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Searched refs:max_allele_slen (Results 1 – 21 of 21) sorted by relevance

/dports/biology/plink/plink-ng-79b2df8c/2.0/
H A Dplink2_data.h63 …t1_select), const double* variant_cms, uint32_t variant_ct, uint32_t max_allele_slen, char delim, …
73 …onst uint32_t* new_variant_idx_to_old, uint32_t chr_fo_idx, uint32_t max_allele_slen, UnsortedVar …
95 …aw_variant_ct, uint32_t variant_ct, uint32_t max_allele_ct, uint32_t max_allele_slen, uint32_t max…
97 …aw_variant_ct, uint32_t variant_ct, uint32_t max_allele_ct, uint32_t max_allele_slen, uint32_t max…
H A Dplink2_pvar.cc417 …2_t VaridWorstCaseSlen(const VaridTemplate* vtp, uint32_t max_chr_slen, uint32_t max_allele_slen) { in VaridWorstCaseSlen() argument
419 return (max_allele_slen * vtp->alleles_needed + vtp->base_len + max_chr_slen + 10); in VaridWorstCaseSlen()
809 uint32_t max_allele_slen = 1; in LoadPvar() local
1655 if (ref_slen > max_allele_slen) { in LoadPvar()
1656 max_allele_slen = ref_slen; in LoadPvar()
1683 if (cur_allele_slen > max_allele_slen) { in LoadPvar()
1684 max_allele_slen = cur_allele_slen; in LoadPvar()
1705 if (remaining_alt_char_ct > max_allele_slen) { in LoadPvar()
1706 max_allele_slen = remaining_alt_char_ct; in LoadPvar()
1798 … uint32_t worst_case_id_slen = VaridWorstCaseSlen(varid_templatep, max_chr_slen, max_allele_slen); in LoadPvar()
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H A Dplink2_fasta.h35 …st ChrInfo* cip, const char* fname, uint32_t max_allele_ct, uint32_t max_allele_slen, FaFlags flag…
H A Dplink2_misc.h327 …* alt1_binstr, uint32_t variant_ct, uint32_t max_allele_ct, uint32_t max_allele_slen, FreqRptFlags…
329 …t, uint32_t male_ct, uint32_t variant_ct, uint32_t x_start, uint32_t max_allele_slen, GenoCountsFl…
331 …no_ct, uintptr_t max_pheno_name_blen, uint32_t variant_ct, uintptr_t max_allele_slen, uint32_t fir…
337 …ouble* hwe_x_pvals, uint32_t variant_ct, uint32_t hwe_x_ct, uint32_t max_allele_slen, double outpu…
H A Dplink2_matrix_calc.h184 …aw_variant_ct, uint32_t variant_ct, uint32_t max_allele_ct, uint32_t max_allele_slen, uint32_t pc_…
189 …2_t variant_ct, uint32_t raw_sample_ct, uint32_t sample_ct, uint32_t max_allele_slen, VscoreFlags …
H A Dplink2_adjust.h78 …* ln_pvals, const double* chisqs, uintptr_t orig_allele_ct, uint32_t max_allele_slen, double ln_pf…
H A Dplink2_export.h59 …iant_ct, uint32_t variant_ct, uint32_t max_variant_id_slen, uint32_t max_allele_slen, uint32_t max…
H A Dplink2_glm.h122 …ct, uint32_t orig_variant_ct, uint32_t max_variant_id_slen, uint32_t max_allele_slen, uint32_t xch…
H A Dplink2_adjust.cc83 …* ln_pvals, const double* chisqs, uintptr_t orig_allele_ct, uint32_t max_allele_slen, double ln_pf… in Multcomp() argument
204 …st uintptr_t overflow_buf_size = kCompressStreamBlock + 2 * kMaxIdSlen + 512 + 2 * max_allele_slen; in Multcomp()
785 uint32_t max_allele_slen = 1; in AdjustFile() local
879 …NSTCPCONSTP(a1_storage), &(afip->base), ln_pvals, nullptr, entry_ct, max_allele_slen, ln_pfilter, … in AdjustFile()
H A Dplink2_data.cc48 … const uintptr_t overflow_buf_size = kCompressStreamBlock + kMaxIdSlen + 512 + 2 * max_allele_slen;
80 if (max_allele_slen) {
300 if (max_allele_slen == 1) { in ChrLenLbound()
307 if (cur_bp + max_allele_slen <= bp_end) { in ChrLenLbound()
322 if (max_allele_slen == 1) { in ChrLenLbound()
330 if (cur_bp + max_allele_slen <= bp_end) { in ChrLenLbound()
345 if (max_allele_slen == 1) { in ChrLenLbound()
349 if (bp_end >= max_allele_slen) { in ChrLenLbound()
350 min_check_bp = bp_end + 1 - max_allele_slen; in ChrLenLbound()
3279 … const uintptr_t overflow_buf_size = kCompressStreamBlock + kMaxIdSlen + 512 + 2 * max_allele_slen; in WriteBimSplit()
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H A Dplink2_export.cc48 const uint32_t max_allele_slen = *max_export_allele_slen_ptr; variable
49 uint32_t max_export_allele_slen = max_allele_slen;
117 if (allele_slen <= max_allele_slen) {
1302 writebuf_alloc = max_chr_blen + kMaxIdSlen + 32 + 2 * max_allele_slen;
3307 if (writebuf_len < max_allele_slen + 4) {
3308 writebuf_len = max_allele_slen + 4;
7892 if (max_allele_slen > 14) {
7894 if (max_allele_slen < 128) {
7896 } else if (max_allele_slen < 32768) {
9422 if (max_allele_slen > kMaxMediumLine - 5) {
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H A Dplink2_fasta.cc461 …st ChrInfo* cip, const char* fname, uint32_t max_allele_ct, uint32_t max_allele_slen, FaFlags flag…
511 seqbuf_size += max_allele_slen + 1;
600 seqbuf_end = &(seqbuf[variant_bps[cur_vidx_last] + max_allele_slen]);
H A Dplink2_filter.h85 …t_ct, uint32_t max_allele_ct, uint32_t max_variant_id_slen, uint32_t max_allele_slen, uint32_t maf…
H A Dplink2.cc847 uint32_t max_allele_slen = 0; in Plink2Core() local
1257 …variant_id_htable_size, pcp->max_thread_ct, allele_storage_mutable, &max_allele_slen, outname, out… in Plink2Core()
1921 …ame, raw_variant_ct, variant_ct, max_allele_ct, max_variant_id_slen, max_allele_slen, (pcp->misc_f… in Plink2Core()
1975 …->freq_ref_binstr, pcp->freq_alt1_binstr, variant_ct, max_allele_ct, max_allele_slen, pcp->freq_rp… in Plink2Core()
1984 …le_geno_cts, raw_sample_ct, sample_ct, male_ct, variant_ct, x_start, max_allele_slen, pcp->geno_co… in Plink2Core()
2303 …raw_sample_ct, sample_ct, raw_variant_ct, variant_ct, max_allele_ct, max_allele_slen, pcp->pca_ct,… in Plink2Core()
2331 uint32_t max_allele_slen_backup = max_allele_slen; in Plink2Core()
2398 …gs / kfMiscRefAlleleForce) & 1, pcp->max_thread_ct, allele_storage, &max_allele_slen, refalt1_sele… in Plink2Core()
2404 …s / kfMiscAlt1AlleleForce) & 1, pcp->max_thread_ct, allele_storage, &max_allele_slen, refalt1_sele… in Plink2Core()
2419 … variant_ids, allele_idx_offsets, cip, pcp->fa_fname, max_allele_ct, max_allele_slen, pcp->fa_flag… in Plink2Core()
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H A Dplink2_misc.cc401 uint32_t max_allele_slen = *max_allele_slen_ptr; in UpdateVarAlleles() local
577 *max_allele_slen_ptr = max_allele_slen; in UpdateVarAlleles()
3137 …* alt1_binstr, uint32_t variant_ct, uint32_t max_allele_ct, uint32_t max_allele_slen, FreqRptFlags… in WriteAlleleFreqs() argument
3153 …sStreamBlock + max_chr_blen + kMaxIdSlen + 512 + max_allele_ct * (24 * k1LU) + 2 * max_allele_slen; in WriteAlleleFreqs()
3554 …t, uint32_t male_ct, uint32_t variant_ct, uint32_t x_start, uint32_t max_allele_slen, GenoCountsFl…
3606 …Block + max_chr_blen + kMaxIdSlen + 512 + max_allele_ct * max_allele_ct * 20 + 2 * max_allele_slen;
4103 …no_ct, uintptr_t max_pheno_name_blen, uint32_t variant_ct, uintptr_t max_allele_slen, uint32_t fir… in WriteMissingnessReports() argument
4283 …t overflow_buf_size = kCompressStreamBlock + max_chr_blen + kMaxIdSlen + 512 + 2 * max_allele_slen; in WriteMissingnessReports()
4898 …ouble* hwe_x_pvals, uint32_t variant_ct, uint32_t hwe_x_ct, uint32_t max_allele_slen, double outpu…
4908 …ndUpPow2(kCompressStreamBlock + max_chr_blen + kMaxIdSlen + 512 + 2 * max_allele_slen, kCacheline);
H A Dplink2_matrix_calc.cc4946 …aw_variant_ct, uint32_t variant_ct, uint32_t max_allele_ct, uint32_t max_allele_slen, uint32_t pc_… in CalcPca() argument
5014 …= RoundUpPow2(kCompressStreamBlock + max_chr_blen + kMaxIdSlen + 2 * max_allele_slen + 32 + 16 * p… in CalcPca()
7259 …2_t variant_ct, uint32_t raw_sample_ct, uint32_t sample_ct, uint32_t max_allele_slen, VscoreFlags … in Vscore() argument
7604 …+ kMaxIdSlen + 128 + (24 * k1LU) * vscore_ct + MAXV(ref_col + alt1_col, alt_col) * max_allele_slen; in Vscore()
H A Dplink2_filter.cc2191 …t_ct, uint32_t max_allele_ct, uint32_t max_variant_id_slen, uint32_t max_allele_slen, uint32_t maf… in ReadAlleleFreqs() argument
2720 if (cur_loaded_allele_code_slen <= max_allele_slen) { in ReadAlleleFreqs()
H A Dplink2_import.cc2968 uint32_t max_allele_slen = 1; in VcfToPgen() local
3103 if (cur_max_allele_slen > max_allele_slen) { in VcfToPgen()
3104 max_allele_slen = cur_max_allele_slen; in VcfToPgen()
3309 …const uintptr_t overflow_buf_size = kCompressStreamBlock + MAXV(2 * max_allele_slen + max_qualfilt… in VcfToPgen()
H A Dplink2_glm.cc10653 …ct, uint32_t orig_variant_ct, uint32_t max_variant_id_slen, uint32_t max_allele_slen, uint32_t xch… in GlmMain() argument
10712 …e = kCompressStreamBlock + 2 * kMaxIdSlen + max_chr_blen + kMaxIdSlen + 1024 + 2 * max_allele_slen; in GlmMain()
12554 …, nullptr, adjust_info_ptr, orig_ln_pvals, nullptr, valid_allele_ct, max_allele_slen, ln_pfilter, … in GlmMain()
/dports/biology/plink/plink-ng-79b2df8c/1.9/
H A Dplink_common.h2325 void cleanup_allele_storage(uint32_t max_allele_slen, uintptr_t allele_storage_entry_ct, char** all…
H A Dplink_common.c4929 void cleanup_allele_storage(uint32_t max_allele_slen, uintptr_t allele_storage_entry_ct, char** all… in cleanup_allele_storage() argument
4930 if (allele_storage && (max_allele_slen > 1)) { in cleanup_allele_storage()