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wdist_dosage.c
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#include "wdist_common.h"
// Routines that handle dosage data instead of just 0-1-2 reference allele
// counts. Only Oxford-formatted data is currently supported, but a PLINK
// --dosage loader will probably be added later.
#define MULTIPLEX_DOSAGE_NM (BITCT / 2)
#define MULTIPLEX_DOSAGE_NM3D (MULTIPLEX_DOSAGE_NM / 2)
#if MULTIPLEX_DOSAGE_NM < MULTIPLEX_DOSAGE_NM3D
#error "MULTIPLEX_DOSAGE_NM cannot be less than MULTIPLEX_DOSAGE_NM3D."
#endif
// allowed deviation from 1.0 when summing 0-1-2 reference allele counts, when
// assessing whether missingness should be treated as binary
#define D_EPSILON 0.000244140625 // just want this above .0002
int32_t oxford_sample_load(char* samplename, uintptr_t* unfiltered_indiv_ct_ptr, char** person_ids_ptr, uint32_t* max_person_id_len_ptr, uintptr_t** sex_nm_ptr, uintptr_t** sex_male_ptr, uintptr_t** pheno_nm_ptr, uintptr_t** pheno_c_ptr, double** pheno_d_ptr, uintptr_t** indiv_exclude_ptr, char* missing_code) {
FILE* samplefile = NULL;
unsigned char* wkspace_mark = NULL;
uintptr_t unfiltered_indiv_ct = 0;
uint32_t max_person_id_len = 4;
uint32_t missing_code_ct = 0;
uint32_t indiv_uidx = 0;
char** missing_code_ptrs = NULL;
uint32_t* missing_code_lens = NULL;
int32_t load_sex = 0;
int32_t load_pheno = 0;
uint32_t male_ct = 0;
uint32_t female_ct = 0;
uintptr_t* pheno_nm = NULL;
uintptr_t* pheno_c = NULL;
double* pheno_d = NULL;
int32_t pheno_is_binary = 0;
uintptr_t unfiltered_indiv_ctl;
char* person_ids;
char* item_begin;
char* bufptr;
uint32_t cur_person_id_len;
uint32_t uii;
uint32_t ujj;
uint64_t first_real_line_loc;
int32_t retval;
int32_t is_missing;
double dxx;
if (fopen_checked(&samplefile, samplename, "rb")) {
return RET_OPEN_FAIL;
}
// pass #1: just count number of samples
tbuf[MAXLINELEN - 1] = ' ';
if (!fgets(tbuf, MAXLINELEN, samplefile)) {
if (feof(samplefile)) {
goto oxford_sample_load_ret_INVALID_FORMAT;
} else {
goto oxford_sample_load_ret_READ_FAIL;
}
}
item_begin = skip_initial_spaces(tbuf);
bufptr = next_item_mult(item_begin, 2);
if (no_more_items_kns(bufptr)) {
goto oxford_sample_load_ret_INVALID_FORMAT_3;
}
if (strcmp_se(item_begin, "ID_1", 4) || strcmp_se(next_item(item_begin), "ID_2", 4) || strcmp_se(bufptr, "missing", 7)) {
goto oxford_sample_load_ret_INVALID_FORMAT_3;
}
bufptr = next_item(bufptr);
if (!no_more_items_kns(bufptr)) {
if (strcmp_se(bufptr, "sex", 3)) {
load_pheno = 1;
} else {
load_sex = 1;
bufptr = next_item(bufptr);
if (!no_more_items_kns(bufptr)) {
load_pheno = 1;
}
}
if (load_pheno) {
if (!no_more_items_kns(next_item(bufptr))) {
load_pheno++;
}
}
}
if (!tbuf[MAXLINELEN - 1]) {
goto oxford_sample_load_ret_INVALID_FORMAT_2;
}
if (!fgets(tbuf, MAXLINELEN, samplefile)) {
if (feof(samplefile)) {
goto oxford_sample_load_ret_INVALID_FORMAT;
} else {
goto oxford_sample_load_ret_READ_FAIL;
}
}
item_begin = skip_initial_spaces(tbuf);
bufptr = next_item_mult(item_begin, 2);
if (no_more_items_kns(bufptr)) {
goto oxford_sample_load_ret_INVALID_FORMAT;
}
if (strcmp_se(item_begin, "0", 1) || strcmp_se(next_item(item_begin), "0", 1) || strcmp_se(bufptr, "0", 1)) {
goto oxford_sample_load_ret_INVALID_FORMAT;
}
if (load_sex) {
bufptr = next_item(bufptr);
if (no_more_items_kns(bufptr) || strcmp_se(bufptr, "D", 1)) {
goto oxford_sample_load_ret_INVALID_FORMAT;
}
}
if (load_pheno) {
bufptr = next_item(bufptr);
if (no_more_items_kns(bufptr)) {
goto oxford_sample_load_ret_INVALID_FORMAT;
}
if (!strcmp_se(bufptr, "B", 1)) {
pheno_is_binary = 1;
} else if (strcmp_se(bufptr, "P", 1)) {
goto oxford_sample_load_ret_INVALID_FORMAT;
}
if (load_pheno > 1) {
if (no_more_items_kns(next_item(bufptr))) {
goto oxford_sample_load_ret_INVALID_FORMAT;
}
logprint("Note: Multiple phenotypes/covariates detected. Loading only the first one.\n");
load_pheno = 1;
}
}
if (!tbuf[MAXLINELEN - 1]) {
goto oxford_sample_load_ret_INVALID_FORMAT_2;
}
first_real_line_loc = ftello(samplefile);
unfiltered_indiv_ct = 0;
// first pass: count indivs, determine max ID length
while (fgets(tbuf, MAXLINELEN, samplefile) != NULL) {
if (!tbuf[MAXLINELEN - 1]) {
goto oxford_sample_load_ret_INVALID_FORMAT_2;
}
item_begin = skip_initial_spaces(tbuf);
if (is_eoln_kns(*item_begin)) {
continue;
}
bufptr = item_endnn(item_begin);
if (is_eoln(*bufptr)) {
goto oxford_sample_load_ret_INVALID_FORMAT;
}
cur_person_id_len = 2 + (uint32_t)(bufptr - item_begin);
item_begin = skip_initial_spaces(bufptr);
bufptr = item_endnn(item_begin);
if (is_eoln(*bufptr)) {
goto oxford_sample_load_ret_INVALID_FORMAT;
}
cur_person_id_len += (uint32_t)(bufptr - item_begin);
if (cur_person_id_len > max_person_id_len) {
max_person_id_len = cur_person_id_len;
}
unfiltered_indiv_ct++;
}
if (!feof(samplefile)) {
goto oxford_sample_load_ret_READ_FAIL;
}
if (!unfiltered_indiv_ct) {
sprintf(logbuf, "Error: No %s in .sample file.\n", species_plural);
goto oxford_sample_load_ret_INVALID_FORMAT_4;
}
*unfiltered_indiv_ct_ptr = unfiltered_indiv_ct;
*max_person_id_len_ptr = max_person_id_len;
unfiltered_indiv_ctl = (unfiltered_indiv_ct + (BITCT - 1)) / BITCT;
if (wkspace_alloc_c_checked(person_ids_ptr, unfiltered_indiv_ct * max_person_id_len) ||
wkspace_alloc_ul_checked(sex_nm_ptr, unfiltered_indiv_ctl * sizeof(intptr_t)) ||
wkspace_alloc_ul_checked(sex_male_ptr, unfiltered_indiv_ctl * sizeof(intptr_t)) ||
wkspace_alloc_ul_checked(pheno_nm_ptr, unfiltered_indiv_ctl * sizeof(intptr_t)) ||
wkspace_alloc_ul_checked(indiv_exclude_ptr, unfiltered_indiv_ctl * sizeof(intptr_t))) {
goto oxford_sample_load_ret_NOMEM;
}
if (load_pheno) {
if (pheno_is_binary) {
if (wkspace_alloc_ul_checked(pheno_c_ptr, unfiltered_indiv_ctl * sizeof(intptr_t))) {
goto oxford_sample_load_ret_NOMEM;
}
pheno_c = *pheno_c_ptr;
fill_ulong_zero(pheno_c, unfiltered_indiv_ctl);
} else {
if (wkspace_alloc_d_checked(pheno_d_ptr, unfiltered_indiv_ct * sizeof(double))) {
goto oxford_sample_load_ret_NOMEM;
}
pheno_d = *pheno_d_ptr;
}
} else {
pheno_d_ptr = NULL;
}
person_ids = *person_ids_ptr;
fill_ulong_zero(*sex_nm_ptr, unfiltered_indiv_ctl);
fill_ulong_zero(*sex_male_ptr, unfiltered_indiv_ctl);
fill_ulong_zero(*indiv_exclude_ptr, unfiltered_indiv_ctl);
fill_ulong_zero(*pheno_nm_ptr, unfiltered_indiv_ctl);
pheno_nm = *pheno_nm_ptr;
wkspace_mark = wkspace_base;
if (*missing_code) {
bufptr = missing_code;
do {
if ((*bufptr == ',') || (*bufptr == '\0')) {
// blank string makes no sense
sprintf(logbuf, "Error: Invalid --missing-code parameter '%s'.%s", missing_code, errstr_append);
logprintb();
goto oxford_sample_load_ret_INVALID_CMDLINE;
}
bufptr = strchr(bufptr, ',');
missing_code_ct++;
if (bufptr) {
bufptr++;
}
} while (bufptr);
}
if (missing_code_ct) {
missing_code_ptrs = (char**)wkspace_alloc(missing_code_ct * sizeof(char*)); if (!missing_code_ptrs) {
goto oxford_sample_load_ret_NOMEM;
}
if (wkspace_alloc_ui_checked(&missing_code_lens, missing_code_ct * sizeof(int32_t))) {
goto oxford_sample_load_ret_NOMEM;
}
bufptr = missing_code;
for (uii = 0; uii < missing_code_ct; uii++) {
missing_code_ptrs[uii] = bufptr;
bufptr = strchr(bufptr, ',');
if (bufptr) {
missing_code_lens[uii] = (uint32_t)(bufptr - missing_code_ptrs[uii]);
*bufptr = '\0';
bufptr++;
} else {
missing_code_lens[uii] = strlen(missing_code_ptrs[uii]);
}
}
}
if (fseeko(samplefile, first_real_line_loc, SEEK_SET)) {
goto oxford_sample_load_ret_READ_FAIL;
}
// second pass: actually load stuff
while (fgets(tbuf, MAXLINELEN, samplefile)) {
item_begin = skip_initial_spaces(tbuf);
if (is_eoln_kns(*item_begin)) {
continue;
}
bufptr = item_endnn(item_begin);
uii = (uint32_t)(bufptr - item_begin);
memcpy(&(person_ids[indiv_uidx * max_person_id_len]), item_begin, uii);
person_ids[indiv_uidx * max_person_id_len + uii] = '\t';
item_begin = skip_initial_spaces(bufptr);
bufptr = item_endnn(item_begin);
ujj = (uint32_t)(bufptr - item_begin);
memcpy(&(person_ids[indiv_uidx * max_person_id_len + uii + 1]), item_begin, ujj);
person_ids[indiv_uidx * max_person_id_len + uii + 1 + ujj] = '\0';
item_begin = next_item(skip_initial_spaces(bufptr));
if (load_sex) {
if (no_more_items_kns(item_begin)) {
goto oxford_sample_load_ret_INVALID_FORMAT;
}
if (*item_begin == '1') {
set_bit_noct(*sex_nm_ptr, indiv_uidx);
set_bit_noct(*sex_male_ptr, indiv_uidx);
male_ct++;
} else if (*item_begin == '2') {
set_bit_noct(*sex_nm_ptr, indiv_uidx);
female_ct++;
}
item_begin = next_item(item_begin);
}
if (load_pheno) {
if (no_more_items_kns(item_begin)) {
goto oxford_sample_load_ret_INVALID_FORMAT;
}
bufptr = item_endnn(item_begin);
uii = (uint32_t)(bufptr - item_begin);
is_missing = 0;
for (ujj = 0; ujj < missing_code_ct; ujj++) {
if (uii == missing_code_lens[ujj]) {
if (!memcmp(item_begin, missing_code_ptrs[ujj], uii)) {
is_missing = 1;
break;
}
}
}
if (!is_missing) {
set_bit_noct(pheno_nm, indiv_uidx);
if (pheno_is_binary) {
if (*item_begin == '1') {
set_bit_noct(pheno_c, indiv_uidx);
} else if (*item_begin != '0') {
goto oxford_sample_load_ret_INVALID_FORMAT;
}
} else {
if (sscanf(item_begin, "%lg", &dxx) != 1) {
goto oxford_sample_load_ret_INVALID_FORMAT;
}
pheno_d[indiv_uidx] = dxx;
}
}
}
indiv_uidx++;
}
if (!feof(samplefile)) {
goto oxford_sample_load_ret_READ_FAIL;
}
retval = 0;
if (load_sex) {
uii = unfiltered_indiv_ct - male_ct - female_ct;
if (uii) {
sprintf(logbuf, "%" PRIuPTR " %s (%d male%s, %d female%s, %d unknown) loaded.\n", unfiltered_indiv_ct, species_str(unfiltered_indiv_ct), male_ct, (male_ct == 1)? "" : "s", female_ct, (female_ct == 1)? "" : "s", uii);
} else {
sprintf(logbuf, "%" PRIuPTR " %s (%d male%s, %d female%s) loaded.\n", unfiltered_indiv_ct, species_str(unfiltered_indiv_ct), male_ct, (male_ct == 1)? "" : "s", female_ct, (female_ct == 1)? "" : "s");
}
} else {
sprintf(logbuf, "%" PRIuPTR " %s loaded.\n", unfiltered_indiv_ct, species_str(unfiltered_indiv_ct));
}
logprintb();
while (0) {
oxford_sample_load_ret_NOMEM:
retval = RET_NOMEM;
break;
oxford_sample_load_ret_READ_FAIL:
retval = RET_READ_FAIL;
break;
oxford_sample_load_ret_INVALID_CMDLINE:
retval = RET_INVALID_CMDLINE;
break;
oxford_sample_load_ret_INVALID_FORMAT:
logprint("Error: Improperly formatted .sample file.\n");
retval = RET_INVALID_FORMAT;
break;
oxford_sample_load_ret_INVALID_FORMAT_2:
sprintf(logbuf, "Error: Excessively long line in .sample file (max %d chars).\n", MAXLINELEN - 3);
oxford_sample_load_ret_INVALID_FORMAT_4:
logprintb();
retval = RET_INVALID_FORMAT;
break;
oxford_sample_load_ret_INVALID_FORMAT_3:
logprint("Unsupported .sample file format. (First three columns are expected to be\n'ID_1', 'ID_2', and 'missing', in that order.)\n");
retval = RET_INVALID_FORMAT;
break;
}
if (wkspace_mark) {
wkspace_reset(wkspace_mark);
}
fclose_cond(samplefile);
return retval;
}
int32_t oxford_gen_load1(FILE* genfile, uint32_t* gen_buf_len_ptr, uintptr_t* unfiltered_marker_ct_ptr, double** set_allele_freqs_ptr, uint32_t* is_missing_01_ptr, uintptr_t unfiltered_indiv_ct, uint32_t maf_succ) {
// Determine maximum line length, calculate reference allele frequencies,
// and check if all missingness probabilities are 0 or ~1.
uintptr_t unfiltered_marker_ct = 0;
uintptr_t unfiltered_indiv_ct8m = unfiltered_indiv_ct & 0xfffffff8U;
uint32_t gen_buf_len = 0;
char* stack_base = (char*)wkspace_base;
char* loadbuf = (&(stack_base[sizeof(double)]));
uint32_t is_missing_01 = 1;
uint32_t pct = 1;
uint64_t file_length;
uint64_t file_pos_100;
char* bufptr;
int32_t max_load;
uint32_t uii;
uint32_t indiv_uidx;
double total_ref_allele_ct;
double total_allele_wt;
double cur_ref_allele_cts[8];
double cur_allele_wts[8];
double cur_ref_homs[8];
double cur_ref_allele_ct;
double cur_allele_wt;
double dxx;
if (wkspace_left > 0x7fffffc0) {
max_load = 0x7fffffc0;
} else {
max_load = wkspace_left;
}
*set_allele_freqs_ptr = (double*)wkspace_base;
if (fseeko(genfile, 0, SEEK_END)) {
return RET_READ_FAIL;
}
fflush(stdout);
file_length = ftello(genfile);
rewind(genfile);
max_load -= sizeof(double);
if (max_load <= 0) {
return RET_NOMEM;
}
while (fgets(loadbuf, max_load, genfile)) {
bufptr = skip_initial_spaces(loadbuf);
if (is_eoln_kns(*bufptr)) {
continue;
}
bufptr = next_item_mult(bufptr, 4);
if (maf_succ) {
total_ref_allele_ct = 1.0;
total_allele_wt = 1.0;
} else {
total_ref_allele_ct = 0.0;
total_allele_wt = 0.0;
}
for (indiv_uidx = 0; indiv_uidx < unfiltered_indiv_ct;) {
bufptr = next_item(bufptr);
if (no_more_items_kns(bufptr)) {
goto oxford_gen_load1_ret_INVALID_FORMAT;
}
if (indiv_uidx >= unfiltered_indiv_ct8m) {
if (sscanf(bufptr, "%lg %lg %lg", &cur_allele_wt, &cur_ref_allele_ct, &dxx) != 3) {
goto oxford_gen_load1_ret_INVALID_FORMAT;
}
bufptr = next_item_mult(bufptr, 2);
cur_allele_wt += dxx + cur_ref_allele_ct;
cur_ref_allele_ct += 2 * dxx;
if (is_missing_01) {
if ((cur_allele_wt != 0.0) && ((cur_allele_wt < 1.0 - D_EPSILON) || (cur_allele_wt > 1.0 + D_EPSILON))) {
is_missing_01 = 0;
}
}
total_ref_allele_ct += cur_ref_allele_ct;
total_allele_wt += cur_allele_wt;
indiv_uidx++;
} else {
// sadly, this kludge is an important performance optimization
if (sscanf(bufptr, "%lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg %lg", &(cur_allele_wts[0]), &(cur_ref_allele_cts[0]), &(cur_ref_homs[0]), &(cur_allele_wts[1]), &(cur_ref_allele_cts[1]), &(cur_ref_homs[1]), &(cur_allele_wts[2]), &(cur_ref_allele_cts[2]), &(cur_ref_homs[2]), &(cur_allele_wts[3]), &(cur_ref_allele_cts[3]), &(cur_ref_homs[3]), &(cur_allele_wts[4]), &(cur_ref_allele_cts[4]), &(cur_ref_homs[4]), &(cur_allele_wts[5]), &(cur_ref_allele_cts[5]), &(cur_ref_homs[5]), &(cur_allele_wts[6]), &(cur_ref_allele_cts[6]), &(cur_ref_homs[6]), &(cur_allele_wts[7]), &(cur_ref_allele_cts[7]), &(cur_ref_homs[7])) != 24) {
goto oxford_gen_load1_ret_INVALID_FORMAT;
}
bufptr = next_item_mult(bufptr, 23);
if (is_missing_01) {
for (uii = 0; uii < 8; uii++) {
cur_allele_wts[uii] += cur_ref_homs[uii] + cur_ref_allele_cts[uii];
cur_ref_allele_cts[uii] += 2 * cur_ref_homs[uii];
if ((cur_allele_wts[uii] != 0.0) && ((cur_allele_wts[uii] < 1.0 - D_EPSILON) || (cur_allele_wts[uii] > 1.0 + D_EPSILON))) {
is_missing_01 = 0;
}
total_ref_allele_ct += cur_ref_allele_cts[uii];
total_allele_wt += cur_allele_wts[uii];
}
} else {
for (uii = 0; uii < 8; uii++) {
cur_allele_wts[uii] += cur_ref_homs[uii] + cur_ref_allele_cts[uii];
cur_ref_allele_cts[uii] += 2 * cur_ref_homs[uii];
total_ref_allele_ct += cur_ref_allele_cts[uii];
total_allele_wt += cur_allele_wts[uii];
}
}
indiv_uidx += 8;
}
}
uii = strlen(bufptr) + (uint32_t)(bufptr - loadbuf);
if (loadbuf[uii - 1] != '\n') {
logprint("Excessively long line in .gen file.\n");
return RET_NOMEM;
}
if (uii >= gen_buf_len) {
gen_buf_len = uii + 1;
}
if (total_allele_wt == 0.0) {
(*set_allele_freqs_ptr)[unfiltered_marker_ct] = 0.5;
} else {
(*set_allele_freqs_ptr)[unfiltered_marker_ct] = (total_ref_allele_ct * 0.5) / total_allele_wt;
}
unfiltered_marker_ct++;
loadbuf = &(loadbuf[sizeof(double)]);
max_load -= sizeof(double);
file_pos_100 = ftello(genfile) * 100LLU;
if (file_pos_100 >= pct * file_length) {
pct = (uint32_t)(file_pos_100 / file_length);
printf("\rScanning .gen file (%u%%)...", pct);
fflush(stdout);
}
}
if (!feof(genfile)) {
return RET_READ_FAIL;
}
if (!unfiltered_marker_ct) {
logprint("Error: No markers in .gen file.\n");
return RET_INVALID_FORMAT;
}
putchar('\r');
sprintf(logbuf, ".gen scan complete. %" PRIuPTR " marker%s and %" PRIuPTR " pe%s present.\n", unfiltered_marker_ct, (unfiltered_marker_ct == 1)? "" : "s", unfiltered_indiv_ct, (unfiltered_indiv_ct == 1)? "rson" : "ople");
logprintb();
*set_allele_freqs_ptr = (double*)wkspace_alloc(unfiltered_marker_ct * sizeof(double));
*unfiltered_marker_ct_ptr = unfiltered_marker_ct;
*gen_buf_len_ptr = gen_buf_len;
*is_missing_01_ptr = is_missing_01;
while (0) {
oxford_gen_load1_ret_INVALID_FORMAT:
logprint("Error: Improperly formatted .gen file.\n");
return RET_INVALID_FORMAT;
}
return 0;
}
// ----- multithread globals -----
static double* g_distance_matrix;
// If missingness is binary, this is a sum of sparse intersection weights;
// otherwise, this is a sum of ALL weights.
static double* g_distance_wt_matrix;
static uint32_t g_thread_start[MAX_THREADS_P1];
static double* g_dosage_vals; // (usually) [0..2] dosages for current markers
// If missingness is binary
static uintptr_t* g_missing_vals; // bit array marking missing values
// If missingness is continuous
static double* g_nonmissing_vals;
#if BITCT < MULTIPLEX_DOSAGE_NM
#error "Insufficient g_missing_wts[] size in wdist_dosage.c."
#endif
// static double g_marker_wts[BITCT]; // --exponent marker weights
static double g_missing_wts[BITCT]; // missingness rescale weights
#ifdef __LP64__
static double* g_missing_dmasks; // 0x7fff... if non-missing, 0x0000... otherwise
#else
// double times signed int32_t tends to be faster than double times uint32_t
static int32_t* g_missing_dmasks; // 1 or 0, multiply instead of mask
#endif
void incr_distance_dosage_2d_01(double* distance_matrix_slice, int32_t thread_idx) {
#ifdef __LP64__
// take absolute value = force sign bit to zero
__m128d* dptr_start;
__m128d* dptr_end;
__m128d* dptr;
__m128d* dptr2;
__m128d* mptr_start;
__m128d* mptr;
__m128d* mptr2;
__uni16 acc;
#else
double* dptr_start;
double* dptr_end;
double* dptr;
double* dptr2;
int32_t* mptr_start;
int32_t* mptr;
int32_t* mptr2;
double acc;
#endif
uintptr_t ulii;
uintptr_t uljj;
for (ulii = g_thread_start[thread_idx]; ulii < g_thread_start[thread_idx + 1]; ulii++) {
#ifdef __LP64__
dptr_start = (__m128d*)(&(g_dosage_vals[ulii * BITCT]));
dptr_end = &(dptr_start[BITCT2]);
dptr2 = (__m128d*)g_dosage_vals;
mptr2 = (__m128d*)g_missing_dmasks;
#else
dptr_start = &(g_dosage_vals[ulii * BITCT]);
dptr_end = &(dptr_start[BITCT]);
dptr2 = g_dosage_vals;
mptr2 = g_missing_dmasks;
#endif
if (g_missing_vals[ulii]) {
#ifdef __LP64__
mptr_start = (__m128d*)(&(g_missing_dmasks[ulii * BITCT]));
#else
mptr_start = &(g_missing_dmasks[ulii * BITCT]);
#endif
for (uljj = 0; uljj < ulii; uljj++) {
dptr = dptr_start;
mptr = mptr_start;
#ifdef __LP64__
acc.vd = _mm_setzero_pd();
do {
acc.vd = _mm_add_pd(acc.vd, _mm_and_pd(_mm_and_pd(*mptr++, *mptr2++), _mm_sub_pd(*dptr++, *dptr2++)));
} while (dptr != dptr_end);
*distance_matrix_slice += acc.d8[0] + acc.d8[1];
#else
acc = 0.0;
do {
acc += (*mptr++) * (*mptr2++) * fabs((*dptr++) - (*dptr2++));
} while (dptr != dptr_end);
*distance_matrix_slice += acc;
#endif
distance_matrix_slice++;
}
} else {
for (uljj = 0; uljj < ulii; uljj++) {
dptr = dptr_start;
#ifdef __LP64__
acc.vd = _mm_setzero_pd();
do {
acc.vd = _mm_add_pd(acc.vd, _mm_and_pd(*mptr2++, _mm_sub_pd(*dptr++, *dptr2++)));
} while (dptr != dptr_end);
*distance_matrix_slice += acc.d8[0] + acc.d8[1];
#else
acc = 0.0;
do {
acc += (*mptr2++) * fabs((*dptr++) - (*dptr2++));
} while (dptr != dptr_end);
*distance_matrix_slice += acc;
#endif
distance_matrix_slice++;
}
}
}
}
THREAD_RET_TYPE incr_distance_dosage_2d_01_thread(void* arg) {
intptr_t tidx = (intptr_t)arg;
int32_t ts = g_thread_start[tidx];
int32_t ts0 = g_thread_start[0];
incr_distance_dosage_2d_01(&(g_distance_matrix[((int64_t)ts * (ts - 1) - (int64_t)ts0 * (ts0 - 1)) / 2]), (int)tidx);
THREAD_RETURN;
}
void incr_distance_dosage_2d_flat(double* distance_matrix_slice, double* distance_wt_matrix_slice, int32_t thread_idx) {
#ifdef __LP64__
// take absolute value = force sign bit to zero
const __m128i absmask_raw = {0x7fffffffffffffffLLU, 0x7fffffffffffffffLLU};
__m128d* absmask_ptr = (__m128d*)(&absmask_raw);
__m128d absmask = *absmask_ptr;
__m128d* dptr_start;
__m128d* dptr_end;
__m128d* dptr;
__m128d* dptr2;
__m128d* mptr_start;
__m128d* mptr;
__m128d* mptr2;
__m128d cur_nonmissing_wts;
__uni16 acc;
__uni16 accm;
#else
double* dptr_start;
double* dptr_end;
double* dptr;
double* dptr2;
double* mptr_start;
double* mptr;
double* mptr2;
double cur_nonmissing_wt;
double acc;
double accm;
#endif
uintptr_t ulii;
uintptr_t uljj;
for (ulii = g_thread_start[thread_idx]; ulii < g_thread_start[thread_idx + 1]; ulii++) {
#ifdef __LP64__
dptr_start = (__m128d*)(&(g_dosage_vals[ulii * MULTIPLEX_DOSAGE_NM]));
dptr_end = &(dptr_start[MULTIPLEX_DOSAGE_NM / 2]);
dptr2 = (__m128d*)g_dosage_vals;
mptr_start = (__m128d*)(&(g_nonmissing_vals[ulii * MULTIPLEX_DOSAGE_NM]));
mptr2 = (__m128d*)g_nonmissing_vals;
#else
dptr_start = &(g_dosage_vals[ulii * MULTIPLEX_DOSAGE_NM]);
dptr_end = &(dptr_start[MULTIPLEX_DOSAGE_NM]);
dptr2 = g_dosage_vals;
mptr_start = &(g_nonmissing_vals[ulii * MULTIPLEX_DOSAGE_NM]);
mptr2 = g_nonmissing_vals;
#endif
for (uljj = 0; uljj < ulii; uljj++) {
dptr = dptr_start;
mptr = mptr_start;
#ifdef __LP64__
acc.vd = _mm_setzero_pd();
accm.vd = _mm_setzero_pd();
do {
cur_nonmissing_wts = _mm_mul_pd(*mptr++, *mptr2++);
acc.vd = _mm_add_pd(acc.vd, _mm_mul_pd(cur_nonmissing_wts, _mm_and_pd(absmask, _mm_sub_pd(*dptr++, *dptr2++))));
accm.vd = _mm_add_pd(accm.vd, cur_nonmissing_wts);
} while (dptr != dptr_end);
*distance_matrix_slice += acc.d8[0] + acc.d8[1];
*distance_wt_matrix_slice += accm.d8[0] + accm.d8[1];
#else
acc = 0.0;
accm = 0.0;
do {
cur_nonmissing_wt = (*mptr++) * (*mptr2++);
acc += cur_nonmissing_wt * fabs((*dptr++) - (*dptr2++));
accm += cur_nonmissing_wt;
} while (dptr != dptr_end);
*distance_matrix_slice += acc;
*distance_wt_matrix_slice += accm;
#endif
distance_matrix_slice++;
distance_wt_matrix_slice++;
}
}
}
THREAD_RET_TYPE incr_distance_dosage_2d_flat_thread(void* arg) {
intptr_t tidx = (intptr_t)arg;
int32_t ts = g_thread_start[tidx];
int32_t ts0 = g_thread_start[0];
int64_t offset = ((int64_t)ts * (ts - 1) - (int64_t)ts0 * (ts0 - 1)) / 2;
incr_distance_dosage_2d_flat(&(g_distance_matrix[offset]), &(g_distance_wt_matrix[offset]), (int)tidx);
THREAD_RETURN;
}
void incr_distance_dosage_2d(double* distance_matrix_slice, double* distance_wt_matrix_slice, int32_t thread_idx) {
#ifdef __LP64__
const __m128i absmask_raw = {0x7fffffffffffffffLLU, 0x7fffffffffffffffLLU};
__m128d* absmask_ptr = (__m128d*)(&absmask_raw);
__m128d absmask = *absmask_ptr;
__m128d* dptr_start;
__m128d* dptr_end;
__m128d* dptr;
__m128d* dptr2;
__m128d* mptr_start;
__m128d* mptr;
__m128d* mptr2;
__m128d* mwptr;
__m128d cur_nonmissing_wts;
__uni16 acc;
__uni16 accm;
#else
double* dptr_start;
double* dptr_end;
double* dptr;
double* dptr2;
double* mptr_start;
double* mptr;
double* mptr2;
double* mwptr;
double cur_nonmissing_wt;
double acc;
double accm;
#endif
uintptr_t ulii;
uintptr_t uljj;
for (ulii = g_thread_start[thread_idx]; ulii < g_thread_start[thread_idx + 1]; ulii++) {
#ifdef __LP64__
dptr_start = (__m128d*)(&(g_dosage_vals[ulii * MULTIPLEX_DOSAGE_NM]));
dptr_end = &(dptr_start[MULTIPLEX_DOSAGE_NM / 2]);
dptr2 = (__m128d*)g_dosage_vals;
mptr_start = (__m128d*)(&(g_nonmissing_vals[ulii * MULTIPLEX_DOSAGE_NM]));
mptr2 = (__m128d*)g_nonmissing_vals;
#else
dptr_start = &(g_dosage_vals[ulii * MULTIPLEX_DOSAGE_NM]);
dptr_end = &(dptr_start[MULTIPLEX_DOSAGE_NM]);
dptr2 = g_dosage_vals;
mptr_start = &(g_nonmissing_vals[ulii * MULTIPLEX_DOSAGE_NM]);
mptr2 = g_nonmissing_vals;
#endif
for (uljj = 0; uljj < ulii; uljj++) {
dptr = dptr_start;
mptr = mptr_start;
#ifdef __LP64__
mwptr = (__m128d*)g_missing_wts;
acc.vd = _mm_setzero_pd();
accm.vd = _mm_setzero_pd();
do {
cur_nonmissing_wts = _mm_mul_pd(*mptr++, *mptr2++);
acc.vd = _mm_add_pd(acc.vd, _mm_mul_pd(cur_nonmissing_wts, _mm_and_pd(absmask, _mm_sub_pd(*dptr++, *dptr2++))));
accm.vd = _mm_add_pd(accm.vd, _mm_mul_pd(*mwptr++, cur_nonmissing_wts));
} while (dptr != dptr_end);
*distance_matrix_slice += acc.d8[0] + acc.d8[1];
*distance_wt_matrix_slice += accm.d8[0] + accm.d8[1];
#else
mwptr = g_missing_wts;
acc = 0.0;
accm = 0.0;
do {
cur_nonmissing_wt = (*mptr++) * (*mptr2++);
acc += cur_nonmissing_wt * fabs((*dptr++) - (*dptr2++));
accm += cur_nonmissing_wt * (*mwptr++);
} while (dptr != dptr_end);
*distance_matrix_slice += acc;
*distance_wt_matrix_slice += accm;
#endif
distance_matrix_slice++;
distance_wt_matrix_slice++;
}
}
}
THREAD_RET_TYPE incr_distance_dosage_2d_thread(void* arg) {
intptr_t tidx = (intptr_t)arg;
int32_t ts = g_thread_start[tidx];
int32_t ts0 = g_thread_start[0];
int64_t offset = ((int64_t)ts * (ts - 1) - (int64_t)ts0 * (ts0 - 1)) / 2;
incr_distance_dosage_2d(&(g_distance_matrix[offset]), &(g_distance_wt_matrix[offset]), (int)tidx);
THREAD_RETURN;
}
void incr_distance_dosage_3d_flat(double* distance_matrix_slice, double* distance_wt_matrix_slice, int32_t thread_idx) {
// 3d distance: P_1(0) * (P_2(1) + 2 * P_2(2)) + P_1(1) * (P_2(0) + P_2(2)) +
// P_1(2) * (2 * P_2(0) + P_2(1))
// weight: (P_1(0) + P_1(1) + P_1(2)) * (P_2(0) + P_2(1) + P_2(2))
//
#ifdef __LP64__
const __m128d vec_two = {2.0, 2.0};
__m128d dptr_buf[2 * MULTIPLEX_DOSAGE_NM3D];
__m128d* dptr_buf_end1 = &(dptr_buf[MULTIPLEX_DOSAGE_NM3D / 2]);
__m128d* dptr_buf_end2 = &(dptr_buf[MULTIPLEX_DOSAGE_NM3D]);
__m128d* dptr_buf_end3 = &(dptr_buf[3 * MULTIPLEX_DOSAGE_NM3D / 2]);
__m128d* dptr_buf_end = &(dptr_buf[2 * MULTIPLEX_DOSAGE_NM3D]);
__m128d* dptr;
__m128d* dptr_start;
__m128d* dptr2;
__m128d* dptr3;
__uni16 acc;
#else
double dptr_buf[4 * MULTIPLEX_DOSAGE_NM3D];
double* dptr_buf_end1 = &(dptr_buf[MULTIPLEX_DOSAGE_NM3D]);
double* dptr_buf_end2 = &(dptr_buf[2 * MULTIPLEX_DOSAGE_NM3D]);
double* dptr_buf_end3 = &(dptr_buf[3 * MULTIPLEX_DOSAGE_NM3D]);
double* dptr_buf_end = &(dptr_buf[4 * MULTIPLEX_DOSAGE_NM3D]);
double* dptr;
double* dptr_start;
double* dptr2;
double* dptr3;
double acc;
#endif
uintptr_t ulii;
uintptr_t uljj;
for (ulii = g_thread_start[thread_idx]; ulii < g_thread_start[thread_idx + 1]; ulii++) {
#ifdef __LP64__
dptr = dptr_buf;
dptr_start = (__m128d*)(&(g_dosage_vals[ulii * 4 * MULTIPLEX_DOSAGE_NM3D]));
dptr2 = &(dptr_start[MULTIPLEX_DOSAGE_NM3D / 2]);
dptr3 = &(dptr_start[MULTIPLEX_DOSAGE_NM3D]);
do {
*dptr++ = _mm_add_pd(_mm_mul_pd(vec_two, *dptr3++), *dptr2++);
} while (dptr != dptr_buf_end1);
dptr3 = dptr_start;
do {
*dptr++ = _mm_add_pd(*dptr2++, *dptr3++);
} while (dptr != dptr_buf_end2);
dptr2 = dptr_start;
do {
*dptr++ = _mm_add_pd(_mm_mul_pd(vec_two, *dptr2++), *dptr3++);
} while (dptr != dptr_buf_end3);
dptr2 = &(dptr_start[3 * MULTIPLEX_DOSAGE_NM3D / 2]);
do {
*dptr++ = *dptr2++;
} while (dptr != dptr_buf_end);
dptr2 = (__m128d*)g_dosage_vals;
#else
dptr = dptr_buf;
dptr_start = &(g_dosage_vals[ulii * 4 * MULTIPLEX_DOSAGE_NM3D]);
dptr2 = &(dptr_start[MULTIPLEX_DOSAGE_NM3D]);
dptr3 = &(dptr_start[2 * MULTIPLEX_DOSAGE_NM3D]);
do {
*dptr++ = (*dptr2++) + 2 * (*dptr3++);
} while (dptr != dptr_buf_end1);
dptr3 = dptr_start;
do {
*dptr++ = (*dptr2++) + (*dptr3++);
} while (dptr != dptr_buf_end2);
dptr2 = dptr_start;
do {
*dptr++ = 2 * (*dptr2++) + (*dptr3++);
} while (dptr != dptr_buf_end3);
dptr2 = &(dptr_start[3 * MULTIPLEX_DOSAGE_NM3D]);
do {
*dptr++ = *dptr2++;
} while (dptr != dptr_buf_end);
dptr2 = g_dosage_vals;
#endif
for (uljj = 0; uljj < ulii; uljj++) {
dptr = dptr_buf;
#ifdef __LP64__
acc.vd = _mm_setzero_pd();
do {
acc.vd = _mm_add_pd(acc.vd, _mm_mul_pd(*dptr++, *dptr2++));
} while (dptr != dptr_buf_end3);
*distance_matrix_slice += acc.d8[0] + acc.d8[1];
acc.vd = _mm_setzero_pd();
do {
acc.vd = _mm_add_pd(acc.vd, _mm_mul_pd(*dptr++, *dptr2++));
} while (dptr != dptr_buf_end);
*distance_wt_matrix_slice += acc.d8[0] + acc.d8[1];
#else
acc = 0.0;
do {
acc += (*dptr++) * (*dptr2++);
} while (dptr != dptr_buf_end3);
*distance_matrix_slice += acc;
acc = 0.0;
do {
acc += (*dptr++) * (*dptr2++);
} while (dptr != dptr_buf_end);
*distance_wt_matrix_slice += acc;
#endif
distance_matrix_slice++;
distance_wt_matrix_slice++;
}
}
}
THREAD_RET_TYPE incr_distance_dosage_3d_flat_thread(void* arg) {
intptr_t tidx = (intptr_t)arg;
int32_t ts = g_thread_start[tidx];
int32_t ts0 = g_thread_start[0];
int64_t offset = ((int64_t)ts * (ts - 1) - (int64_t)ts0 * (ts0 - 1)) / 2;
incr_distance_dosage_3d_flat(&(g_distance_matrix[offset]), &(g_distance_wt_matrix[offset]), (int)tidx);
THREAD_RETURN;
}
void incr_distance_dosage_3d(double* distance_matrix_slice, double* distance_wt_matrix_slice, int32_t thread_idx) {
#ifdef __LP64__
const __m128d vec_two = {2.0, 2.0};
__m128d dptr_buf[2 * MULTIPLEX_DOSAGE_NM3D];
__m128d* dptr_buf_end1 = &(dptr_buf[MULTIPLEX_DOSAGE_NM3D / 2]);
__m128d* dptr_buf_end2 = &(dptr_buf[MULTIPLEX_DOSAGE_NM3D]);
__m128d* dptr_buf_end3 = &(dptr_buf[3 * MULTIPLEX_DOSAGE_NM3D / 2]);
__m128d* dptr_buf_end = &(dptr_buf[2 * MULTIPLEX_DOSAGE_NM3D]);
__m128d* dptr;
__m128d* dptr_start;
__m128d* dptr2;
__m128d* dptr3;
__m128d* mwptr;
__uni16 acc;
#else
double dptr_buf[4 * MULTIPLEX_DOSAGE_NM3D];
double* dptr_buf_end1 = &(dptr_buf[MULTIPLEX_DOSAGE_NM3D]);
double* dptr_buf_end2 = &(dptr_buf[2 * MULTIPLEX_DOSAGE_NM3D]);
double* dptr_buf_end3 = &(dptr_buf[3 * MULTIPLEX_DOSAGE_NM3D]);
double* dptr_buf_end = &(dptr_buf[4 * MULTIPLEX_DOSAGE_NM3D]);
double* dptr;
double* dptr_start;
double* dptr2;
double* dptr3;
double* mwptr;
double acc;
#endif
uintptr_t ulii;
uintptr_t uljj;
for (ulii = g_thread_start[thread_idx]; ulii < g_thread_start[thread_idx + 1]; ulii++) {
#ifdef __LP64__
dptr = dptr_buf;
dptr_start = (__m128d*)(&(g_dosage_vals[ulii * 4 * MULTIPLEX_DOSAGE_NM3D]));
dptr2 = &(dptr_start[MULTIPLEX_DOSAGE_NM3D / 2]);
dptr3 = &(dptr_start[MULTIPLEX_DOSAGE_NM3D]);
do {
*dptr++ = _mm_add_pd(_mm_mul_pd(vec_two, *dptr3++), *dptr2++);
} while (dptr != dptr_buf_end1);
dptr3 = dptr_start;
do {
*dptr++ = _mm_add_pd(*dptr2++, *dptr3++);
} while (dptr != dptr_buf_end2);
dptr2 = dptr_start;
do {
*dptr++ = _mm_add_pd(_mm_mul_pd(vec_two, *dptr2++), *dptr3++);
} while (dptr != dptr_buf_end3);
dptr2 = &(dptr_start[3 * MULTIPLEX_DOSAGE_NM3D / 2]);
mwptr = (__m128d*)g_missing_wts;
do {
*dptr++ = _mm_mul_pd(*mwptr++, *dptr2++);
} while (dptr != dptr_buf_end);
dptr2 = (__m128d*)g_dosage_vals;
#else
dptr = dptr_buf;
dptr_start = &(g_dosage_vals[ulii * 4 * MULTIPLEX_DOSAGE_NM3D]);
dptr2 = &(dptr_start[MULTIPLEX_DOSAGE_NM3D]);
dptr3 = &(dptr_start[2 * MULTIPLEX_DOSAGE_NM3D]);
do {
*dptr++ = (*dptr2++) + 2 * (*dptr3++);
} while (dptr != dptr_buf_end1);
dptr3 = dptr_start;
do {
*dptr++ = (*dptr2++) + (*dptr3++);
} while (dptr != dptr_buf_end2);
dptr2 = dptr_start;
do {
*dptr++ = 2 * (*dptr2++) + (*dptr3++);
} while (dptr != dptr_buf_end3);
dptr2 = &(dptr_start[3 * MULTIPLEX_DOSAGE_NM3D]);
mwptr = g_missing_wts;
do {
*dptr++ = (*mwptr++) * (*dptr2++);
} while (dptr != dptr_buf_end);
dptr2 = g_dosage_vals;
#endif
for (uljj = 0; uljj < ulii; uljj++) {
dptr = dptr_buf;
#ifdef __LP64__
acc.vd = _mm_setzero_pd();
do {
acc.vd = _mm_add_pd(acc.vd, _mm_mul_pd(*dptr++, *dptr2++));
} while (dptr != dptr_buf_end3);
*distance_matrix_slice += acc.d8[0] + acc.d8[1];
acc.vd = _mm_setzero_pd();
do {
acc.vd = _mm_add_pd(acc.vd, _mm_mul_pd(*dptr++, *dptr2++));
} while (dptr != dptr_buf_end);
*distance_wt_matrix_slice += acc.d8[0] + acc.d8[1];
#else
acc = 0.0;
do {
acc += (*dptr++) * (*dptr2++);
} while (dptr != dptr_buf_end3);
*distance_matrix_slice += acc;
acc = 0.0;
do {
acc += (*dptr++) * (*dptr2++);
} while (dptr != dptr_buf_end);
*distance_wt_matrix_slice += acc;
#endif
distance_matrix_slice++;
distance_wt_matrix_slice++;
}
}