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io.cpp
1377 lines (1137 loc) · 53.9 KB
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io.cpp
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#include "io.h"
#include "gl_methods.h"
#include "version.h"
#include "build.h"
#include <time.h> // asctime
#include <sys/stat.h> // stat()
extern void(*calculate_gls)(simRecord* sim);
extern unsigned short int rng1_seeder[3];
extern unsigned short int rng1_seeder_save[3];
extern unsigned short int rng2_seeder[3];
extern unsigned short int rng2_seeder_save[3];
extern const char* nonref_str;
/// @brief read_qs_bins_file - read the file containing the quality score binning description
/// @return uint8_t** - array of quality score binning ranges
/// @details
/// The file should contain lines with the following format:
/// [RangeStart],[RangeEnd],[QualityScoreToAssign]
/// where the ranges are inclusive. All values should be comma-separated, >=0 and <=255.
/// The file is assumed to be sorted.
/// The ranges must cover the entire range from the first RangeStart to the last RangeEnd.
///
/// (1) Example file for NovaSeq 6000 RTA3 binning:
///
/// 0,2,2
/// 3,14,12
/// 15,30,23
/// 31,40,37
///
/// Assigns quality score 2 to reads with quality scores 0-2, 12 to reads with quality scores 3-14, etc. Any quality score above 40 will be assigned 37. First range start must be 0.
///
/// (2) Example 2:
///
/// 0,0,2
/// 1,14,11
/// 15,30,25
/// 31,40,37
///
/// This example demonstrates how to assign a specific quality score to a single quality score value. In this example, quality score 2 is assigned when the simulated quality score is exactly 0.
uint8_t** read_qs_bins_file(void) {
if (args->verbose > 0) {
fprintf(stderr, "-> Reading quality score binning file: %s\n", args->qs_bins_fn);
}
FILE* fp = NULL;
if ((fp = fopen(args->qs_bins_fn, "r")) == NULL) {
ERROR("Could not open file: %s\n", args->qs_bins_fn);
}
int rangeStart[256] = { -1 };
int rangeEnd[256] = { -1 };
int qualityScore[256] = { -1 };
int i = 0;
while (1) {
if (EOF == fscanf(fp, "%d,%d,%d\n", &rangeStart[i], &rangeEnd[i], &qualityScore[i])) {
break;
}
if (rangeStart[i] > rangeEnd[i]) {
ERROR("Range start value is greater than range end value in line %d of file: %s\n", i + 1, args->qs_bins_fn);
}
if (rangeStart[i] < 0) {
ERROR("Range start value is less than 0 in line %d of file: %s\n", i + 1, args->qs_bins_fn);
} else if (rangeStart[i] > 255) {
ERROR("Range start value is greater than 255 in line %d of file: %s\n", i + 1, args->qs_bins_fn);
}
if (rangeEnd[i] < 0) {
ERROR("Range end value is less than 0 in line %d of file: %s\n", i + 1, args->qs_bins_fn);
} else if (rangeEnd[i] > 255) {
ERROR("Range end value is greater than 255 in line %d of file: %s\n", i + 1, args->qs_bins_fn);
}
if (qualityScore[i] < 0) {
ERROR("Quality score value is less than 0 in line %d of file: %s\n", i + 1, args->qs_bins_fn);
} else if (qualityScore[i] > 255) {
ERROR("Quality score value is greater than 255 in line %d of file: %s\n", i + 1, args->qs_bins_fn);
}
if (i == 0) {
if (rangeStart[i] != 0) {
ERROR("Quality score range does not start from 0 in line %d of file: %s\n", i + 1, args->qs_bins_fn);
}
}else{
if (rangeStart[i] != (rangeEnd[i - 1] + 1)) {
ERROR("Quality score range is not continuous in line %d of file: %s. Previous range end: %d, current range start: %d\n", i + 1, args->qs_bins_fn, rangeEnd[i - 1], rangeStart[i]);
}
}
i++;
}
if (args->verbose > 0) {
fprintf(stderr, "\n-> Read %d quality score binning ranges from file: %s\n", i, args->qs_bins_fn);
if (args->verbose > 1) {
fprintf(stderr, "\t-> Ranges: ");
for (int j = 0;j < i;j++) {
fprintf(stderr, "%d-%d:%d ", rangeStart[j], rangeEnd[j], qualityScore[j]);
}
fprintf(stderr, "\n");
}
}
const size_t nRanges = i;
if (nRanges == 0) {
ERROR("Could not read any quality score binning ranges from file: %s\n", args->qs_bins_fn);
}
/// qs_bins[nRanges]
/// qs_bins[i][0] = start of i-th range
/// qs_bins[i][1] = end of i-th range
/// qs_bins[i][2] = qs value to assign for i-th range
args->n_qs_bins = nRanges;
uint8_t** ret = (uint8_t**)malloc(nRanges * sizeof(uint8_t*));
ASSERT(NULL != ret);
for (size_t j = 0;j < nRanges;j++) {
ret[j] = (uint8_t*)malloc(3 * sizeof(uint8_t));
ASSERT(NULL != ret[j]);
ret[j][0] = rangeStart[j];
ret[j][1] = rangeEnd[j];
ret[j][2] = qualityScore[j];
}
fclose(fp);
fp = NULL;
return(ret);
}
FILE* get_FILE(const char* fname, const char* mode) {
FILE* fp;
if (NULL == (fp = fopen(fname, mode))) {
fprintf(stderr,
"[%s:%s()]\t->Error opening FILE handle for file:%s exiting\n",
__FILE__, __FUNCTION__, fname);
exit(0);
}
return fp;
}
FILE* open_FILE(const char* prefix, const char* suffix) {
char* str = (char*)malloc(strlen(prefix) + strlen(suffix) + 1);
strcpy(str, prefix);
strcat(str, suffix);
// fprintf(stderr, "\t-> Opening output file: %s\n", str);
FILE* fp = get_FILE(str, "w");
free(str);
str = NULL;
return(fp);
}
htsFile* open_htsFile(const char* fn, const char* mode) {
htsFile* fp = hts_open(fn, mode);
if (NULL == fp) {
ERROR("Could not open file: %s with mode %s", fn, mode);
}
return(fp);
}
BGZF* open_BGZF(const char* fn, const char* mode) {
BGZF* fp = bgzf_open(fn, mode);
if (NULL == fp) {
ERROR("Could not open file: %s with mode %s", fn, mode);
}
return(fp);
}
void write_BGZF(BGZF* fp, const void* data, const int size) {
if ((bgzf_write(fp, data, size)) != size) {
ERROR("Could not write to BGZF file");
}
return;
}
void version_page() {
fprintf(stderr, "vcfgl [version: %s] [build: %s %s] [htslib: %s]\n", VCFGL_VERSION, __DATE__, __TIME__, hts_version());
fprintf(stderr, "\n");
fprintf(stderr, "Build details:\n");
fprintf(stderr, "\t-> CXX=%s\n", VCFGL_MAKE_CXX);
fprintf(stderr, "\t-> CXXFLAGS=%s\n", VCFGL_MAKE_CXXFLAGS);
fprintf(stderr, "\t-> CPPFLAGS=%s\n", VCFGL_MAKE_CPPFLAGS);
fprintf(stderr, "\t-> LIBS=%s\n", VCFGL_MAKE_LIBS);
fprintf(stderr, "\t-> FLAGS=%s\n", VCFGL_MAKE_FLAGS);
fprintf(stderr, "\t-> HTSSRC=%s\n", VCFGL_MAKE_HTSSRC);
fprintf(stderr, "\n");
}
void version_number() {
fprintf(stderr, "%s\n", VCFGL_VERSION);
}
void help_page() {
// fprintf(stderr, "vcfgl [version: %s] [build: %s %s] [htslib: %s]\n", VCFGL_VERSION, __DATE__, __TIME__, hts_version());
fprintf(stderr, "\n");
fprintf(stderr, "Program: vcfgl\n");
fprintf(stderr, "License: GNU GPLv3.0\n");
fprintf(stderr, "Version: %s (htslib: %s)\n", VCFGL_VERSION, hts_version());
fprintf(stderr, "Build: %s %s\n", __DATE__, __TIME__);
fprintf(stderr, "\n");
fprintf(stderr, "Usage: vcfgl -i <input> [options]\n");
fprintf(stderr, "\n");
fprintf(stderr, " -h, --help _____________________ Print this help message and exit\n");
fprintf(stderr, " -v, --version __________________ Print version and build information and exit\n");
fprintf(stderr, "\n");
fprintf(stderr, "Option descriptions:\n");
fprintf(stderr, " -s, --long-option TYPE [X] _____ Description\n");
fprintf(stderr, " -s Short option (if any)\n");
fprintf(stderr, " --long-option Long option\n");
fprintf(stderr, " TYPE Type of the argument value, can be:\n");
fprintf(stderr, " - INT (integer)\n");
fprintf(stderr, " - INT+ (additive integer: sum values to use together\n");
fprintf(stderr, " - FLOAT (floating point number)\n");
fprintf(stderr, " - STRING (string)\n");
fprintf(stderr, " - FILE (filename)\n");
fprintf(stderr, " - x|y|z (one of the listed values x, y or z)\n");
fprintf(stderr, " [X] Default argument value (if any)\n");
fprintf(stderr, " _____ Connector to the option description for better readability\n");
fprintf(stderr, "\n");
fprintf(stderr, "\n");
fprintf(stderr, "General options:\n");
fprintf(stderr, " -V, --verbose INT [0] ___________ Verbosity level\n");
fprintf(stderr, " -@, --threads INT [1] ___________ Number of threads\n");
fprintf(stderr, " -s, --seed INT [time] ___________ Random seed for initializing the random number generator\n");
fprintf(stderr, "\n");
fprintf(stderr, "Input/Output:\n");
fprintf(stderr, " -i, --input FILE ________________ Input VCF/BCF file\n");
fprintf(stderr, " --source [0]|1 ______________ 0: Input REF/ALT alleles are in binary format (REF=0, ALT=1; typically outputted from msprime BinaryMutationModel)\n");
fprintf(stderr, " 1: Input REF/ALT alleles are in VCF format (REF=i, ALT=j(,k..); i, j and k from {A,C,G,T}; i.e. the regular VCF format)\n");
fprintf(stderr, " -o, --output STRING ['output'] __ Output filename prefix\n");
fprintf(stderr, " -O, --output-mode [b]|u|z|v _____ b: Compressed BCF (.bcf), u: uncompressed BCF (.bcf), z: compressed VCF (.vcf.gz), v: uncompressed VCF (.vcf)\n");
fprintf(stderr, "\n");
fprintf(stderr, "Simulation parameters:\n");
fprintf(stderr, " -d, --depth FLOAT|'inf' _________ Mean per-site read depth\n");
fprintf(stderr, " ('inf') Simulate true values (requires: -addFormatDP 0 -addInfoDP 0)\n");
fprintf(stderr, " -df, --depths-file FILE __________ File containing mean per-site read depth values for each sample. One value per line.\n");
fprintf(stderr, " -e, --error-rate FLOAT __________ Base-calling error probability\n");
fprintf(stderr, " -eq, --error-qs [0]|1|2 __________ 0: Do not simulate errors in quality scores. Assumes all quality score assignments are correct\n");
fprintf(stderr, " 1: Simulate site-specific errors in the probability of wrong base calls (requires: -bv FLOAT)\n");
fprintf(stderr, " 2: Simulate the errors in the reported quality scores and genotype likelihoods (requires: -bv FLOAT)\n");
fprintf(stderr, " -bv, --beta-variance FLOAT _______ Designated variance for the beta distribution\n");
fprintf(stderr, " -GL, --gl-model 1|[2] ____________ Genotype likelihood model to be used in simulation\n");
fprintf(stderr, " 1: Genotype likelihood model with correlated errors (a.k.a. Li model, samtools model, angsd -GL 1)\n");
fprintf(stderr, " 2: Canonical genotype likelihood model with independent errors (a.k.a. McKenna model, GATK model, angsd -GL 2)\n");
fprintf(stderr, " --gl1-theta FLOAT [0.83] ___ Theta parameter for the genotype likelihood model 1 (requires: -GL 1)\n");
fprintf(stderr, " --qs-bins FILE _____________ File containing the quality score binning to be used in the simulation\n");
fprintf(stderr, " --precise-gl [0]|1 _________ 0: Use the discrete phred-scaled error probabilities in the genotype likelihood calculation\n");
fprintf(stderr, " 1: Use precise error probabilities in the genotype likelihood calculation (requires: -GL 2)\n");
fprintf(stderr, " --i16-mapq INT [20] ________ Mapping quality score for I16 tag (requires: -addI16 1)\n");
fprintf(stderr, " --gvcf-dps INT(,INT..) _____ Minimum per-sample read depth range(s) for constructing gVCF blocks (requires: -doGVCF 1)\n");
fprintf(stderr, " Example: `--gvcf-dps 5,10,20` will group invariable sites into three types of gVCF blocks: [5,10), [10,20) and [20,inf)\n");
fprintf(stderr, " Sites with minimum depth < 5 will be printed as regular VCF records.\n");
fprintf(stderr, " --adjust-qs INT+ [%d] _______ %d: Do not adjust quality scores\n", args->adjustQs, ARG_QS_ADJUST_DISABLED);
fprintf(stderr, " %d: Use adjusted quality scores in genotype likelihoods (requires: --precise-gl 0)\n", ARG_QS_ADJUST_FOR_GL);
fprintf(stderr, " %d: Use adjusted quality scores in calculating the quality score sum (QS) tag (requires: -addQS 1)\n", ARG_QS_ADJUST_FOR_QSUM);
fprintf(stderr, " %d: Use adjusted quality scores in pileup output (requires: --printPileup 1)\n", ARG_QS_ADJUST_FOR_PILEUP);
fprintf(stderr, " %d: Use adjusted quality scores in --printQScores output (requires: --printQScores 1)\n", ARG_QS_ADJUST_FOR_PRINTQSCORES);
fprintf(stderr, " %d: Use adjusted quality scores in --printGlError output (requires: --printGlError 1)\n", ARG_QS_ADJUST_FOR_PRINTGLERROR);
fprintf(stderr, " --adjust-by FLOAT [0.499] __ Adjustment value for quality scores (requires: --adjust-qs > 0)\n");
fprintf(stderr, " -explode [0]|1 _____________ 1: Explode to sites that are not in input file.\n");
fprintf(stderr, " Useful for simulating invariable sites when the input file only contains variable sites.\n");
fprintf(stderr, " Sets all genotypes in exploded sites to homozygous reference.\n");
fprintf(stderr, " --rm-invar-sites INT+ [%s]___ %d: Do not remove invariable sites\n", ARG_RM_INVAR_DISABLED, ARG_RM_INVAR_DISABLED);
fprintf(stderr, " %d: Remove sites where all individuals' true genotypes in the input file are homozygous reference\n", ARG_RM_INVAR_INPUT_HOMOREFGT);
fprintf(stderr, " %d: Remove sites where all individuals' true genotypes in the input file are homozygous alternative\n", ARG_RM_INVAR_INPUT_HOMOALTGT);
fprintf(stderr, " %d: Remove sites where the all simulated reads among all individuals are the same base\n", ARG_RM_INVAR_INPUT_SIM_INVAR);
fprintf(stderr, " Example: '--rm-invar-sites 3' (1+2) will do both 1 and 2 (i.e. remove all homozygous sites)\n");
fprintf(stderr, " --rm-empty-sites [0]|1 _____ 0: Do not remove empty sites\n");
fprintf(stderr, " 1: Remove empty sites (i.e. sites where no reads were simulated)\n");
fprintf(stderr, " -doUnobserved INT [1] ______ 0: Trim unobserved alleles. Only alleles that are observed will be listed in REF and ALT fields\n");
fprintf(stderr, " 1: Use '<*>' notation to represent unobserved alleles\n");
fprintf(stderr, " 2: Use '<NON_REF>' notation to represent unobserved alleles (a.k.a. GATK notation)\n");
fprintf(stderr, " 3: Explode unobserved bases from {A,C,G,T} list\n");
fprintf(stderr, " 4: Use '<*>' notation to represent unobserved alleles and explode unobserved bases from {A,C,G,T} list\n");
fprintf(stderr, " 5: Use '<NON_REF>' notation to represent unobserved alleles and explode unobserved bases from {A,C,G,T} list\n");
fprintf(stderr, " -doGVCF [0]|1 ______________ 0: Disabled, 1: Output in gVCF format (requires: --rm-invar-sites 0, -doUnobserved 2, -addPL 1 and --gvcf-dps INT)\n");
fprintf(stderr, " -printPileup [0]|1 _________ 0: Disabled, 1: Also output in pileup format (<output_prefix>.pileup.gz)\n");
fprintf(stderr, " -printTruth [0]|1 __________ 0: Disabled, 1: Also output the VCF file containing the true genotypes (named <output_prefix>.truth.vcf)\n");
fprintf(stderr, " -printBasePickError [0]|1 __ 0: Disabled, 1: Print the base picking error probability to stdout.\n");
fprintf(stderr, " If --error-qs 1 is used, writes per-read base picking error probabilities to stdout.\n");
fprintf(stderr, " If --error-qs 0 or 2 is used, writes a single value which is used for all samples and sites.\n");
fprintf(stderr, " The columns are: type, sample_id, contig, site, read_index, base_pick_error_prob\n");
fprintf(stderr, " -printQsError [0]|1 ________ 0: Disabled, 1: Print the error probability used in quality score calculations to stdout.\n");
fprintf(stderr, " If --error-qs 2 is used, writes per-read quality score error probabilities to stdout.\n");
fprintf(stderr, " If --error-qs 0 or 1 is used, writes a single value which is used for all samples and sites.\n");
fprintf(stderr, " The columns are: type, sample_id, contig, site, read_index, error_prob\n");
fprintf(stderr, " -printGlError [0]|1 ________ 0: Disabled, 1: Print the error probability used in genotype likelihood calculations to stdout. (requires: -GL 2)\n");
fprintf(stderr, " Since -GL 1 works directly with quality scores, this option is only available when -GL 2 is used.\n");
fprintf(stderr, " If --error-qs 2 is used, writes per-read error probabilities to stdout.\n");
fprintf(stderr, " If --error-qs 0 or 1 is used, writes a single value which is used for all samples and sites.\n");
fprintf(stderr, " If --precise-gl 1 is used, the printed values are the same as those printed by -printQsError.\n");
fprintf(stderr, " The columns are: type, sample_id, contig, site, read_index, error_prob\n");
fprintf(stderr, " -printQScores [0]|1 ________ 0: Disabled, 1: Print the quality scores to stdout.\n");
fprintf(stderr, " The columns are: type, sample_id, contig, site, read_index, qScore\n");
fprintf(stderr, "\n");
fprintf(stderr, "Output VCF/BCF tags: 0: Do not add, 1: Add\n");
fprintf(stderr, " -addGL 0|[1] _______________ Genotype likelihoods (GL) tag\n");
fprintf(stderr, " -addGP [0]|1 _______________ Genotype probabilities (GP) tag\n");
fprintf(stderr, " -addPL [0]|1 _______________ Phred-scaled genotype likelihoods (PL) tag\n");
fprintf(stderr, " -addI16 [0]|1 ______________ I16 tag\n");
fprintf(stderr, " -addQS [0]|1 _______________ Quality score sum (QS) tag\n");
fprintf(stderr, " -addFormatDP [1]|0 _________ Per-sample read depth (FORMAT/DP) tag\n");
fprintf(stderr, " -addFormatAD [0]|1 _________ Per-sample allelic read depth (FORMAT/AD) tag\n");
fprintf(stderr, " -addFormatADF [0]|1 ________ Per-sample forward-strand allelic read depth (FORMAT/ADF) tag\n");
fprintf(stderr, " -addFormatADR [0]|1 ________ Per-sample reverse-strand allelic read depth (FORMAT/ADR) tag\n");
fprintf(stderr, " -addInfoDP [0]|1 ___________ Total read depth (INFO/DP) tag\n");
fprintf(stderr, " -addInfoAD [0]|1 ___________ Total allelic read depth (INFO/AD) tag\n");
fprintf(stderr, " -addInfoADF [0]|1 __________ Total forward-strand allelic read depth (INFO/ADF) tag\n");
fprintf(stderr, " -addInfoADR [0]|1 __________ Total reverse-strand allelic read depth (INFO/ADR) tag\n");
fprintf(stderr, "\n");
}
/// @brief args_init - initialize the args struct and set arguments to default values
/// @return argStruct* - pointer to the args struct
argStruct* args_init() {
args = (argStruct*)calloc(1, sizeof(argStruct));
// -------------------------------------------- //
// read in from command line
args->verbose = 0;
args->n_threads = 1;
args->seed = -1;
// --> Input/Output
args->in_fn = NULL;
args->gtSource = ARG_GTSOURCE_BINARY;
args->out_fnprefix = NULL;
args->output_mode = NULL;
// --> Simulation parameters
args->mps_depth = ARG_DEPTH_UNDEF;
args->mps_depths_fn = NULL;
args->error_rate = ARG_ERROR_RATE_UNDEF;
args->error_qs = 0;
args->beta_variance = -1.0;
args->GL = 2;
args->glModel1_theta = 0.83;
args->qs_bins_fn = NULL;
args->usePreciseGlError = 0;
args->i16_mapq = ARG_I16_MAPQ_DEFAULT;
args->gvcf_dps_str = NULL;
args->adjustQs = ARG_QS_ADJUST_DISABLED;
args->adjustBy = 0.499;
args->explode = 0;
args->rmInvarSites = 0;
args->rmEmptySites = 0;
args->doUnobserved = ARG_DOUNOBSERVED_STAR;
args->doGVCF = 0;
args->printPileup = 0;
args->printTruth = 0;
args->printBasePickError = 0;
args->printQsError = 0;
args->printGlError = 0;
args->printQScores = 0;
args->addGL = 1;
args->addGP = 0;
args->addPL = 0;
args->addI16 = 0;
args->addQS = 0;
args->addFormatDP = 1;
args->addInfoDP = 0;
args->addFormatAD = 0;
args->addInfoAD = 0;
args->addFormatADF = 0;
args->addInfoADF = 0;
args->addFormatADR = 0;
args->addInfoADR = 0;
// -------------------------------------------- //
// set during program execution
args->out_fn = NULL;
args->out_truth_fn = NULL;
args->out_pileup_fn = NULL;
args->output_mode_str = NULL;
args->in_fp = NULL;
args->arg_fp = NULL;
args->out_fp = NULL;
args->out_truth_fp = NULL;
args->out_pileup_fp = NULL;
args->datetime = NULL;
args->command = NULL;
args->versionInfo = NULL;
// -------------------------------------------- //
// for internal use
args->mps_depths = NULL;
args->n_mps_depths = 1;
args->betaSampler = NULL;
args->poissonSampler = NULL;
args->base_pick_error_prob = -1.0;
args->preCalc = NULL;
args->gl1errmod = NULL;
args->qs_bins = NULL;
args->n_qs_bins = 0;
return(args);
}
argStruct* args_get(int argc, char** argv) {
args = args_init();
if (0 == argc) {
help_page();
exit(0);
}
while (*argv) {
char* arv = *argv;
char* val = *(++argv);
if ((strcmp("--help", arv) == 0) || (strcmp("-h", arv) == 0)) {
help_page();
exit(0);
}
else if ((strcmp("--version", arv) == 0) || (strcmp("-v", arv) == 0)) {
version_page();
exit(0);
}
else if ((strcmp("-vv", arv) == 0)){
version_number();
exit(0);
}
else if ((strcmp("--verbose", arv) == 0) || (strcmp("-V", arv) == 0)) {
args->verbose = atoi(val);
}
else if ((strcmp("--threads", arv) == 0) || (strcmp("-@", arv) == 0)) {
args->n_threads = atoi(val);
}
else if ((strcmp("--seed", arv) == 0) || (strcmp("-s", arv) == 0)) {
args->seed = atoi(val);
}
else if ((strcmp("--input", arv) == 0) || (strcmp("-i", arv) == 0)) {
args->in_fn = strdup(val);
}
else if ((strcmp("--source", arv) == 0)) {
args->gtSource = atoi(val);
}
else if ((strcmp("--output", arv) == 0) || (strcmp("-o", arv) == 0)) {
args->out_fnprefix = strdup(val);
}
else if ((strcmp("--output-mode", arv) == 0) || (strcmp("-O", arv) == 0)) {
args->output_mode = strdup(val);
}
else if ((strcmp("--depth", arv) == 0) || (strcmp("-d", arv) == 0)) {
char* tmp = strdup(val);
int isNumber = 1;
int i = 0;
if (tmp[0] == '-')
i = 1;
for (; tmp[i] != 0; ++i) {
if (!isdigit(tmp[i])) {
if (tmp[i] == '.')
continue;
isNumber = 0;
if (strcasecmp("inf", tmp + i) == 0) {
args->mps_depth = ARG_DEPTH_INF;
}
}
}
free(tmp);
tmp = NULL;
if (isNumber) {
args->mps_depth = atof(val);
} else if (ARG_DEPTH_INF != args->mps_depth) {
NEVER;
}
}
else if ((strcmp("--depths-file", arv) == 0) || (strcmp("-df", arv) == 0)) {
args->mps_depths_fn = strdup(val);
args->mps_depth = ARG_DEPTH_FILE;
}
else if ((strcmp("--error-rate", arv) == 0) || (strcmp("-e", arv) == 0)) {
args->error_rate = atof(val);
}
else if ((strcasecmp("--error-qs", arv) == 0) || (strcasecmp("-eq", arv) == 0)) {
args->error_qs = atoi(val);
}
else if ((strcasecmp("--beta-variance", arv) == 0) || (strcasecmp("-bv", arv) == 0)) {
args->beta_variance = atof(val);
}
else if ((strcasecmp("--gl-model", arv) == 0) || (strcasecmp("-GL", arv) == 0)) {
args->GL = atoi(val);
}
else if (strcasecmp("--gl1-theta", arv) == 0) {
args->glModel1_theta = atof(val);
}
else if (strcasecmp("--qs-bins", arv) == 0) {
args->qs_bins_fn = strdup(val);
}
else if (strcasecmp("--precise-gl", arv) == 0) {
args->usePreciseGlError = atoi(val);
}
else if (strcasecmp("--i16-mapq", arv) == 0) {
args->i16_mapq = atoi(val);
}
else if (strcasecmp("--gvcf-dps", arv) == 0) {
args->gvcf_dps_str = strdup(val);
}
else if (strcasecmp("--adjust-qs", arv) == 0) {
args->adjustQs = atoi(val);
}
else if (strcasecmp("--adjust-by", arv) == 0) {
args->adjustBy = atof(val);
}
else if (strcasecmp("-explode", arv) == 0) {
args->explode = atoi(val);
}
else if (strcasecmp("--rm-invar-sites", arv) == 0) {
args->rmInvarSites = atoi(val);
}
else if (strcasecmp("--rm-empty-sites", arv) == 0) {
args->rmEmptySites = atoi(val);
}
else if (strcasecmp("-doUnobserved", arv) == 0) {
args->doUnobserved = atoi(val);
}
else if (strcasecmp("-doGVCF", arv) == 0) {
args->doGVCF = atoi(val);
}
else if (strcasecmp("-printPileup", arv) == 0) {
args->printPileup = atoi(val);
}
else if (strcasecmp("-printTruth", arv) == 0) {
args->printTruth = atoi(val);
}
else if (strcasecmp("-printBasePickError", arv) == 0) {
args->printBasePickError = atoi(val);
}
else if (strcasecmp("-printQsError", arv) == 0) {
args->printQsError = atoi(val);
}
else if (strcasecmp("-printGlError", arv) == 0) {
args->printGlError = atoi(val);
}
else if (strcasecmp("-printQScores", arv) == 0) {
args->printQScores = atoi(val);
}
else if ((strcasecmp("-addGL", arv) == 0) || (strcasecmp("-addFormatGL", arv) == 0)) {
args->addGL = atoi(val);
}
else if ((strcasecmp("-addGP", arv) == 0) || (strcasecmp("-addFormatGP", arv) == 0)) {
args->addGP = atoi(val);
}
else if ((strcasecmp("-addPL", arv) == 0) || (strcasecmp("-addFormatPL", arv) == 0)) {
args->addPL = atoi(val);
}
else if ((strcasecmp("-addI16", arv) == 0) || (strcasecmp("-addFormatI16", arv) == 0)) {
args->addI16 = atoi(val);
}
else if ((strcasecmp("-addQS", arv) == 0) || (strcasecmp("-addFormatQS", arv) == 0)) {
args->addQS = atoi(val);
}
else if (strcasecmp("-addFormatDP", arv) == 0)
args->addFormatDP = atoi(val);
else if (strcasecmp("-addInfoDP", arv) == 0)
args->addInfoDP = atoi(val);
else if (strcasecmp("-addFormatAD", arv) == 0)
args->addFormatAD = atoi(val);
else if (strcasecmp("-addInfoAD", arv) == 0)
args->addInfoAD = atoi(val);
else if (strcasecmp("-addFormatADF", arv) == 0)
args->addFormatADF = atoi(val);
else if (strcasecmp("-addInfoADF", arv) == 0)
args->addInfoADF = atoi(val);
else if (strcasecmp("-addFormatADR", arv) == 0)
args->addFormatADR = atoi(val);
else if (strcasecmp("-addInfoADR", arv) == 0)
args->addInfoADR = atoi(val);
else {
ERROR("Unknown arg:%s\n", arv);
}
++argv;
}
// ---------------------------------------------------------------------- //
// ARGUMENT VALIDATION
CHECK_ARG_INTERVAL_INT(args->verbose, 0, 5, "--verbose");
CHECK_ARG_INTERVAL_INT(args->n_threads, 0, ARG_NTHREADS_MAXVAL, "--threads");
CHECK_ARG_INTERVAL_INT(args->seed, INT_MIN, INT_MAX, "--seed");
// --> Input/Output
// ** MUST BE SET **
if (args->in_fn == NULL) {
ERROR(
"Input file is not specified. Please use -i/--input option to "
"specify the input file.");
}
CHECK_ARG_INTERVAL_INT(args->gtSource, 0, 1, "--source");
if (NULL == args->output_mode) {
args->output_mode = strdup("b");
}
// --> Simulation parameters
if (ARG_DEPTH_INF == args->mps_depth) {
if (PROGRAM_WILL_SKIP_INPUT_HOMOREFGT_SITES) {
ERROR("--rm-invar-sites %d cannot be used with -depth inf", args->rmInvarSites);
}
if (PROGRAM_WILL_SKIP_INPUT_HOMOALTGT_SITES) {
ERROR("--rm-invar-sites %d cannot be used with -depth inf", args->rmInvarSites);
}
if (args->printPileup != 0) {
ERROR(
"(-printPileup 1) Cannot output pileup file when --depth inf is set.");
}
if (args->addFormatDP) {
ERROR(
"(-addFormatDP 1) FORMAT/DP tag cannot be added when --depth "
"inf is set.");
}
if (args->addInfoDP) {
ERROR(
"(-addInfoDP 1) INFO/DP tag cannot be added when --depth inf "
"is set.");
}
if (args->addI16 != 0) {
ERROR(
"(-addI16 != 0) I16 tag cannot be added when --depth inf is set.");
}
if (1 == args->addQS) {
ERROR("(-addQS 1) QS tag cannot be added when --depth inf is set.");
}
if (args->addFormatAD) {
ERROR(
"(-addFormatAD 1) FORMAT/AD tag cannot be added when --depth "
"inf is set.");
}
if (args->addFormatADF) {
ERROR(
"(-addFormatADF 1) FORMAT/ADF tag cannot be added when --depth "
"inf is set.");
}
if (args->addFormatADR) {
ERROR(
"(-addFormatADR 1) FORMAT/ADR tag cannot be added when --depth "
"inf is set.");
}
if (args->addInfoAD) {
ERROR(
"(-addInfoAD 1) INFO/AD tag cannot be added when --depth inf "
"is set.");
}
if (args->addInfoADF) {
ERROR(
"(-addInfoADF 1) INFO/ADF tag cannot be added when --depth inf "
"is set.");
}
if (args->addInfoADR) {
ERROR(
"(-addInfoADR 1) INFO/ADR tag cannot be added when --depth inf "
"is set.");
}
if (0 != args->error_rate) {
ERROR(
"Cannot simulate true values (--depth inf) with error rate "
"(--error-rate) set to %f. Please set --error-rate to 0 and "
"rerun.",
args->error_rate);
}
} else if (ARG_DEPTH_UNDEF == args->mps_depth) {
ERROR("Average per-site read depth value is required. Please set it using --depth or --depths-file and re-run.");
} else if (ARG_DEPTH_FILE == args->mps_depth) {
//
} else {
CHECK_ARG_INTERVAL_DBL(args->mps_depth, 0.0, ARG_DEPTH_MAXVAL, "--depth");
}
if (args->error_rate == ARG_ERROR_RATE_UNDEF) {
ERROR("Error rate is not specified. Please use --error-rate option to specify the error rate. Allowed range: [0.0, 1.0]");
}
CHECK_ARG_INTERVAL_IE_DBL(args->error_rate, 0.0, 1.0, "--error-rate");
CHECK_ARG_INTERVAL_INT(args->error_qs, 0, 2, "--error-qs");
if (!PROGRAM_BETA_VAR_IS_UNDEF) {
CHECK_ARG_INTERVAL_DBL(args->beta_variance, 0.0, 1.0, "--beta-variance");
}
CHECK_ARG_INTERVAL_INT(args->GL, 1, 2, "--gl-model");
CHECK_ARG_INTERVAL_DBL(args->glModel1_theta, 0.0, 1.0, "--gl1-theta");
CHECK_ARG_INTERVAL_01(args->usePreciseGlError, "--precise-gl");
CHECK_ARG_INTERVAL_INT(args->i16_mapq, 0, 60, "--i16-mapq");
CHECK_ARG_INTERVAL_INT(args->adjustQs, 0, ARGMAX_QS_ADJUST, "--adjust-qs");
if (PROGRAM_WILL_ADJUST_QS && args->adjustBy == 0.0) {
ERROR("--adjust-qs %d requires a non-zero value for --adjust-by. Please set --adjust-by and rerun.", args->adjustQs);
}
if (PROGRAM_WILL_ADJUST_QS_FOR_GL && args->usePreciseGlError) {
ERROR("--adjust-qs %d requires --precise-gl 0. Please set --precise-gl 0 and rerun.", ARG_QS_ADJUST_FOR_GL);
}
if (PROGRAM_WILL_ADJUST_QS_FOR_QSUM && !args->addQS) {
ERROR("--adjust-qs %d requires -addQS 1. Please set -addQS 1 and rerun.", ARG_QS_ADJUST_FOR_QSUM);
}
if (PROGRAM_WILL_ADJUST_QS_FOR_PILEUP && !args->printPileup) {
ERROR("--adjust-qs %d requires --printPileup 1. Please set --printPileup 1 and rerun.", ARG_QS_ADJUST_FOR_PILEUP);
}
if (PROGRAM_WILL_ADJUST_QS_FOR_PRINTQSCORES && !args->printQScores) {
ERROR("--adjust-qs %d requires --printQScores 1. Please set --printQScores and rerun.", ARG_QS_ADJUST_FOR_PRINTQSCORES);
}
if (PROGRAM_WILL_ADJUST_QS_FOR_PRINTGLERROR && !args->printGlError) {
ERROR("--adjust-qs %d requires --printGlError 1. Please set --printGlError and rerun.", ARG_QS_ADJUST_FOR_PRINTGLERROR);
}
CHECK_ARG_INTERVAL_01(args->explode, "-explode");
CHECK_ARG_INTERVAL_INT(args->rmInvarSites, 0, ARGMAX_RM_INVAR, "--rm-invar-sites");
CHECK_ARG_INTERVAL_01(args->rmEmptySites, "--rm-empty-sites");
CHECK_ARG_INTERVAL_INT(args->doUnobserved, 0, 5, "-doUnobserved");
CHECK_ARG_INTERVAL_01(args->doGVCF, "-doGVCF");
CHECK_ARG_INTERVAL_01(args->printPileup, "-printPileup");
CHECK_ARG_INTERVAL_01(args->printTruth, "-printTruth");
CHECK_ARG_INTERVAL_01(args->printBasePickError, "-printBasePickError");
CHECK_ARG_INTERVAL_01(args->printQsError, "-printQsError");
CHECK_ARG_INTERVAL_01(args->printGlError, "-printGlError");
CHECK_ARG_INTERVAL_01(args->printQScores, "-printQScores");
CHECK_ARG_INTERVAL_01(args->addGL, "-addGL");
CHECK_ARG_INTERVAL_01(args->addGP, "-addGP");
CHECK_ARG_INTERVAL_01(args->addPL, "-addPL");
CHECK_ARG_INTERVAL_INT(args->addI16, 0, 2, "-addI16");
CHECK_ARG_INTERVAL_01(args->addQS, "-addQS");
CHECK_ARG_INTERVAL_01(args->addFormatDP, "-addFormatDP");
CHECK_ARG_INTERVAL_01(args->addInfoDP, "-addInfoDP");
CHECK_ARG_INTERVAL_01(args->addFormatAD, "-addFormatAD");
CHECK_ARG_INTERVAL_01(args->addInfoAD, "-addInfoAD");
CHECK_ARG_INTERVAL_01(args->addFormatADF, "-addFormatADF");
CHECK_ARG_INTERVAL_01(args->addInfoADF, "-addInfoADF");
CHECK_ARG_INTERVAL_01(args->addFormatADR, "-addFormatADR");
CHECK_ARG_INTERVAL_01(args->addInfoADR, "-addInfoADR");
// ---------------------------------------------------------------------- //
// ARGUMENT COMBINATION COMPATIBILITY CHECKS
if (args->usePreciseGlError && (1 == args->GL)) {
ERROR("Precise genotype likelihood error (--precise-gl 1) is not supported with genotype likelihood model 1 (--gl-model 1).");
}
if ((args->beta_variance >= 0) && (0 == args->error_qs)) {
ERROR("--beta-variance %e requires --error-qs 1 or 2.", args->beta_variance);
}
if (1 == args->error_qs || 2 == args->error_qs) {
if (0.0 == args->error_rate) {
ERROR("--error-qs 1 or 2 requires --error-rate > 0 (found %f). If you want to simulate reads without errors, please use --error-qs 0 instead.", args->error_rate);
} else if (args->error_rate > 0.0) {
if (0.0 == args->beta_variance) {
ERROR("--error-qs 1 or 2 requires --beta-variance > 0 (found %e). If you want to simulate quality scores without errors, please use --error-qs 0 instead.", args->beta_variance);
} else if (args->beta_variance > 0.0) {
} else {
ERROR("--beta-variance should be set to a positive value. Please set --beta-variance and rerun.");
}
} else {
ERROR("Error rate (--error-rate) should be set to a positive value. Please set --error-rate and rerun.");
}
}
if (1 == args->doGVCF) {
if (!args->addFormatDP) {
ERROR("[-doGVCF 1] -addFormatDP 1 is required for gVCF output. Please set -addFormatDP 1 and rerun.");
}
WARN("\n-> [-doGVCF 1] GVCF mode is under development. Please use with caution and report any issues.");
if (0 != args->rmInvarSites) {
ERROR("\n-> [-doGVCF 1] --rm-invar-sites 0 is required. Please set --rm-invar-sites 0 and rerun.");
}
if (NULL == args->gvcf_dps_str) {
ERROR("\n-> [-doGVCF 1] --gvcf-dps is required. Please set --gvcf-dps and rerun.");
}
if (!PROGRAM_WILL_ADD_UNOBSERVED) {
ERROR("\n-> [-doGVCF 1] Adding unobserved alleles is required for gVCF output. Please set -doUnobserved to %d or %d and rerun.", ARG_DOUNOBSERVED_STAR, ARG_DOUNOBSERVED_NONREF);
}
if (ARG_DEPTH_INF == args->mps_depth) {
ERROR("\n-> [-doGVCF 1] --depth inf is not supported with gVCF output. Please set --depth to a finite value and rerun.");
}
} else {
if (args->gvcf_dps_str != NULL) {
ERROR("\n-> [--gvcf-dps] --gvcf-dps requires -doGVCF 1. Please set -doGVCF 1 and rerun.");
}
}
if (args->printGlError && (1 == args->GL)) {
ERROR("\n-> [-printGlError 1] Printing the error probability used in genotype likelihood calculations (-printGlError 1) is not supported with genotype likelihood model 1 (--gl-model 1).");
}
if ((0 == args->addI16) && (ARG_I16_MAPQ_DEFAULT != args->i16_mapq)) {
ERROR("\n-> [--i16-mapq] --i16-mapq is set, but printing I16 tag is disabled. Please set -addI16 to 1, or remove --i16-mapq and rerun.");
}
// ---------------------------------------------------------------------- //
// SET ARGUMENT VARIABLES
if (NULL == args->out_fnprefix) {
WARN("Output file prefix is not specified. Setting it to 'output'.\n");
args->out_fnprefix = strdup("output");
}
if (PROGRAM_WILL_ADD_STAR) {
nonref_str = "<*>";
} else if (PROGRAM_WILL_ADD_NONREF) {
nonref_str = "<NON_REF>";
}
if (ARG_DEPTH_INF == args->mps_depth) {
if (PROGRAM_WILL_SKIP_SIM_INVAR_SITES) {
ERROR("[--rm-invar-sites %d] Cannot skip invariable sites when --depth inf is set.", args->rmInvarSites);
}
if (1 == args->doGVCF) {
ERROR("[-doGVCF 1] Cannot output gVCF when --depth inf is set.");
}
}
if (ARG_DEPTH_FILE == args->mps_depth) {
args->mps_depths = args->read_depthsFile();
}
if (args->qs_bins_fn != NULL) {
args->qs_bins = read_qs_bins_file();
}
args->arg_fp = open_FILE(args->out_fnprefix, ".arg");
args->datetime = (char*)malloc(256 * sizeof(char));
ASSERT(NULL != args->datetime);
if (args->error_qs != 0) {
#if __USE_STD_BETA__ == 1
args->betaSampler = new BetaSampler(args->error_rate, args->beta_variance, args->seed);
#else
args->betaSampler = BetaSampler_init(args->error_rate, args->beta_variance, args->seed);
#endif
}
// -> SEED
if (args->seed == -1) {
int rseed = time(NULL);
fprintf(stderr, "\n-> No seed was given. Setting the random seed to the randomly chosen value: %d\n", rseed);
args->seed = rseed;
}
// set seed for rng0
srand48(args->seed);
// set seed for rng1
rng1_seeder[1] = (unsigned short)((long)args->seed);
rng1_seeder[2] = (unsigned short)(((long)args->seed) >> 16);
rng2_seeder[1] = (unsigned short)((long)args->seed);
rng2_seeder[2] = (unsigned short)(((long)args->seed) >> 16);
if (ARG_DEPTH_INF != args->mps_depth) {
if (1 == args->n_mps_depths) {
args->poissonSampler = (PoissonSampler**)malloc(sizeof(PoissonSampler*));
args->poissonSampler[0] = PoissonSampler_init(args->mps_depth);
} else {
//array of poisson samplers
args->poissonSampler = (PoissonSampler**)malloc(args->n_mps_depths * sizeof(PoissonSampler*));
for (int i = 0; i < args->n_mps_depths; ++i) {
args->poissonSampler[i] = PoissonSampler_init(args->mps_depths[i]);
}
}
}
if (args->printBasePickError) {
fprintf(stderr, "[-printBasePickError 1] Program will print the base picking error probability to stdout.\n");
}
if (args->printGlError) {
fprintf(stderr, "[-printGlError 1] Program will print the error probability used in genotype likelihood calculations to stdout.\n");
}
if (args->printQScores) {
fprintf(stderr, "[-printQScores 1] Program will print the quality scores to stdout.\n");
}
if (0 == args->error_qs) {
args->base_pick_error_prob = args->error_rate;
if (args->printBasePickError) {
fprintf(stdout, "base_pick_error_prob\tNA\tNA\tNA\tNA\t%f\n", args->base_pick_error_prob);
}
} else if (1 == args->error_qs) {
args->base_pick_error_prob = -1.0; // sampled
} else if (2 == args->error_qs) {
args->base_pick_error_prob = args->error_rate;
if (args->printBasePickError) {
fprintf(stdout, "base_pick_error_prob\tNA\tNA\tNA\tNA\t%f\n", args->base_pick_error_prob);
}
}
// ---------------------------------------------------------------------- //
// PRINT ARGUMENTS
ASSERT(asprintf(&args->versionInfo, "vcfgl [version: %s] [build: %s %s] [htslib: %s]\n", VCFGL_VERSION, __DATE__, __TIME__, hts_version()));
fprintf(stderr, "\n%s\n", args->versionInfo);
fprintf(args->arg_fp, args->versionInfo);
char depth_val[1024];