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gtc2vcf.c
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/* The MIT License
Copyright (c) 2018-2022 Giulio Genovese
Author: Giulio Genovese <[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.
*/
#include <getopt.h>
#include <errno.h>
#include <sys/resource.h>
#include <htslib/vcf.h>
#include <htslib/kseq.h>
#include "bcftools.h"
#include "tsv2vcf.h"
#include "htslib/khash_str2int.h"
#include "gtc2vcf.h"
#define GTC2VCF_VERSION "2022-05-18"
#define GT_NC 0
#define GT_AA 1
#define GT_AB 2
#define GT_BB 3
#define TAG_LIST_DFLT "GT,GQ,IGC,BAF,LRR,NORMX,NORMY,R,THETA,X,Y"
#define GC_WIN_DFLT "200"
#define CAPACITY_DFLT "32768"
#define GENOME_BUILD_DFLT "GRCh38"
#define VERBOSE (1 << 0)
#define BPM_LOADED (1 << 1)
#define CSV_LOADED (1 << 2)
#define EGT_LOADED (1 << 3)
#define LOAD_IDAT (1 << 4)
#define ADJUST_CLUSTERS (1 << 5)
#define GENOME_STUDIO (1 << 6)
#define NO_INFO_GC (1 << 7)
#define FORMAT_GT (1 << 8)
#define FORMAT_GQ (1 << 9)
#define FORMAT_IGC (1 << 10)
#define FORMAT_BAF (1 << 11)
#define FORMAT_LRR (1 << 12)
#define FORMAT_NORMX (1 << 13)
#define FORMAT_NORMY (1 << 14)
#define FORMAT_R (1 << 15)
#define FORMAT_THETA (1 << 16)
#define FORMAT_X (1 << 17)
#define FORMAT_Y (1 << 18)
#define USE_ORIGINAL_BAF_LRR (1 << 19) //WRITE ORIGINAL BAF AND LRR VALUES TO THE TARGET VCF WITHOUT NORMALIZING THEM
/****************************************
* hFILE READING FUNCTIONS *
****************************************/
// read or skip a fixed length array
static inline void read_array(hFILE *hfile, void **arr, size_t *m_arr, size_t nmemb, size_t size, size_t term) {
if (arr) {
if (!m_arr) {
*arr = malloc((nmemb + term) * size);
if (!*arr) error("Failed to allocate memory for array\n");
} else if (*m_arr < nmemb + term) {
void *tmp = realloc(*arr, (nmemb + term) * size);
if (!tmp) error("Failed to allocate memory for array\n");
*arr = tmp;
*m_arr = nmemb + term;
}
if (hread(hfile, *arr, nmemb * size) < nmemb * size) {
error("Failed to read %ld bytes from stream\n", nmemb * size);
}
} else {
int c = 0;
for (int i = 0; i < nmemb * size; i++) c = hgetc(hfile);
if (c == EOF) error("Failed to reposition stream forward %ld bytes\n", nmemb * size);
}
}
// read or skip a length-prefixed array
static inline void read_pfx_array(hFILE *hfile, void **arr, size_t *m_arr, size_t item_size) {
int32_t n;
if (hread(hfile, (void *)&n, 4) < 4) {
error("Failed to read 4 bytes from stream\n");
}
read_array(hfile, arr, m_arr, n, item_size, 0);
}
// read or skip a length-prefixed string
// http://en.wikipedia.org/wiki/LEB128#Decode_unsigned_integer
static inline void read_pfx_string(hFILE *hfile, char **str, size_t *m_str) {
uint8_t byte;
size_t n = 0, shift = 0;
while (1) {
if (hread(hfile, (void *)&byte, 1) < 1) {
error("Failed to read 1 byte from stream\n");
}
n |= (size_t)(byte & 0x7F) << shift;
if (!(byte & 0x80)) break;
shift += 7;
}
if (n || m_str) {
read_array(hfile, (void **)str, m_str, n, 1, 1);
if (str) (*str)[n] = '\0';
}
}
// check whether file is compressed with gzip
static inline int is_gzip(hFILE *hfile) {
uint8_t buffer[2];
if (hpeek(hfile, (void *)buffer, 2) < 2) error("Failed to read 2 bytes from stream\n");
return (buffer[0] == 0x1f && buffer[1] == 0x8b);
}
/****************************************
* BUFFER ARRAY IMPLEMENTATION *
****************************************/
typedef struct {
hFILE *hfile;
off_t offset;
int32_t item_num;
int32_t item_offset;
size_t item_capacity;
size_t item_size;
char *buffer;
} buffer_array_t;
static buffer_array_t *buffer_array_init(hFILE *hfile, size_t capacity, size_t item_size) {
buffer_array_t *arr = (buffer_array_t *)malloc(1 * sizeof(buffer_array_t));
arr->hfile = hfile;
read_bytes(hfile, (void *)&arr->item_num, sizeof(int32_t));
arr->offset = htell(arr->hfile);
arr->item_offset = 0;
arr->item_capacity = (capacity <= 0) ? (size_t)strtol(CAPACITY_DFLT, NULL, 0) : capacity;
arr->item_size = item_size;
arr->buffer = (char *)malloc(arr->item_capacity * item_size);
read_bytes(hfile, (void *)arr->buffer,
(arr->item_num < arr->item_capacity ? arr->item_num : arr->item_capacity) * item_size);
return arr;
}
static inline int get_element(buffer_array_t *arr, void *dst, size_t item_idx) {
if (!arr || item_idx >= arr->item_num) {
return -1;
} else if (item_idx - arr->item_offset < arr->item_capacity) {
memcpy(dst, (void *)(arr->buffer + (item_idx - arr->item_offset) * arr->item_size), arr->item_size);
return 0;
}
arr->item_offset = item_idx;
if (hseek(arr->hfile, arr->offset + item_idx * arr->item_size, SEEK_SET) < 0) {
error("Fail to seek to position %ld in file\n", arr->offset + item_idx * arr->item_size);
}
read_bytes(arr->hfile, (void *)arr->buffer,
((arr->item_num - arr->item_offset) < arr->item_capacity ? (arr->item_num - arr->item_offset)
: arr->item_capacity)
* arr->item_size);
memcpy(dst, (void *)arr->buffer, arr->item_size);
return 0;
}
static void buffer_array_destroy(buffer_array_t *arr) {
if (!arr) return;
free(arr->buffer);
free(arr);
}
/****************************************
* BPM FILE IMPLEMENTATION *
****************************************/
// http://github.com/snewhouse/glu-genetics/blob/master/glu/lib/illumina.py
// http://github.com/Illumina/BeadArrayFiles/blob/develop/module/BeadPoolManifest.py
typedef struct {
int32_t version;
uint8_t norm_id; // Normalization lookups from manifest. This indexes into list of
// normalization transforms read from GTC file
char *ilmn_id; // IlmnID (probe identifier) of locus
char *name; // Name (variant identifier) of locus
int32_t index;
char *ilmn_strand; // TOP BOT PLUS MINUS or Top Bot P M
char *snp; // SNP value for locus (e.g., [A/C])
char *chrom; // Chromosome for the locus (e.g., XY)
char *ploidy;
char *species;
char *map_info; // Mapping location of locus
char *customer_strand;
int32_t address_a; // AddressA ID of locus
char *allele_a_probe_seq; // CSV files or BPM files with version 4 data block
int32_t address_b; // AddressB ID of locus (0 if none)
char *allele_b_probe_seq; // CSV files or BPM files with version 4 data block (empty if
// none)
char *genome_build;
char *source;
char *source_version;
char *source_strand;
char *source_seq; // CSV files or BPM files with version 4 data block
char *top_genomic_seq; // CSV files or BPM files with version 4 data block
int32_t beadset_id; // CSV files
uint8_t exp_clusters;
uint8_t intensity_only;
uint8_t assay_type; // Identifies type of assay (0 - Infinium II, 1 - Infinium I (A/T),
// 2 - Infinium I (G/C)
uint8_t assay_type_csv;
float frac_a;
float frac_c;
float frac_g;
float frac_t;
char *ref_strand; // RefStrand annotation
} LocusEntry;
// retrieve assay type following (allele_a_probe_seq, source_seq) -> assay_type map
// (...W., ...W[./.]W...) -> 1
// (...S., ...S[./.]S...) -> 2
// (...S., ...S[./.]W...) -> 1
// (...S., ...W[./.]S...) -> 1
// (...W., ...S[./.]W...) -> 2
// (...W., ...W[./.]S...) -> 2
static uint8_t get_assay_type(const char *allele_a_probe_seq, const char *allele_b_probe_seq, const char *source_seq) {
if (!allele_a_probe_seq || !source_seq) return 0xFF;
if (!allele_b_probe_seq) return 0;
const char *left = strchr(source_seq, '[');
const char *right = strchr(source_seq, ']');
if (!left || !right) error("Source sequence is malformed: %s\n", source_seq);
char trail_left = toupper(*(left - 1));
char trail_right = toupper(*(right + 1));
if ((trail_left == 'A' || trail_left == 'T') && (trail_right == 'A' || trail_right == 'T')) return 1;
if ((trail_left == 'C' || trail_left == 'G') && (trail_right == 'C' || trail_right == 'G')) return 2;
int i = 2;
while (!(iupac2bitmask(allele_a_probe_seq[strlen(allele_a_probe_seq) - i])
& iupac2bitmask(allele_b_probe_seq[strlen(allele_b_probe_seq) - i])))
i++;
char trail_a_probe_seq = toupper(allele_a_probe_seq[strlen(allele_a_probe_seq) - i]);
if (trail_a_probe_seq == 'C' || trail_a_probe_seq == 'G' || trail_a_probe_seq == 'S') return 1;
if (trail_a_probe_seq == 'A' || trail_a_probe_seq == 'T' || trail_a_probe_seq == 'W') return 2;
// these weird rule were deduced from manifests for array GDA_PGx-8v1-0_20042614
if (trail_a_probe_seq == 'Y' && trail_right == 'G') return 1;
if (trail_a_probe_seq == 'Y' && trail_right == 'T') return 1;
if (trail_a_probe_seq == 'Y' && trail_right == 'A') return 2;
if (trail_a_probe_seq == 'K' && trail_right == 'C') return 1;
if (trail_a_probe_seq == 'K' && trail_right == 'A') return 2;
if (trail_a_probe_seq == 'M' && trail_right == 'G') return 1;
if (trail_a_probe_seq == 'M' && trail_right == 'T') return 2;
if (trail_a_probe_seq == 'R' && trail_right == 'C') return 1;
if (trail_a_probe_seq == 'R' && trail_right == 'T') return 2;
fprintf(stderr, "Warning: Unable to retrieve assay type: %s %s %s\n", allele_a_probe_seq, allele_b_probe_seq,
source_seq);
return 0xFF;
}
static void locusentry_read(LocusEntry *locus_entry, hFILE *hfile) {
locus_entry->norm_id = 0xFF;
read_bytes(hfile, (void *)&locus_entry->version, sizeof(int32_t));
if (locus_entry->version < 4 || locus_entry->version == 5 || locus_entry->version > 8)
error("Locus version %d in manifest file not supported\n", locus_entry->version);
read_pfx_string(hfile, &locus_entry->ilmn_id, NULL);
read_pfx_string(hfile, &locus_entry->name, NULL);
read_pfx_string(hfile, NULL, NULL);
read_pfx_string(hfile, NULL, NULL);
read_pfx_string(hfile, NULL, NULL);
read_bytes(hfile, (void *)&locus_entry->index, sizeof(int32_t));
read_pfx_string(hfile, NULL, NULL);
read_pfx_string(hfile, &locus_entry->ilmn_strand, NULL);
read_pfx_string(hfile, &locus_entry->snp, NULL);
read_pfx_string(hfile, &locus_entry->chrom, NULL);
read_pfx_string(hfile, &locus_entry->ploidy, NULL);
read_pfx_string(hfile, &locus_entry->species, NULL);
read_pfx_string(hfile, &locus_entry->map_info, NULL);
read_pfx_string(hfile, &locus_entry->top_genomic_seq, NULL); // only version 4
read_pfx_string(hfile, &locus_entry->customer_strand, NULL);
read_bytes(hfile, (void *)&locus_entry->address_a, sizeof(int32_t));
read_bytes(hfile, (void *)&locus_entry->address_b, sizeof(int32_t));
read_pfx_string(hfile, &locus_entry->allele_a_probe_seq, NULL); // only version 4
read_pfx_string(hfile, &locus_entry->allele_b_probe_seq, NULL); // only version 4
read_pfx_string(hfile, &locus_entry->genome_build, NULL);
read_pfx_string(hfile, &locus_entry->source, NULL);
read_pfx_string(hfile, &locus_entry->source_version, NULL);
read_pfx_string(hfile, &locus_entry->source_strand, NULL);
read_pfx_string(hfile, &locus_entry->source_seq, NULL); // only version 4
if (locus_entry->source_seq) {
char *ptr = strchr(locus_entry->source_seq, '-');
if (ptr && *(ptr - 1) == '/') {
*ptr = *(ptr - 2);
*(ptr - 2) = '-';
}
}
if (locus_entry->version >= 6) {
read_bytes(hfile, NULL, 1);
read_bytes(hfile, (void *)&locus_entry->exp_clusters, sizeof(int8_t));
read_bytes(hfile, (void *)&locus_entry->intensity_only, sizeof(int8_t));
read_bytes(hfile, (void *)&locus_entry->assay_type, sizeof(uint8_t));
if (locus_entry->assay_type < 0 || locus_entry->assay_type > 2)
error("Format error in reading assay type from locus entry\n");
if (locus_entry->address_b == 0 && locus_entry->assay_type != 0)
error("Manifest format error: Assay type is inconsistent with address B\n");
if (locus_entry->address_b != 0 && locus_entry->assay_type == 0)
error("Manifest format error: Assay type is inconsistent with address B\n");
} else {
locus_entry->assay_type =
get_assay_type(locus_entry->allele_a_probe_seq, locus_entry->allele_b_probe_seq, locus_entry->source_seq);
}
if (locus_entry->version >= 7) {
read_bytes(hfile, &locus_entry->frac_a, sizeof(float));
read_bytes(hfile, &locus_entry->frac_c, sizeof(float));
read_bytes(hfile, &locus_entry->frac_t, sizeof(float));
read_bytes(hfile, &locus_entry->frac_g, sizeof(float));
}
if (locus_entry->version >= 8) read_pfx_string(hfile, &locus_entry->ref_strand, NULL);
}
typedef struct {
char *fn;
hFILE *hfile; // bpm file
htsFile *fp; // csv file
int32_t version;
char *manifest_name; // Name of manifest
char *control_config; // Control description from manifest
int32_t num_loci; // Number of loci in manifest
int32_t *indexes;
char **names; // Names of loci from manifest
void *names2index;
uint8_t *norm_ids;
LocusEntry *locus_entries;
uint8_t *norm_lookups;
char **header;
size_t m_header;
} bpm_t;
static uint8_t *bpm_norm_lookups(bpm_t *bpm) {
uint8_t sorted_norm_ids[256];
for (int i = 0; i < 256; i++) sorted_norm_ids[i] = 0xFF;
for (int i = 0; i < bpm->num_loci; i++) {
int norm_id = bpm->locus_entries[i].norm_id;
sorted_norm_ids[norm_id] = norm_id;
}
int j = 0;
for (int i = 0; i < 256; i++)
if (sorted_norm_ids[i] != 0xFF) sorted_norm_ids[j++] = sorted_norm_ids[i];
uint8_t *norm_lookups = (uint8_t *)malloc(256 * sizeof(uint8_t *));
memset((void *)norm_lookups, 0xFF, 256 * sizeof(uint8_t *));
for (int i = 0; i < j; i++) norm_lookups[sorted_norm_ids[i]] = i;
return norm_lookups;
}
static bpm_t *bpm_init(const char *fn, int make_dict) {
bpm_t *bpm = (bpm_t *)calloc(1, sizeof(bpm_t));
bpm->fn = strdup(fn);
bpm->hfile = hopen(bpm->fn, "rb");
if (bpm->hfile == NULL) error("Could not open %s: %s\n", bpm->fn, strerror(errno));
if (is_gzip(bpm->hfile)) error("File %s is gzip compressed and currently cannot be sought\n", bpm->fn);
uint8_t buffer[4];
if (hread(bpm->hfile, (void *)buffer, 4) < 4) error("Failed to read magic number from %s file\n", bpm->fn);
if (memcmp(buffer, "BPM", 3) != 0) error("BPM file %s format identifier is bad\n", bpm->fn);
if (buffer[3] != 1) error("BPM file %s version is unknown\n", bpm->fn);
read_bytes(bpm->hfile, (void *)&bpm->version, sizeof(int32_t));
if (bpm->version & 0x1000) bpm->version ^= 0x1000;
if (bpm->version > 5 || bpm->version < 3) error("BPM file %s version %d is unsupported\n", bpm->fn, bpm->version);
read_pfx_string(bpm->hfile, &bpm->manifest_name, NULL);
if (bpm->version > 1) read_pfx_string(bpm->hfile, &bpm->control_config, NULL);
read_bytes(bpm->hfile, (void *)&bpm->num_loci, sizeof(int32_t));
read_array(bpm->hfile, (void **)&bpm->indexes, NULL, bpm->num_loci, sizeof(int32_t), 0);
bpm->names = (char **)malloc(bpm->num_loci * sizeof(char *));
for (int i = 0; i < bpm->num_loci; i++) read_pfx_string(bpm->hfile, &bpm->names[i], NULL);
if (make_dict) {
bpm->names2index = khash_str2int_init();
for (int i = 0; i < bpm->num_loci; i++) {
if (khash_str2int_has_key(bpm->names2index, bpm->names[i]))
error("Illumina probe %s present multiple times in file %s\n", bpm->names[i], fn);
khash_str2int_inc(bpm->names2index, bpm->names[i]);
}
}
read_array(bpm->hfile, (void **)&bpm->norm_ids, NULL, bpm->num_loci, sizeof(uint8_t), 0);
bpm->locus_entries = (LocusEntry *)malloc(bpm->num_loci * sizeof(LocusEntry));
LocusEntry locus_entry;
for (int i = 0; i < bpm->num_loci; i++) {
memset(&locus_entry, 0, sizeof(LocusEntry));
locusentry_read(&locus_entry, bpm->hfile);
int idx = locus_entry.index - 1;
if (idx < 0 || idx >= bpm->num_loci) error("Locus entry index %d is out of boundaries\n", locus_entry.index);
if (bpm->norm_ids[idx] > 100)
error("Manifest format error: read invalid normalization ID %d\n", bpm->norm_ids[idx]);
// To mimic the flawed byte-wrapping behavior from GenomeStudio, AutoCall, and
// IAAP, this value is allowed to overflow beyond 255, which happens with some
// probes in the Omni5 arrays
locus_entry.norm_id = bpm->norm_ids[idx] + 100 * locus_entry.assay_type;
memcpy(&bpm->locus_entries[idx], &locus_entry, sizeof(LocusEntry));
}
bpm->norm_lookups = bpm_norm_lookups(bpm);
for (int i = 0; i < bpm->num_loci; i++) {
if (i != bpm->locus_entries[i].index - 1)
error("Manifest format error: read invalid number of assay entries\n");
}
if (bpm->locus_entries[0].version < 8)
fprintf(stderr, "Warning: RefStrand annotation missing from manifest file %s\n", bpm->fn);
read_bytes(bpm->hfile, (void *)&bpm->m_header, sizeof(int32_t));
bpm->header = (char **)malloc(bpm->m_header * sizeof(char *));
for (int i = 0; i < bpm->m_header; i++) read_pfx_string(bpm->hfile, &bpm->header[i], NULL);
if (!heof(bpm->hfile))
error("BPM reader did not reach the end of file %s at position %ld\n", bpm->fn, htell(bpm->hfile));
return bpm;
}
static void bpm_destroy(bpm_t *bpm) {
if (!bpm) return;
if (bpm->hfile && hclose(bpm->hfile) < 0) error("Error closing BPM file %s\n", bpm->fn);
free(bpm->fn);
if (bpm->fp && hts_close(bpm->fp) < 0) error("Error closing CSV file %s\n", bpm->fp->fn);
free(bpm->manifest_name);
free(bpm->control_config);
free(bpm->indexes);
if (bpm->names) {
for (int i = 0; i < bpm->num_loci; i++) free(bpm->names[i]);
free(bpm->names);
}
khash_str2int_destroy(bpm->names2index);
free(bpm->norm_ids);
for (int i = 0; i < bpm->num_loci; i++) {
LocusEntry *locus_entry = &bpm->locus_entries[i];
free(locus_entry->ilmn_id);
free(locus_entry->name);
free(locus_entry->ilmn_strand);
free(locus_entry->snp);
free(locus_entry->chrom);
free(locus_entry->ploidy);
free(locus_entry->species);
free(locus_entry->map_info);
free(locus_entry->customer_strand);
free(locus_entry->allele_a_probe_seq);
free(locus_entry->allele_b_probe_seq);
free(locus_entry->genome_build);
free(locus_entry->source);
free(locus_entry->source_version);
free(locus_entry->source_strand);
free(locus_entry->source_seq);
free(locus_entry->top_genomic_seq);
free(locus_entry->ref_strand);
}
free(bpm->locus_entries);
free(bpm->norm_lookups);
for (int i = 0; i < bpm->m_header; i++) free(bpm->header[i]);
free(bpm->header);
free(bpm);
}
static void bpm_to_csv(const bpm_t *bpm, FILE *stream, int flags) {
for (int i = 0; i < bpm->m_header; i++) fprintf(stream, "%s\n", bpm->header[i]);
if (flags & BPM_LOADED) {
fprintf(stream,
"Index,NormID,IlmnID,Name,IlmnStrand,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_"
"ID,AlleleB_ProbeSeq,GenomeBuild,Chr,MapInfo,Ploidy,Species,Source,"
"SourceVersion,SourceStrand,SourceSeq,TopGenomicSeq,BeadSetID,Exp_Clusters,"
"Intensity_Only,Assay_Type,Frac A,Frac C,Frac G,Frac T,RefStrand");
if (flags & CSV_LOADED) fprintf(stream, ",Assay_Type_CSV");
fputc('\n', stream);
} else {
fprintf(stream,
"IlmnID,Name,IlmnStrand,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_ID,AlleleB_"
"ProbeSeq,GenomeBuild,Chr,MapInfo,Ploidy,Species,Source,SourceVersion,"
"SourceStrand,SourceSeq,TopGenomicSeq,BeadSetID,Exp_Clusters,RefStrand\n");
}
if (flags & VERBOSE) {
kstring_t address_b = {0, 0, NULL};
if (flags & BPM_LOADED) {
for (int i = 0; i < bpm->num_loci; i++) {
LocusEntry *locus_entry = &bpm->locus_entries[i];
address_b.l = 0;
ksprintf(&address_b, locus_entry->address_b ? "%010d" : "", locus_entry->address_b);
fprintf(stream,
"%d,%d,%s,%s,%s,%s,%010d,%-s,%s,%-s,%s,%s,%s,%s,%s,%s,%s,%s,%-s,%-s,%d,"
"%d,%d,%d,%f,%f,%f,%f,%s",
locus_entry->index, locus_entry->norm_id, locus_entry->ilmn_id, locus_entry->name,
locus_entry->ilmn_strand, locus_entry->snp, locus_entry->address_a,
locus_entry->allele_a_probe_seq ? locus_entry->allele_a_probe_seq : "", address_b.s,
locus_entry->allele_b_probe_seq ? locus_entry->allele_b_probe_seq : "",
locus_entry->genome_build, locus_entry->chrom, locus_entry->map_info, locus_entry->ploidy,
locus_entry->species, locus_entry->source, locus_entry->source_version,
locus_entry->source_strand, locus_entry->source_seq ? locus_entry->source_seq : "",
locus_entry->top_genomic_seq ? locus_entry->top_genomic_seq : "", locus_entry->beadset_id,
locus_entry->exp_clusters, locus_entry->intensity_only, locus_entry->assay_type,
locus_entry->frac_a, locus_entry->frac_c, locus_entry->frac_g, locus_entry->frac_t,
locus_entry->ref_strand ? locus_entry->ref_strand : "");
if (flags & CSV_LOADED) fprintf(stream, ",%d", locus_entry->assay_type_csv);
fputc('\n', stream);
}
} else {
for (int i = 0; i < bpm->num_loci; i++) {
LocusEntry *locus_entry = &bpm->locus_entries[i];
address_b.l = 0;
ksprintf(&address_b, locus_entry->address_b ? "%010d" : "", locus_entry->address_b);
fprintf(stream, "%s,%s,%s,%s,%010d,%-s,%s,%-s,%s,%s,%s,%s,%s,%s,%s,%s,%-s,%-s,%d,%d,%s\n",
locus_entry->ilmn_id, locus_entry->name, locus_entry->ilmn_strand, locus_entry->snp,
locus_entry->address_a, locus_entry->allele_a_probe_seq, address_b.s,
locus_entry->allele_b_probe_seq ? locus_entry->allele_b_probe_seq : "",
locus_entry->genome_build, locus_entry->chrom, locus_entry->map_info, locus_entry->ploidy,
locus_entry->species, locus_entry->source, locus_entry->source_version,
locus_entry->source_strand, locus_entry->source_seq, locus_entry->top_genomic_seq,
locus_entry->beadset_id, locus_entry->exp_clusters,
locus_entry->ref_strand ? locus_entry->ref_strand : "");
}
}
free(address_b.s);
} else {
fprintf(stream, "... use --verbose to visualize Assay data ...\n");
}
fprintf(stream, "[Controls]\n");
fprintf(stream, "%s", bpm->control_config);
}
/****************************************
* CSV FILE IMPLEMENTATION *
****************************************/
static int tsv_read_uint8(tsv_t *tsv, bcf1_t *rec, void *usr) {
uint8_t *uint8 = (uint8_t *)usr;
char tmp = *tsv->se;
*tsv->se = 0;
char *endptr;
*uint8 = (uint8_t)strtol(tsv->ss, &endptr, 0);
*tsv->se = tmp;
return 0;
}
static int tsv_read_int32(tsv_t *tsv, bcf1_t *rec, void *usr) {
int32_t *int32 = (int32_t *)usr;
char tmp = *tsv->se;
*tsv->se = 0;
char *endptr;
*int32 = (int32_t)strtol(tsv->ss, &endptr, 10);
*tsv->se = tmp;
return 0;
}
static int tsv_read_float(tsv_t *tsv, bcf1_t *rec, void *usr) {
float *single = (float *)usr;
char tmp = *tsv->se;
*tsv->se = 0;
char *endptr;
*single = (float)strtof(tsv->ss, &endptr);
*tsv->se = tmp;
return 0;
}
static int tsv_read_string(tsv_t *tsv, bcf1_t *rec, void *usr) {
char **str = (char **)usr;
if (tsv->se == tsv->ss) {
*str = NULL;
} else {
char tmp = *tsv->se;
*tsv->se = 0;
*str = strdup(tsv->ss);
*tsv->se = tmp;
}
return 0;
}
// Petr Danecek's similar implementation in bcftools/tsv2vcf.c
static int csv_parse(tsv_t *tsv, bcf1_t *rec, char *str) {
int status = 0;
tsv->icol = 0;
tsv->ss = tsv->se = str;
while (*tsv->ss && tsv->icol < tsv->ncols) {
while (*tsv->se && *tsv->se != ',') tsv->se++;
if (tsv->cols[tsv->icol].setter) {
int ret = tsv->cols[tsv->icol].setter(tsv, rec, tsv->cols[tsv->icol].usr);
if (ret < 0) return -1;
status++;
}
if (*tsv->se) tsv->se++;
tsv->ss = tsv->se;
tsv->icol++;
}
return status ? 0 : -1;
}
static void locus_merge(LocusEntry *dest, LocusEntry *src) {
if (src->version) dest->version = src->version;
if (src->norm_id != 0xFF) dest->norm_id = src->norm_id;
if (strcmp(dest->ilmn_id, src->ilmn_id)) {
error("BPM and CSV manifests have conflicting IDs: %s and %s\n", dest->ilmn_id, src->ilmn_id);
} else {
free(dest->ilmn_id);
dest->ilmn_id = src->ilmn_id;
}
if (src->name) {
free(dest->name);
dest->name = src->name;
}
if (src->index != 0) dest->index = src->index;
if (src->ilmn_strand) {
free(dest->ilmn_strand);
dest->ilmn_strand = src->ilmn_strand;
}
if (src->snp) {
free(dest->snp);
dest->snp = src->snp;
}
if (src->chrom) {
free(dest->chrom);
dest->chrom = src->chrom;
}
if (src->ploidy) {
free(dest->ploidy);
dest->ploidy = src->ploidy;
}
if (src->species) {
free(dest->species);
dest->species = src->species;
}
if (src->map_info) {
free(dest->map_info);
dest->map_info = src->map_info;
}
if (src->customer_strand) {
free(dest->customer_strand);
dest->customer_strand = src->customer_strand;
}
if (src->address_a != 0) dest->address_a = src->address_a;
if (src->allele_a_probe_seq) {
free(dest->allele_a_probe_seq);
dest->allele_a_probe_seq = src->allele_a_probe_seq;
}
if (src->address_b != 0) dest->address_b = src->address_b;
if (src->allele_b_probe_seq) {
free(dest->allele_b_probe_seq);
dest->allele_b_probe_seq = src->allele_b_probe_seq;
}
if (src->genome_build) {
free(dest->genome_build);
dest->genome_build = src->genome_build;
}
if (src->source) {
free(dest->source);
dest->source = src->source;
}
if (src->source_version) {
free(dest->source_version);
dest->source_version = src->source_version;
}
if (src->source_strand) {
free(dest->source_strand);
dest->source_strand = src->source_strand;
}
if (src->source_seq) {
free(dest->source_seq);
dest->source_seq = src->source_seq;
}
if (src->top_genomic_seq) {
free(dest->top_genomic_seq);
dest->top_genomic_seq = src->top_genomic_seq;
}
if (src->beadset_id) dest->beadset_id = src->beadset_id;
if (src->exp_clusters) dest->exp_clusters = src->exp_clusters;
if (src->intensity_only) dest->intensity_only = src->intensity_only;
if (src->assay_type != 0xFF) dest->assay_type = src->assay_type;
if (src->assay_type_csv != 0xFF) dest->assay_type_csv = src->assay_type_csv;
if (src->frac_a) dest->frac_a = src->frac_a;
if (src->frac_c) dest->frac_c = src->frac_c;
if (src->frac_g) dest->frac_g = src->frac_g;
if (src->frac_t) dest->frac_t = src->frac_t;
if (src->ref_strand) {
free(dest->ref_strand);
dest->ref_strand = src->ref_strand;
}
}
// this line will read a CSV file and if a BPM object is provided it will fill it rather than
// create a new one
static bpm_t *bpm_csv_init(const char *fn, bpm_t *bpm, int make_dict) {
int bpm_available = bpm != NULL;
if (!bpm_available) bpm = (bpm_t *)calloc(1, sizeof(bpm_t));
int bpm_prev_num_loci = bpm->num_loci;
bpm->fp = hts_open(fn, "r");
if (bpm->fp == NULL) error("Could not open %s: %s\n", fn, strerror(errno));
kstring_t str = {0, 0, NULL};
kstring_t hdr = {0, 0, NULL};
if (hts_getline(bpm->fp, KS_SEP_LINE, &str) <= 0) error("Empty file: %s\n", fn);
if (strncmp(str.s, "Illumina", 8) && strncmp(str.s, "\"Illumina", 9))
error("Header of file %s is incorrect: %s\n", fn, str.s);
kputs(str.s, &hdr);
kputc('\n', &hdr);
char *tmp = NULL;
size_t prev = 0;
while (strncmp(str.s + prev, "[Assay]", 7)) {
if (strncmp(str.s + prev, "Descriptor File Name,", 21) == 0) {
free(bpm->manifest_name);
bpm->manifest_name = strdup(str.s + prev + 21);
char *ptr = strchr(bpm->manifest_name, ',');
if (ptr) *ptr = '\0';
} else if (strncmp(str.s + prev, "Loci Count ,", 12) == 0) {
bpm->num_loci = (int)strtol(str.s + prev + 12, &tmp, 0);
} else if (strncmp(str.s + prev, "Loci Count,", 11) == 0) {
bpm->num_loci = (int)strtol(str.s + prev + 11, &tmp, 0);
}
if (hts_getline(bpm->fp, KS_SEP_LINE, &str) <= 0) error("Error reading from file: %s\n", fn);
kputs(str.s, &hdr);
kputc('\n', &hdr);
}
if (bpm->num_loci == 0)
error("Could not understand number of loci from header of manifest file %s\n", fn);
else if (bpm_available && bpm_prev_num_loci != bpm->num_loci)
error("BPM manifest file has %d loci while CSV manifest file %s has %d loci\n", bpm_prev_num_loci, fn,
bpm->num_loci);
int moff = 0, *off = NULL;
for (int i = 0; i < bpm->m_header; i++) free(bpm->header[i]);
bpm->m_header = ksplit_core(hdr.s, '\n', &moff, &off);
free(bpm->header);
bpm->header = (char **)malloc(bpm->m_header * sizeof(char *));
for (int i = 0; i < bpm->m_header; i++) bpm->header[i] = strdup(&hdr.s[off[i]]);
free(off);
free(hdr.s);
if (hts_getline(bpm->fp, KS_SEP_LINE, &str) <= 0) error("Error reading from file: %s\n", fn);
LocusEntry locus_entry;
tsv_t *tsv = tsv_init(str.s);
tsv_register(tsv, "Index", tsv_read_int32, &locus_entry.index);
int norm_id = tsv_register(tsv, "NormID", tsv_read_uint8, &locus_entry.norm_id);
tsv_register(tsv, "IlmnID", tsv_read_string, &locus_entry.ilmn_id);
tsv_register(tsv, "Name", tsv_read_string, &locus_entry.name);
tsv_register(tsv, "IlmnStrand", tsv_read_string, &locus_entry.ilmn_strand);
tsv_register(tsv, "SNP", tsv_read_string, &locus_entry.snp);
tsv_register(tsv, "AddressA_ID", tsv_read_int32, &locus_entry.address_a);
tsv_register(tsv, "AlleleA_ProbeSeq", tsv_read_string, &locus_entry.allele_a_probe_seq);
tsv_register(tsv, "AddressB_ID", tsv_read_int32, &locus_entry.address_b);
tsv_register(tsv, "AlleleB_ProbeSeq", tsv_read_string, &locus_entry.allele_b_probe_seq);
tsv_register(tsv, "GenomeBuild", tsv_read_string, &locus_entry.genome_build);
tsv_register(tsv, "Chr", tsv_read_string, &locus_entry.chrom);
tsv_register(tsv, "MapInfo", tsv_read_string, &locus_entry.map_info);
tsv_register(tsv, "Ploidy", tsv_read_string, &locus_entry.ploidy);
tsv_register(tsv, "Species", tsv_read_string, &locus_entry.species);
tsv_register(tsv, "Source", tsv_read_string, &locus_entry.source);
tsv_register(tsv, "SourceVersion", tsv_read_string, &locus_entry.source_version);
tsv_register(tsv, "SourceStrand", tsv_read_string, &locus_entry.source_strand);
tsv_register(tsv, "SourceSeq", tsv_read_string, &locus_entry.source_seq);
tsv_register(tsv, "TopGenomicSeq", tsv_read_string, &locus_entry.top_genomic_seq);
int beadset_id = tsv_register(tsv, "BeadSetID", tsv_read_int32, &locus_entry.beadset_id);
tsv_register(tsv, "Exp_Clusters", tsv_read_uint8, &locus_entry.exp_clusters);
tsv_register(tsv, "Intensity_Only", tsv_read_uint8, &locus_entry.intensity_only);
tsv_register(tsv, "Frac A", tsv_read_float, &locus_entry.frac_a);
tsv_register(tsv, "Frac C", tsv_read_float, &locus_entry.frac_c);
tsv_register(tsv, "Frac G", tsv_read_float, &locus_entry.frac_g);
tsv_register(tsv, "Frac T", tsv_read_float, &locus_entry.frac_t);
int ref_strand = tsv_register(tsv, "RefStrand", tsv_read_string, &locus_entry.ref_strand);
if (ref_strand < 0) fprintf(stderr, "Warning: RefStrand annotation missing from manifest file %s\n", fn);
if (!bpm_available) bpm->locus_entries = (LocusEntry *)malloc(bpm->num_loci * sizeof(LocusEntry));
for (int i = 0; i < bpm->num_loci; i++) {
memset(&locus_entry, 0, sizeof(LocusEntry));
locus_entry.norm_id = 0xFF;
locus_entry.assay_type = 0xFF;
locus_entry.assay_type_csv = 0xFF;
if (hts_getline(bpm->fp, KS_SEP_LINE, &str) <= 0) error("Error reading from file: %s\n", fn);
if (csv_parse(tsv, NULL, str.s) < 0) error("Could not parse the manifest file: %s\n", str.s);
if (beadset_id == 0 && locus_entry.beadset_id == 0)
error("BeadSetID value 0 for probe %s is not allowed\n", locus_entry.ilmn_id);
if (locus_entry.source_seq) {
char *ptr = strchr(locus_entry.source_seq, '-');
if (ptr && *(ptr - 1) == '/') {
*ptr = *(ptr - 2);
*(ptr - 2) = '-';
}
}
locus_entry.assay_type_csv =
get_assay_type(locus_entry.allele_a_probe_seq, locus_entry.allele_b_probe_seq, locus_entry.source_seq);
if (locus_entry.index == 0) locus_entry.index = i + 1;
int idx = locus_entry.index - 1;
if (idx < 0 || idx >= bpm->num_loci) error("Locus entry index %d is out of boundaries\n", idx);
if (!bpm_available) {
memcpy(&bpm->locus_entries[idx], &locus_entry, sizeof(LocusEntry));
} else {
locus_merge(&bpm->locus_entries[idx], &locus_entry);
if (bpm->locus_entries[idx].assay_type != 0xff
&& bpm->locus_entries[idx].assay_type != bpm->locus_entries[idx].assay_type_csv)
fprintf(stderr, "Warning: Failed to retrieve assay type %d: %s %s %s\n",
bpm->locus_entries[idx].assay_type, bpm->locus_entries[idx].allele_a_probe_seq,
bpm->locus_entries[idx].allele_b_probe_seq, bpm->locus_entries[idx].source_seq);
}
}
tsv_destroy(tsv);
if (hts_getline(bpm->fp, KS_SEP_LINE, &str) <= 0) error("Error reading from file: %s\n", fn);
if (strncmp(str.s, "[Controls]", 10) != 0)
error(
"Missing [Controls] section from manifest file: %s\n"
"Found the following line instead: %s\n",
fn, str.s);
while (hts_getline(bpm->fp, KS_SEP_LINE, &str) > 0) kputc('\n', &str);
free(bpm->control_config);
bpm->control_config = str.s;
if (make_dict && !bpm->names2index) {
bpm->names2index = khash_str2int_init();
for (int i = 0; i < bpm->num_loci; i++) {
if (khash_str2int_has_key(bpm->names2index, bpm->locus_entries[i].name))
error("Illumina probe %s present multiple times in file %s\n", bpm->locus_entries[i].name, fn);
khash_str2int_inc(bpm->names2index, bpm->locus_entries[i].name);
}
}
if (norm_id == 0) {
free(bpm->norm_lookups);
bpm->norm_lookups = bpm_norm_lookups(bpm);
}
return bpm;
}
/****************************************
* EGT FILE IMPLEMENTATION *
****************************************/
// http://github.com/broadinstitute/picard/blob/master/src/main/java/picard/arrays/illumina/InfiniumEGTFile.java
// http://github.com/Illumina/BeadArrayFiles/blob/develop/module/ClusterFile.py
typedef struct {
int32_t N; // Number of samples assigned to cluster during training
float r_dev; // R (intensity) std deviation value
float r_mean; // R (intensity) mean value
float theta_dev; // Theta std devation value
float theta_mean; // Theta mean value
} ClusterStats;
typedef struct {
float cluster_separation; // A score measure the separation between genotype clusters
float total_score; // The GenTrain score
float original_score; // The original score before editing this cluster
uint8_t edited; // Whether this cluster has been manually manipulated
} ClusterScore;
typedef struct {
ClusterStats aa_cluster_stats; // Describes AA genotype cluster
ClusterStats ab_cluster_stats; // Describes AB genotype cluster
ClusterStats bb_cluster_stats; // Describes BB genotype cluster
float intensity_threshold; // Intensity threshold for no-call
ClusterScore cluster_score; // Various scores for cluster
int32_t address; // Bead type identifier for probe A
float r_mean; // precomputed clusters mean
} ClusterRecord;
typedef struct {
char *fn;
hFILE *hfile;
int32_t version;
char *gencall_version; // The GenCall version
char *cluster_version; // The clustering algorithm version
char *call_version; // The genotyping algorithm version
char *normalization_version; // The normalization algorithm version
char *date_created; // The date the cluster file was created (e.g., 3/9/2017 2:18:30 PM)
uint8_t is_wgt;
int32_t data_block_version;
char *opa;
char *manifest_name; // The manifest name used to build this cluster file
int32_t num_records;
ClusterRecord *cluster_records;
char **names; // Names of records from manifest
char **names2index;
} egt_t;
static void clusterscore_read(ClusterScore *clusterscore, hFILE *hfile) {
read_bytes(hfile, (void *)&clusterscore->cluster_separation, sizeof(float));
read_bytes(hfile, (void *)&clusterscore->total_score, sizeof(float));
read_bytes(hfile, (void *)&clusterscore->original_score, sizeof(float));
read_bytes(hfile, (void *)&clusterscore->edited, sizeof(uint8_t));
}
static void clusterrecord_read(ClusterRecord *clusterrecord, hFILE *hfile, int32_t data_block_version) {
read_bytes(hfile, (void *)&clusterrecord->aa_cluster_stats.N, sizeof(int32_t));
read_bytes(hfile, (void *)&clusterrecord->ab_cluster_stats.N, sizeof(int32_t));
read_bytes(hfile, (void *)&clusterrecord->bb_cluster_stats.N, sizeof(int32_t));
read_bytes(hfile, (void *)&clusterrecord->aa_cluster_stats.r_dev, sizeof(float));
read_bytes(hfile, (void *)&clusterrecord->ab_cluster_stats.r_dev, sizeof(float));
read_bytes(hfile, (void *)&clusterrecord->bb_cluster_stats.r_dev, sizeof(float));
read_bytes(hfile, (void *)&clusterrecord->aa_cluster_stats.r_mean, sizeof(float));
read_bytes(hfile, (void *)&clusterrecord->ab_cluster_stats.r_mean, sizeof(float));
read_bytes(hfile, (void *)&clusterrecord->bb_cluster_stats.r_mean, sizeof(float));
read_bytes(hfile, (void *)&clusterrecord->aa_cluster_stats.theta_dev, sizeof(float));
read_bytes(hfile, (void *)&clusterrecord->ab_cluster_stats.theta_dev, sizeof(float));
read_bytes(hfile, (void *)&clusterrecord->bb_cluster_stats.theta_dev, sizeof(float));
read_bytes(hfile, (void *)&clusterrecord->aa_cluster_stats.theta_mean, sizeof(float));
read_bytes(hfile, (void *)&clusterrecord->ab_cluster_stats.theta_mean, sizeof(float));
read_bytes(hfile, (void *)&clusterrecord->bb_cluster_stats.theta_mean, sizeof(float));
if (data_block_version >= 7) {
read_bytes(hfile, (void *)&clusterrecord->intensity_threshold, sizeof(float));
read_bytes(hfile, NULL, 14 * sizeof(float));
} else {
clusterrecord->intensity_threshold = NAN;
}
}
static egt_t *egt_init(const char *fn) {
egt_t *egt = (egt_t *)calloc(1, sizeof(egt_t));
egt->fn = strdup(fn);
egt->hfile = hopen(egt->fn, "rb");
if (egt->hfile == NULL) error("Could not open %s: %s\n", egt->fn, strerror(errno));
if (is_gzip(egt->hfile)) error("File %s is gzip compressed and currently cannot be sought\n", egt->fn);
read_bytes(egt->hfile, (void *)&egt->version, sizeof(int32_t));
if (egt->version != 3) error("EGT cluster file version %d not supported\n", egt->version);
read_pfx_string(egt->hfile, &egt->gencall_version, NULL);
read_pfx_string(egt->hfile, &egt->cluster_version, NULL);
read_pfx_string(egt->hfile, &egt->call_version, NULL);
read_pfx_string(egt->hfile, &egt->normalization_version, NULL);
read_pfx_string(egt->hfile, &egt->date_created, NULL);
read_bytes(egt->hfile, (void *)&egt->is_wgt, sizeof(uint8_t));
if (egt->is_wgt != 1) error("Only WGT cluster file version supported\n");
read_pfx_string(egt->hfile, &egt->manifest_name, NULL);
read_bytes(egt->hfile, (void *)&egt->data_block_version, sizeof(int32_t));
if (egt->data_block_version < 5 || egt->data_block_version == 6 || egt->data_block_version > 9)
error("Data block version %d in cluster file not supported\n", egt->data_block_version);
read_pfx_string(egt->hfile, &egt->opa, NULL);
read_bytes(egt->hfile, (void *)&egt->num_records, sizeof(int32_t));
egt->cluster_records = (ClusterRecord *)malloc(egt->num_records * sizeof(ClusterRecord));
for (int i = 0; i < egt->num_records; i++)
clusterrecord_read(&egt->cluster_records[i], egt->hfile, egt->data_block_version);
for (int i = 0; i < egt->num_records; i++) clusterscore_read(&egt->cluster_records[i].cluster_score, egt->hfile);
// toss useless strings such as aa_ab_bb/aa_ab/aa_bb/ab_bb
for (int i = 0; i < egt->num_records; i++) read_pfx_string(egt->hfile, NULL, NULL);
egt->names = (char **)malloc(egt->num_records * sizeof(char *));
egt->names2index = khash_str2int_init();
for (int i = 0; i < egt->num_records; i++) {
read_pfx_string(egt->hfile, &egt->names[i], NULL);
if (khash_str2int_has_key(egt->names2index, egt->names[i]))
error("Illumina probe %s present multiple times in file %s\n", egt->names[i], fn);
khash_str2int_inc(egt->names2index, egt->names[i]);
}
for (int i = 0; i < egt->num_records; i++)
read_bytes(egt->hfile, (void *)&egt->cluster_records[i].address, sizeof(int32_t));
int32_t aa_n, ab_n, bb_n;
for (int i = 0; i < egt->num_records; i++) {
read_bytes(egt->hfile, (void *)&aa_n, sizeof(int32_t));
read_bytes(egt->hfile, (void *)&ab_n, sizeof(int32_t));
read_bytes(egt->hfile, (void *)&bb_n, sizeof(int32_t));
if (egt->cluster_records[i].aa_cluster_stats.N != aa_n || egt->cluster_records[i].ab_cluster_stats.N != ab_n
|| egt->cluster_records[i].bb_cluster_stats.N != bb_n)
error("Cluster counts don't match with EGT cluster file %s\n", egt->fn);
}
if (egt->data_block_version == 9) read_bytes(egt->hfile, NULL, egt->num_records * sizeof(float));
if (!heof(egt->hfile))
error("EGT reader did not reach the end of file %s at position %ld\n", egt->fn, htell(egt->hfile));
for (int i = 0; i < egt->num_records; i++) {
ClusterStats *aa = &egt->cluster_records[i].aa_cluster_stats;
ClusterStats *ab = &egt->cluster_records[i].ab_cluster_stats;
ClusterStats *bb = &egt->cluster_records[i].bb_cluster_stats;
egt->cluster_records[i].r_mean =
(aa->N * aa->r_mean + ab->N * ab->r_mean + bb->N * bb->r_mean) / (aa->N + ab->N + bb->N);
}
return egt;
}
static void egt_destroy(egt_t *egt) {
if (!egt) return;
if (hclose(egt->hfile) < 0) error("Error closing EGT file %s\n", egt->fn);
free(egt->fn);
free(egt->gencall_version);
free(egt->cluster_version);
free(egt->call_version);
free(egt->normalization_version);
free(egt->date_created);