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liftover.c
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liftover.c
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/* The MIT License
Copyright (C) 2022-2024 Giulio Genovese
Author: Giulio Genovese <giulio.genovese@gmail.com>
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 <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <getopt.h>
#include <htslib/kseq.h>
#include <htslib/vcf.h>
#include <htslib/faidx.h>
#include "bcftools.h"
#include "regidx.h" // cannot use htslib/regdix.h see https://github.com/samtools/htslib/pull/761
#include "htslib/khash.h" // required to reset the contigs dictionary and table
KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
#define LIFTOVER_VERSION "2024-05-05"
#define FLIP_TAG "FLIP"
#define SWAP_TAG "SWAP"
#define DROP_TAGS "."
#define AC_TAGS "INFO/AC,FMT/AC"
#define AF_TAGS "INFO/AF,FMT/AF,FMT/AP1,FMT/AP2"
#define DS_TAGS "FMT/DS"
#define GT_TAGS "INFO/ALLELE_A,INFO/ALLELE_B"
#define ES_TAGS "FMT/EZ,FMT/ES,FMT/ED"
#define NO_RULE 0
#define RULE_DROP 1
#define RULE_AC 2
#define RULE_AF 3
#define RULE_DS 4
#define RULE_GT 5
#define RULE_ES 6
#define RULE_AGR 7
const char *rules_str[] = {"DROP", "AC", "AF", "DS", "GT", "FLIP", "AGR"};
static inline char rev_nt(char iupac) {
static const char iupac_complement[128] = {
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, '-', 0, '/', 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 'T',
'V', 'G', 'H', 0, 0, 'C', 'D', 0, 0, 'M', 0, 'K', 'N', 0, 0, 0, 'Y', 'S', 'A', 0, 'B', 'W',
0, 'R', 0, ']', 0, '[', 0, 0, 0, 'T', 'V', 'G', 'H', 0, 0, 'C', 'D', 0, 0, 'M', 0, 'K',
'N', 0, 0, 0, 'Y', 'S', 'A', 0, 'B', 'W', 0, 'R', 0, 0, 0, 0, 0, 0,
};
return iupac_complement[(int)(iupac & 0x7F)];
}
static inline void reverse_complement(char *str) {
int i, len = strlen(str);
for (i = 0; i < len / 2; i++) {
char tmp = str[i];
str[i] = rev_nt(str[len - i - 1]);
str[len - i - 1] = rev_nt(tmp);
}
if (len % 2 == 1) str[len / 2] = rev_nt(str[len / 2]);
}
typedef struct {
int tStart;
int qStart;
int size;
int chain_ind; // index of chain the block belongs to
int tStart_gap; // size of gap to reach previous contiguous block in target space
int tEnd_gap; // size of gap to reach next contiguous block in target space
int qStart_gap; // size of gap to reach previous contiguous block in query space
int qEnd_gap; // size of gap to reach next contiguous block in query space
} block_t;
typedef struct {
uint64_t score;
int t_rid;
int tSize;
int tStart;
int tEnd;
int q_rid;
int qSize;
int qStrand;
int qStart;
int qEnd;
int id;
int block_ind; // index of first block of the chain
int n_blocks; // number of blocks in the chain
} chain_t;
// return previous block from the same chain (NULL if it is the first block)
static inline const block_t *prev_block(const block_t *block, const block_t *blocks, const chain_t *chains) {
int ind = (block - blocks) - chains[block->chain_ind].block_ind;
return ind == 0 ? NULL : block - 1;
}
// return next block from the same chain (NULL if it is the last block)
static inline const block_t *next_block(const block_t *block, const block_t *blocks, const chain_t *chains) {
int ind = (block - blocks) - chains[block->chain_ind].block_ind;
return ind == chains[block->chain_ind].n_blocks - 1 ? NULL : block + 1;
}
typedef struct {
int int_id; // VCF header int_id
int coltype; // whether BCF_HL_INFO or BCF_HL_FMT
int rule; // which rule should apply (DROP, AC, AF, DS, GT, FLIP, or AGR)
} tag_t;
typedef struct {
bcf_hdr_t *in_hdr;
bcf_hdr_t *out_hdr;
faidx_t *src_fai;
faidx_t *dst_fai;
int n_chains;
chain_t *chains;
block_t *blocks;
regidx_t *idx;
regitr_t *itr;
htsFile *reject_fh;
int max_indel_inc;
int aln_win;
int in_mt_rid;
int out_mt_rid;
int lift_mt;
int no_left_align;
int write_src;
int write_fail;
int write_nw;
int info_end_id;
int info_an_id;
int fmt_gt_id;
int fmt_an_id;
int *af_arr;
int *ploidy_arr;
const char *flip_tag;
const char *swap_tag;
int n_tags;
tag_t *tags;
int warning_symbolic;
int warning_indel;
int ntotal;
int nswapped;
int nref_added;
int nrejected;
kstring_t tmp_kstr;
kstring_t tmp_pad;
kstring_t *tmp_als;
int m_tmp_als;
int8_t *tmp_arr;
int m_tmp_arr;
int32_t *int32_arr;
int m_int32_arr;
} args_t;
args_t *args;
/****************************************
* CHAIN FUNCTIONS *
****************************************/
static inline int bcf_hdr_name2id_flexible(const bcf_hdr_t *hdr, char *chr) {
if (!chr) return -1;
char buf[] = {'c', 'h', 'r', '\0', '\0', '\0'};
int rid = bcf_hdr_name2id(hdr, chr);
if (rid >= 0) return rid;
if (strncmp(chr, "chr", 3) == 0) rid = bcf_hdr_name2id(hdr, chr + 3);
if (rid >= 0) return rid;
strncpy(buf + 3, chr, 2);
rid = bcf_hdr_name2id(hdr, buf);
if (rid >= 0) return rid;
if (strcmp(chr, "23") == 0 || strcmp(chr, "25") == 0 || strcmp(chr, "XY") == 0 || strcmp(chr, "XX") == 0
|| strcmp(chr, "PAR1") == 0 || strcmp(chr, "PAR2") == 0) {
rid = bcf_hdr_name2id(hdr, "X");
if (rid >= 0) return rid;
rid = bcf_hdr_name2id(hdr, "chrX");
} else if (strcmp(chr, "24") == 0) {
rid = bcf_hdr_name2id(hdr, "Y");
if (rid >= 0) return rid;
rid = bcf_hdr_name2id(hdr, "chrY");
} else if (strcmp(chr, "26") == 0 || strcmp(chr, "MT") == 0 || strcmp(chr, "chrM") == 0) {
rid = bcf_hdr_name2id(hdr, "MT");
if (rid >= 0) return rid;
rid = bcf_hdr_name2id(hdr, "chrM");
}
return rid;
}
// load the chain file (see http://genome.ucsc.edu/goldenPath/help/chain.html)
static int read_chains(htsFile *fp, const bcf_hdr_t *in_hdr, const bcf_hdr_t *out_hdr, int max_snp_gap,
chain_t **chains, block_t **blocks) {
int n_chains = 0;
int n_blocks = 0;
int m_chains = 0;
int m_blocks = 0;
char *tmp = NULL;
kstring_t str = {0, 0, NULL};
int moff = 0, *off = NULL;
while (hts_getline(fp, KS_SEP_LINE, &str) >= 0) {
hts_expand(chain_t, n_chains + 1, m_chains, *chains);
chain_t *chain = &(*chains)[n_chains++];
int ncols = ksplit_core(str.s, 0, &moff, &off);
if (ncols != 13) error("Wrong number of columns in the chain file: %s\n", fp->fn);
// read Header Lines
if (strcmp(&str.s[off[0]], "chain") != 0)
error("Chain line should start with word \"chain\" but \"%s\" found in the chain file: %s\n",
&str.s[off[0]], fp->fn);
chain->score = (uint64_t)strtoll(&str.s[off[1]], &tmp, 0);
if (*tmp) error("Could not parse integer %s in the chain file: %s\n", &str.s[off[1]], fp->fn);
chain->t_rid = bcf_hdr_name2id_flexible(in_hdr, &str.s[off[2]]);
chain->tSize = strtol(&str.s[off[3]], &tmp, 0);
if (*tmp) error("Could not parse integer %s in the chain file: %s\n", &str.s[off[3]], fp->fn);
if (chain->t_rid >= 0) {
uint64_t len = in_hdr->id[BCF_DT_CTG][chain->t_rid].val->info[0];
if (len != 0 && chain->tSize != len)
fprintf(stderr,
"Warning: source contig %s has length %" PRId64 " in the VCF and length %s in the chain file\n",
&str.s[off[2]], len, &str.s[off[3]]);
}
if (str.s[off[4]] != '+')
error("Chain line fifth column should be \"+\" but \"%s\" found in the chain file: %s\n", &str.s[off[4]],
fp->fn);
chain->tStart = strtol(&str.s[off[5]], &tmp, 0);
if (*tmp) error("Could not parse integer %s in the chain file: %s\n", &str.s[off[5]], fp->fn);
chain->tEnd = strtol(&str.s[off[6]], &tmp, 0);
if (*tmp) error("Could not parse integer %s in the chain file: %s\n", &str.s[off[6]], fp->fn);
chain->q_rid = bcf_hdr_name2id_flexible(out_hdr, &str.s[off[7]]);
chain->qSize = strtol(&str.s[off[8]], &tmp, 0);
if (*tmp) error("Could not parse integer %s in the chain file: %s\n", &str.s[off[8]], fp->fn);
if (chain->q_rid >= 0) {
uint64_t len = out_hdr->id[BCF_DT_CTG][chain->q_rid].val->info[0];
if (len != 0 && chain->qSize != len)
fprintf(stderr,
"Warning: query contig %s has length %" PRId64 " in the VCF and length %s in the chain file\n",
&str.s[off[7]], len, &str.s[off[8]]);
}
if (str.s[off[9]] != '+' && str.s[off[9]] != '-')
error("Chain line tenth column should be \"+\" or \"-\" but \"%s\" found in the chain file: %s\n",
&str.s[off[9]], fp->fn);
chain->qStrand = str.s[off[9]] == '-';
chain->qStart = strtol(&str.s[off[10]], &tmp, 0);
if (*tmp) error("Could not parse integer %s in the chain file: %s\n", &str.s[off[10]], fp->fn);
chain->qEnd = strtol(&str.s[off[11]], &tmp, 0);
if (*tmp) error("Could not parse integer %s in the chain file: %s\n", &str.s[off[11]], fp->fn);
chain->id = strtol(&str.s[off[12]], &tmp, 0);
if (*tmp) error("Could not parse integer %s in the chain file: %s\n", &str.s[off[12]], fp->fn);
// read Data Lines
int tStart = 0;
int qStart = 0;
int dt = -1;
int dq = -1;
chain->block_ind = n_blocks;
chain->n_blocks = 0;
block_t *block;
int merge_in_progress = 0;
while (hts_getline(fp, KS_SEP_LINE, &str) > 0) {
int ncols = ksplit_core(str.s, 0, &moff, &off);
if (ncols != 1 && ncols != 3) error("Wrong number of columns in the chain file: %s\n", fp->fn);
int size = strtol(&str.s[off[0]], &tmp, 0);
if (*tmp) error("Could not parse integer %s in the chain file: %s\n", &str.s[off[0]], fp->fn);
if (merge_in_progress) {
block->size += size;
} else {
hts_expand(block_t, n_blocks + 1, m_blocks, *blocks);
block = &(*blocks)[n_blocks++];
block->tStart = tStart;
block->qStart = qStart;
block->size = size;
block->chain_ind = n_chains - 1;
block->tStart_gap = dt;
block->tEnd_gap = -1;
block->qStart_gap = dq;
block->qEnd_gap = -1;
chain->n_blocks++;
}
if (ncols == 1) {
tStart += size;
if (chain->tStart + tStart != chain->tEnd)
error("Chain malformed as target interval %s:%d-%d not fully covered in the chain file: %s\n",
bcf_hdr_id2name(in_hdr, chain->t_rid), chain->tStart, chain->tEnd, fp->fn);
qStart += size;
if (chain->qStart + qStart != chain->qEnd)
error("Chain malformed as query interval %s:%d-%d not fully covered in the chain file: %s\n",
bcf_hdr_id2name(in_hdr, chain->q_rid), chain->qStart, chain->qEnd, fp->fn);
} else {
dt = strtol(&str.s[off[1]], &tmp, 0);
if (*tmp) error("Could not parse integer %s in the chain file: %s\n", &str.s[off[1]], fp->fn);
dq = strtol(&str.s[off[2]], &tmp, 0);
if (*tmp) error("Could not parse integer %s in the chain file: %s\n", &str.s[off[2]], fp->fn);
tStart += size + dt;
qStart += size + dq;
merge_in_progress = dt == dq && dt <= max_snp_gap;
if (merge_in_progress) {
block->size += dt;
} else {
block->tEnd_gap = dt;
block->qEnd_gap = dq;
}
}
}
}
free(off);
free(str.s);
return n_chains;
}
static void write_chains(FILE *stream, const bcf_hdr_t *in_hdr, const bcf_hdr_t *out_hdr, const chain_t *chains,
int n_chains, block_t *blocks) {
int i, j;
for (i = 0; i < n_chains; i++) {
const chain_t *chain = &chains[i];
const char *tName = bcf_hdr_id2name(in_hdr, chain->t_rid);
const char *qName = bcf_hdr_id2name(out_hdr, chain->q_rid);
fprintf(stream, "chain %" PRIhts_pos " %s %d + %d %d %s %d %c %d %d %d\n", chain->score, tName, chain->tSize,
chain->tStart, chain->tEnd, qName, chain->qSize, chain->qStrand ? '-' : '+', chain->qStart, chain->qEnd,
chain->id);
for (j = 0; j < chain->n_blocks; j++) {
const block_t *block = &blocks[chain->block_ind + j];
fprintf(stream, "%s\t%d\t%d\t%d\t%" PRIhts_pos "\t%c\t%s\t%d\t%d\n", tName, chain->tStart + block->tStart,
chain->tStart + block->tStart + block->size, chain->id, chain->score, chain->qStrand ? '-' : '+',
qName,
chain->qStrand ? chain->qSize - chain->qStart - block->qStart - block->size
: chain->qStart + block->qStart,
chain->qStrand ? chain->qSize - chain->qStart - block->qStart
: chain->qStart + block->qStart + block->size);
}
}
}
KHASH_MAP_INIT_INT(32, char)
static regidx_t *regidx_init_chains(const bcf_hdr_t *in_hdr, const chain_t *chains, int n_chains, block_t *blocks) {
khash_t(32) *h = kh_init(32);
regidx_t *idx = regidx_init(NULL, NULL, NULL, sizeof(uint64_t), NULL);
int i, j;
for (i = 0; i < n_chains; i++) {
const chain_t *chain = &chains[i];
if (chain->t_rid < 0 || chain->q_rid < 0) continue;
// check whether the chain has already been added as Ensembl duplicates chains in the chain file
if (chain->id) {
khiter_t k = kh_get(32, h, chain->id);
int ret, is_missing = (k == kh_end(h));
if (!is_missing) continue;
kh_put(32, h, chain->id, &ret);
}
const char *name = bcf_hdr_id2name(in_hdr, chain->t_rid);
int len = strlen(name);
for (j = 0; j < chain->n_blocks; j++) {
int block_ind = chain->block_ind + j;
const block_t *block = &blocks[block_ind];
regidx_push(idx, (char *)name, (char *)name + len, chain->tStart + block->tStart + 1,
chain->tStart + block->tStart + block->size, (void *)&block_ind);
}
}
kh_destroy(32, h);
return idx;
}
/****************************************
* TAGS FUNCTIONS *
****************************************/
// assign AGR tags rules
static void find_AGR_tags(const bcf_hdr_t *hdr, int *info_rules, int *fmt_rules) {
const int coltypes[2] = {BCF_HL_INFO, BCF_HL_FMT};
int i, j;
for (i = 0; i < 2; i++) {
int *rules = i == 0 ? info_rules : fmt_rules;
for (j = 0; j < hdr->n[BCF_DT_ID]; j++) {
// https://github.com/samtools/htslib/issues/1538
if (!hdr->id[BCF_DT_ID][j].val || bcf_hdr_id2coltype(hdr, coltypes[i], j) == 0xf) continue;
int length = bcf_hdr_id2length(hdr, coltypes[i], j);
if (length == BCF_VL_A || length == BCF_VL_G || length == BCF_VL_R) rules[j] = RULE_AGR;
}
}
}
// assign special tags rules
static void assign_tags(const bcf_hdr_t *hdr, const char *tags, int length_flag, int field_type_flag, int rule,
int *info_rules, int *fmt_rules) {
if (strcmp(tags, ".") == 0) return;
char *s = strdup(tags);
int i, moff = 0, *off = NULL;
int n = ksplit_core(s, ',', &moff, &off);
for (i = 0; i < n; i++) {
char *ss = &s[off[i]];
int coltype = -1;
if (!strncasecmp("INFO/", ss, 5)) {
coltype = BCF_HL_INFO;
ss += 5;
} else if (!strncasecmp("INF/", ss, 4)) {
coltype = BCF_HL_INFO;
ss += 4;
} else if (!strncasecmp("FORMAT/", ss, 7)) {
coltype = BCF_HL_FMT;
ss += 7;
} else if (!strncasecmp("FMT/", ss, 4)) {
coltype = BCF_HL_FMT;
ss += 4;
}
int int_id = bcf_hdr_id2int(hdr, BCF_DT_ID, ss);
if (coltype == -1) {
if (bcf_hdr_idinfo_exists(hdr, BCF_HL_INFO, int_id)) error("Error: did you mean INFO/%s?\n", ss);
if (bcf_hdr_idinfo_exists(hdr, BCF_HL_FMT, int_id)) error("Error: did you mean FORMAT/%s?\n", ss);
error("No matching tag %s\n", ss);
}
if (!bcf_hdr_idinfo_exists(hdr, coltype, int_id)) continue;
unsigned int length = bcf_hdr_id2length(hdr, coltype, int_id);
if (!(1 << length & length_flag)) {
if (length) {
char bcf_vl = length == BCF_VL_A ? 'A' : length == BCF_VL_G ? 'G' : length == BCF_VL_R ? 'R' : '.';
error("The %s tag \"%s\" is a Number=%c tag which is not the expected length for this tag\n",
coltype == BCF_HL_INFO ? "INFO" : "FORMAT", ss, bcf_vl);
} else {
int number = bcf_hdr_id2number(hdr, coltype, int_id);
error("The %s tag \"%s\" is a Number=%d tag which is not the expected length for this tag\n",
coltype == BCF_HL_INFO ? "INFO" : "FORMAT", ss, number);
}
}
int field_type = bcf_hdr_id2type(hdr, coltype, int_id);
if (!(1 << field_type & field_type_flag)) {
const char *bcf_ht = field_type == BCF_HT_FLAG ? "Flag"
: field_type == BCF_HT_INT ? "Integer"
: field_type == BCF_HT_REAL ? "Float"
: field_type == BCF_HT_STR ? "String"
: ".";
error("The %s tag \"%s\" is a Type=%s tag which is not the expected type for this tag\n",
coltype == BCF_HL_INFO ? "INFO" : "FORMAT", ss, bcf_ht);
}
int *rules = coltype == BCF_HL_INFO ? info_rules : fmt_rules;
rules[int_id] = rule;
}
free(off);
free(s);
}
// make list of tags rules
static int compress_tags(int *info_rules, int *fmt_rules, int n, tag_t **tags) {
const int coltypes[2] = {BCF_HL_INFO, BCF_HL_FMT};
int i, j, n_tags = 0, m_tags = 0;
*tags = NULL;
for (i = 0; i < 2; i++) {
int *rules = i == 0 ? info_rules : fmt_rules;
for (j = 0; j < n; j++) {
if (!rules[j]) continue;
hts_expand(tag_t, n_tags + 1, m_tags, *tags);
tag_t *tag = &(*tags)[n_tags++];
tag->int_id = j;
tag->coltype = coltypes[i];
tag->rule = rules[j];
}
}
return n_tags;
}
/****************************************
* PLUGIN *
****************************************/
const char *about(void) { return "Lift over a VCF from one genome build to another.\n"; }
const char *usage(void) {
return "\n"
"About: Lift over a VCF from one genome build to another. "
"(version " LIFTOVER_VERSION
" https://github.com/freeseek/score)\n"
"[ Genovese, G., et al. BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants\n"
"across genome assemblies. Bioinformatics 40, Issue 2 (2024) http://doi.org/10.1093/bioinformatics/btae038 "
"]\n"
"\n"
"Usage: bcftools +liftover [General Options] -- [Plugin Options]\n"
"Options:\n"
" run \"bcftools plugin\" for a list of common options\n"
"\n"
"Plugin options:\n"
" -s, --src-fasta-ref <file> source reference sequence in fasta format\n"
" -f, --fasta-ref <file> destination reference sequence in fasta format\n"
" --set-cache-size <int> select fasta cache size in bytes\n"
" -c, --chain <file> UCSC liftOver chain file\n"
" --max-snp-gap <int> maximum distance to merge contiguous blocks separated by same distance "
"[1]\n"
" --max-indel-inc <int> maximum distance used to increase the size an indel during liftover "
"[250]\n"
" --lift-mt force liftover of MT/chrMT [automatically determined from contig "
"lengths]\n"
" --print-blocks <file> output contiguous blocks used for the liftOver\n"
" --no-left-align do not attempt to left align indels after liftover\n"
" --reject <file> output variants that cannot be lifted over\n"
" -O, --reject-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level "
"[v]\n"
" --write-src write the source contig/position/alleles for lifted variants\n"
" --write-fail write whether the 5' and 3' anchors have failed to lift\n"
" --write-nw write the Needleman-Wunsch alignments when required\n"
"\n"
"Options for how to update INFO/FORMAT records:\n"
" --fix-tags fix Number type for INFO/AC, INFO/AF, FORMAT/GP, and FORMAT/DS tags\n"
" --flip-tag <string> INFO annotation flag to record whether alleles are flipped [FLIP]\n"
" --swap-tag <string> INFO annotation to record when alleles are swapped [SWAP]\n"
" --drop-tags <list> tags to drop when alleles are swapped [" DROP_TAGS
"]\n"
" --ac-tags <list> AC-like tags (must be Number=A,Type=Integer/Float) [" AC_TAGS
"]\n"
" --af-tags <list> AF-like tags (must be Number=A,Type=Float) [" AF_TAGS
"]\n"
" --ds-tags <list> DS-like tags (must be Number=A,Type=Float) [" DS_TAGS
"]\n"
" --gt-tags <list> tags with integers like FORMAT/GT (must be Type=Integer) [" GT_TAGS
"]\n"
" --es-tags <list> GWAS-VCF tags (must be Number=A) [" ES_TAGS
"]\n"
"\n"
"Examples:\n"
" bcftools +liftover -Ou input.hg19.bcf -- -s hg19.fa -f hg38.fa \\\n"
" -c hg19ToHg38.over.chain.gz | bcftools sort -Ob -o output.hg38.bcf -W\n"
" bcftools +liftover -Ou GRCh38_dbSNPv156.vcf.gz -- -s hg38.fa -f chm13v2.0.fa \\\n"
" -c hg38ToHs1.over.chain.gz | bcftools sort -Oz -o chm13v2.0_dbSNPv156.vcf.gz -W=tbi\n"
"\n"
"To obtain liftover chain files:\n"
" wget http://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/hg19ToHg38.over.chain.gz\n"
" wget http://ftp.ensembl.org/pub/assembly_mapping/homo_sapiens/GRCh37_to_GRCh38.chain.gz\n"
" wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHs1.over.chain.gz\n"
"\n";
}
static inline FILE *get_file_handle(const char *str) {
FILE *ret;
if (strcmp(str, "-") == 0)
ret = stdout;
else {
ret = fopen(str, "w");
if (!ret) error("Failed to open %s: %s\n", str, strerror(errno));
}
return ret;
}
int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out) {
args = (args_t *)calloc(1, sizeof(args_t));
args->in_hdr = in;
args->out_hdr = out;
args->max_indel_inc = 250;
args->aln_win = 100;
args->flip_tag = FLIP_TAG;
args->swap_tag = SWAP_TAG;
int i, j, k;
int cache_size = 0;
int output_type = FT_VCF;
int clevel = -1;
int max_snp_gap = 1; // maximum distance between two contiguous blocks to allow merging
int fix_tags = 0;
char *tmp = NULL;
const char *src_ref_fname = NULL;
const char *dst_ref_fname = NULL;
const char *chain_fname = NULL;
const char *blocks_fname = NULL;
const char *reject_fname = NULL;
char *drop_tags = DROP_TAGS;
char *ac_tags = AC_TAGS;
char *af_tags = AF_TAGS;
char *ds_tags = DS_TAGS;
char *gt_tags = GT_TAGS;
char *es_tags = ES_TAGS;
static struct option loptions[] = {{"src-fasta-ref", required_argument, NULL, 's'},
{"fasta-ref", required_argument, NULL, 'f'},
{"set-cache-size", required_argument, NULL, 1},
{"chain", required_argument, NULL, 'c'},
{"max-snp-gap", required_argument, NULL, 2},
{"max-indel-inc", required_argument, NULL, 3},
{"lift-mt", no_argument, NULL, 4},
{"print-blocks", required_argument, NULL, 5},
{"no-left-align", no_argument, NULL, 6},
{"reject", required_argument, NULL, 7},
{"reject-type", required_argument, NULL, 'O'},
{"write-src", no_argument, NULL, 8},
{"write-fail", no_argument, NULL, 9},
{"write-nw", no_argument, NULL, 10},
{"fix-tags", no_argument, NULL, 11},
{"flip-tag", required_argument, NULL, 12},
{"swap-tag", required_argument, NULL, 13},
{"drop-tags", required_argument, NULL, 14},
{"ac-tags", required_argument, NULL, 15},
{"af-tags", required_argument, NULL, 16},
{"ds-tags", required_argument, NULL, 17},
{"gt-tags", required_argument, NULL, 18},
{"es-tags", required_argument, NULL, 19},
{NULL, 0, NULL, 0}};
int c;
while ((c = getopt_long(argc, argv, "h?s:f:c:O:", loptions, NULL)) >= 0) {
switch (c) {
case 's':
src_ref_fname = optarg;
break;
case 'f':
dst_ref_fname = optarg;
break;
case 1:
cache_size = strtol(optarg, &tmp, 0);
if (*tmp) error("Could not parse: --set-cache-size %s\n", optarg);
break;
case 'c':
chain_fname = optarg;
break;
case 2:
max_snp_gap = strtol(optarg, &tmp, 0);
if (*tmp) error("Could not parse: --max-snp-gap %s\n", optarg);
break;
case 3:
args->max_indel_inc = strtol(optarg, &tmp, 0);
if (*tmp) error("Could not parse: --max-indel-inc %s\n", optarg);
break;
case 4:
args->lift_mt = 1;
break;
case 5:
blocks_fname = optarg;
break;
case 6:
args->no_left_align = 1;
break;
case 7:
reject_fname = optarg;
break;
case 'O':
switch (optarg[0]) {
case 'b':
output_type = FT_BCF_GZ;
break;
case 'u':
output_type = FT_BCF;
break;
case 'z':
output_type = FT_VCF_GZ;
break;
case 'v':
output_type = FT_VCF;
break;
default: {
clevel = strtol(optarg, &tmp, 10);
if (*tmp || clevel < 0 || clevel > 9) error("The output type \"%s\" not recognised\n", optarg);
}
}
if (optarg[1]) {
clevel = strtol(optarg + 1, &tmp, 10);
if (*tmp || clevel < 0 || clevel > 9)
error("Could not parse argument: --compression-level %s\n", optarg + 1);
}
break;
case 8:
args->write_src = 1;
break;
case 9:
args->write_fail = 1;
break;
case 10:
args->write_nw = 1;
break;
case 11:
fix_tags = 1;
break;
case 12:
args->flip_tag = optarg;
break;
case 13:
args->swap_tag = optarg;
break;
case 14:
drop_tags = optarg;
break;
case 15:
ac_tags = optarg;
break;
case 16:
af_tags = optarg;
break;
case 17:
ds_tags = optarg;
break;
case 18:
gt_tags = optarg;
break;
case 19:
es_tags = optarg;
break;
case 'h':
case '?':
default:
error("%s", usage());
break;
}
}
if (!in || !out) error("Expected input VCF\n%s", usage());
// load target reference file
if (src_ref_fname) {
args->src_fai = fai_load(src_ref_fname);
if (!args->src_fai) error("Could not load the reference %s\n", src_ref_fname);
if (cache_size) fai_set_cache_size(args->src_fai, cache_size);
} else {
if (!dst_ref_fname || !chain_fname)
error("At least one of --src-fasta-ref or --fasta-ref and --chain options required\n");
}
// does not perform liftover ... only performs the indel extension
if (!dst_ref_fname || !chain_fname) return 0;
// load query reference file
args->dst_fai = fai_load(dst_ref_fname);
if (!args->dst_fai) error("Could not load the reference %s\n", dst_ref_fname);
if (cache_size) fai_set_cache_size(args->dst_fai, cache_size);
// reset contig table for the output header
bcf_hdr_remove(out, BCF_HL_CTG, NULL);
// required to reset the contigs dictionary and table
kh_clear(vdict, out->dict[BCF_DT_CTG]);
for (i = 0; i < out->n[BCF_DT_CTG]; i++) free((void *)out->id[BCF_DT_CTG][i].key);
out->n[BCF_DT_CTG] = 0;
int n = faidx_nseq(args->dst_fai);
for (i = 0; i < n; i++) {
const char *seq = faidx_iseq(args->dst_fai, i);
int len = faidx_seq_len(args->dst_fai, seq);
bcf_hdr_printf(out, "##contig=<ID=%s,length=%d>", seq, len);
}
// fix INFO/AC, INFO/AF, FORMAT/GP, and FORMAT/DS tags from the Michigan imputation server
if (fix_tags) {
bcf_hdr_t *hdrs[] = {in, out};
const char *tags[] = {"AC", "AF", "GP", "DS"};
int coltypes[] = {BCF_HL_INFO, BCF_HL_INFO, BCF_HL_FMT, BCF_HL_FMT};
int numbers[] = {1, 1, 3, 1};
int lengths[] = {BCF_VL_A, BCF_VL_A, BCF_VL_G, BCF_VL_A};
for (i = 0; i < 2; i++) {
for (j = 0; j < 4; j++) {
int int_id = bcf_hdr_id2int(hdrs[i], BCF_DT_ID, tags[j]);
if (int_id < 0) continue;
bcf_idinfo_t *val = (bcf_idinfo_t *)hdrs[i]->id[BCF_DT_ID][int_id].val;
if ((val->info[coltypes[j]] & 0xf) == 0xf) continue;
if ((val->info[coltypes[j]] >> 8 & 0xf) == 0 && val->info[coltypes[j]] >> 12 == numbers[j]) {
val->info[coltypes[j]] &= 0xff;
val->info[coltypes[j]] += lengths[j] << 8;
bcf_hrec_t *hrec = val->hrec[coltypes[j]];
for (k = 0; k < hrec->nkeys; k++) {
if (!strcmp(hrec->keys[k], "Number")) {
if (!strcmp(hrec->vals[k], "1"))
hrec->vals[k][0] = 'A';
else if (!strcmp(hrec->vals[k], "3"))
hrec->vals[k][0] = 'G';
}
}
}
}
}
}
if (bcf_hdr_printf(
out, "##INFO=<ID=%s,Number=0,Type=Flag,Description=\"Whether alleles flipped strand during liftover\">",
args->flip_tag)
< 0)
error_errno("Failed to add \"%s\" INFO header", args->flip_tag);
if (bcf_hdr_printf(out,
"##INFO=<ID=%s,Number=1,Type=Integer,Description=\"Which alternate allele became the reference "
"during liftover (-1 for new reference)\">",
args->swap_tag)
< 0)
error_errno("Failed to add \"%s\" INFO header", args->swap_tag);
if (args->write_src) {
if (bcf_hdr_printf(out,
"##INFO=<ID=SRC_CHROM,Number=1,Type=String,Description=\"The name of the source contig of "
"the variant prior to liftover\">")
< 0)
error_errno("Failed to add \"SRC_CHROM\" INFO header");
if (bcf_hdr_printf(out,
"##INFO=<ID=SRC_POS,Number=1,Type=Integer,Description=\"The position of the variant on the "
"source contig prior to liftover\">")
< 0)
error_errno("Failed to add \"SRC_POS\" INFO header");
if (bcf_hdr_printf(out,
"##INFO=<ID=SRC_REF_ALT,Number=.,Type=String,Description=\"A list of the original alleles "
"of the variant prior to liftover\">")
< 0)
error_errno("Failed to add \"SRC_REF_ALT\" INFO header");
}
if (args->write_fail) {
if (bcf_hdr_printf(
out,
"##INFO=<ID=FAIL5,Number=0,Type=Flag,Description=\"Whether the original 5' anchor failed to lift\">")
< 0)
error_errno("Failed to add \"FAIL5\" INFO header");
if (bcf_hdr_printf(
out,
"##INFO=<ID=FAIL3,Number=0,Type=Flag,Description=\"Whether the original 3' anchor failed to lift\">")
< 0)
error_errno("Failed to add \"FAIL3\" INFO header");
}
if (args->write_nw) {
if (bcf_hdr_printf(out, "##INFO=<ID=NW,Number=.,Type=String,Description=\"Needleman-Wunsch alignments\">") < 0)
error_errno("Failed to add \"NW\" INFO header");
}
if (src_ref_fname)
bcf_hdr_printf(out, "##liftover_target_reference=%s",
strrchr(src_ref_fname, '/') ? strrchr(src_ref_fname, '/') + 1 : src_ref_fname);
if (dst_ref_fname)
bcf_hdr_printf(out, "##liftover_query_reference=%s",
strrchr(dst_ref_fname, '/') ? strrchr(dst_ref_fname, '/') + 1 : dst_ref_fname);
if (chain_fname)
bcf_hdr_printf(out, "##liftover_chain_file=%s",
strrchr(chain_fname, '/') ? strrchr(chain_fname, '/') + 1 : chain_fname);
if (bcf_hdr_sync(out) < 0) error_errno("Failed to update header");
// load chain file
if (max_snp_gap > 20)
fprintf(
stderr,
"Warning: merging contiguous blocks farther than 20 bp apart (--max-snp-gap %d used) is not recommended\n",
max_snp_gap);
if (args->max_indel_inc > 250)
fprintf(stderr,
"Warning: dealing with indels with edges farther apart than 250 bp apart (--max-indel-inc %d used) is "
"not recommended\nThe complexity of the Needleman-Wunsch algorithm used to realign indel sequences "
"near chain gaps grows quadratically in this number",
args->max_indel_inc);
htsFile *fp = hts_open(chain_fname, "r");
if (fp == NULL) error("Could not open %s: %s\n", fp->fn, strerror(errno));
args->n_chains = read_chains(fp, in, out, max_snp_gap, &args->chains, &args->blocks);
if (hts_close(fp) < 0) error("Close failed: %s\n", fp->fn);
if (blocks_fname) {
FILE *blocks_file = get_file_handle(blocks_fname);
write_chains(blocks_file, in, out, args->chains, args->n_chains, args->blocks);
if (blocks_file != stdout && blocks_file != stderr) fclose(blocks_file);
}
args->idx = regidx_init_chains(in, args->chains, args->n_chains, args->blocks);
args->itr = regitr_init(args->idx);
args->info_end_id = bcf_hdr_id2int(in, BCF_DT_ID, "END");
if (!bcf_hdr_idinfo_exists(in, BCF_HL_INFO, args->info_end_id)) args->info_end_id = -1;
args->info_an_id = bcf_hdr_id2int(in, BCF_DT_ID, "AN");
if (!bcf_hdr_idinfo_exists(in, BCF_HL_INFO, args->info_an_id)) args->info_an_id = -1;
args->fmt_gt_id = bcf_hdr_id2int(in, BCF_DT_ID, "GT");
if (!bcf_hdr_idinfo_exists(in, BCF_HL_FMT, args->fmt_gt_id)) args->fmt_gt_id = -1;
args->fmt_an_id = bcf_hdr_id2int(in, BCF_DT_ID, "AN");
if (!bcf_hdr_idinfo_exists(in, BCF_HL_FMT, args->fmt_an_id)) args->fmt_an_id = -1;
args->af_arr = (int *)malloc(sizeof(int) * bcf_hdr_nsamples(in));
for (i = 0; i < bcf_hdr_nsamples(in); i++) args->af_arr[i] = 1;
args->ploidy_arr = (int *)malloc(sizeof(int) * bcf_hdr_nsamples(in));
int *info_rules = (int *)calloc(sizeof(int), in->n[BCF_DT_ID]);
int *fmt_rules = (int *)calloc(sizeof(int), in->n[BCF_DT_ID]);
find_AGR_tags(in, info_rules, fmt_rules);
assign_tags(in, ac_tags, 1 << BCF_VL_A, 1 << BCF_HT_INT | 1 << BCF_HT_REAL, RULE_AC, info_rules, fmt_rules);
assign_tags(in, af_tags, 1 << BCF_VL_A, 1 << BCF_HT_REAL, RULE_AF, info_rules, fmt_rules);
assign_tags(in, ds_tags, 1 << BCF_VL_A, 1 << BCF_HT_REAL, RULE_DS, info_rules, fmt_rules);
assign_tags(in, gt_tags, 1 << BCF_VL_FIXED | 1 << BCF_VL_VAR | 1 << BCF_VL_A | 1 << BCF_VL_G | 1 << BCF_VL_R,
1 << BCF_HT_INT, RULE_GT, info_rules, fmt_rules);
assign_tags(in, es_tags, 1 << BCF_VL_A, 1 << BCF_HT_INT | 1 << BCF_HT_REAL | 1 << BCF_HT_STR, RULE_ES, info_rules,
fmt_rules);
assign_tags(in, drop_tags, 1 << BCF_VL_FIXED | 1 << BCF_VL_VAR | 1 << BCF_VL_A | 1 << BCF_VL_G | 1 << BCF_VL_R,
1 << BCF_HT_FLAG | 1 << BCF_HT_INT | 1 << BCF_HT_REAL | 1 << BCF_HT_STR, RULE_DROP, info_rules,
fmt_rules);
args->n_tags = compress_tags(info_rules, fmt_rules, in->n[BCF_DT_ID], &args->tags);
free(info_rules);
free(fmt_rules);
for (i = 0; i < args->n_tags; i++) {
tag_t *tag = &args->tags[i];
const char *key = bcf_hdr_int2id(in, BCF_DT_ID, tag->int_id);
fprintf(stderr, "%s/%s is handled by %s rule\n", tag->coltype == BCF_HL_INFO ? "INFO" : "FORMAT", key,
rules_str[tag->rule - 1]);
}
// mitochrondria is handled in a special way as GRCh37 has a different mitochondria than hg19
args->in_mt_rid = bcf_hdr_name2id_flexible(in, "MT");
args->out_mt_rid = bcf_hdr_name2id_flexible(out, "chrM");
if (!args->lift_mt && args->in_mt_rid >= 0 && args->out_mt_rid >= 0) {
int in_mt_length = in->id[BCF_DT_CTG][args->in_mt_rid].val->info[0];
int out_mt_length = out->id[BCF_DT_CTG][args->out_mt_rid].val->info[0];
if (in_mt_length == 0 || in_mt_length != out_mt_length) args->lift_mt = 1;
}
if (reject_fname) {
char wmode[8];
set_wmode(wmode, output_type, (char *)reject_fname, clevel);
args->reject_fh = hts_open(reject_fname, hts_bcf_wmode(output_type));
if (args->reject_fh == NULL || bcf_hdr_write(args->reject_fh, args->in_hdr) < 0)
error("Error: cannot write to \"%s\": %s\n", reject_fname, strerror(errno));
}
return 0;
}
/****************************************
* FETCH REFERENCE GENOME SEQUENCE *
****************************************/
// Petr Danecek's code from bcftools/vcfnorm.c
static inline void seq_to_upper(char *seq, int len) {
int i;
for (i = 0; i < len; i++) seq[i] = nt_to_upper(seq[i]);
}
// Petr Danecek's code from bcftools/vcfnorm.c
static inline int replace_iupac_codes(char *seq, int nseq) {
// Replace ambiguity codes with N for now, it awaits to be seen what the VCF spec codifies in the end
int i, n = 0;
for (i = 0; i < nseq; i++) {
char c = toupper(seq[i]);
if (c != 'A' && c != 'C' && c != 'G' && c != 'T' && c != 'N') {
seq[i] = 'N';
n++;
}
}
return n;
}
// fetches sequence in the same way samtools faidx would do using 1-based coordinate system
static inline char *fetch_sequence(const faidx_t *fai, const char *c_name, hts_pos_t p_beg_i, hts_pos_t p_end_i) {
hts_pos_t len;
char *ref = faidx_fetch_seq64(fai, c_name, p_beg_i - 1, p_end_i - 1, &len);
if (!ref || len != p_end_i - p_beg_i + 1) {
free(ref);
return NULL;
}
seq_to_upper(ref, len);
replace_iupac_codes(ref, len);
return ref;
}
/****************************************
* ALLELE EXTENSION FRAMEWORK *
****************************************/
// class to realign alleles using the reference
typedef struct {
const bcf_hdr_t *hdr;
bcf1_t *rec;
kstring_t *als;
faidx_t *fai;
int aln_win;
char *ref;
hts_pos_t beg;
hts_pos_t end;
} bcf1_realign_t;
static void safe_fetch_sequence(bcf1_realign_t *this) {
int seq_len = faidx_seq_len(this->fai, bcf_seqname(this->hdr, this->rec));
if (this->beg + 1 < 1) this->beg = 0;
if (this->end + 1 > seq_len) this->end = seq_len - 1;
this->ref = fetch_sequence(this->fai, bcf_seqname(this->hdr, this->rec), this->beg + 1, this->end + 1);
if (this->ref == NULL)
error("Unable to fetch sequence at %s:%" PRIhts_pos "-%" PRIhts_pos "\n", bcf_seqname(this->hdr, this->rec),
this->beg + 1, this->end + 1);
}
static void shift_left(bcf1_realign_t *this) {
bcf1_t *rec = this->rec;
if (rec->n_allele == 1) return;
while (rec->pos > 0) {
char last_ref = this->als[0].s[this->als[0].l - 1];
int i;
for (i = 1; i < rec->n_allele; i++) {
if (this->als[i].s[0] == '*') continue;
if (this->als[i].s[this->als[i].l - 1] != last_ref) return;
}
if (this->beg == 0 || rec->pos - 1 < this->beg) {
this->beg = rec->pos - this->aln_win;
free(this->ref);
safe_fetch_sequence(this);
}
char first_ref = this->ref[rec->pos - this->beg - 1];
for (i = 0; i < rec->n_allele; i++) {
if (this->als[i].s[0] == '*') continue;