash, dup, original, dup_type, read_group))