htslib.vcfutils

@file htslib/vcfutils.h Allele-related utility functions.

Members

Functions

bcf_acgt2int int bcf_acgt2int(char c): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_calc_ac int bcf_calc_ac(const(bcf_hdr_t)* header, bcf1_t* line, int* ac, int which): bcf_calc_ac() - calculate the number of REF and ALT alleles @header: for access to BCF_DT_ID dictionary @line: VCF line obtained from vcf_parse1 @ac: array of length line->n_allele @which: determine if INFO/AN,AC and indv fields be used
bcf_gt_type int bcf_gt_type(bcf_fmt_t* fmt_ptr, int isample, int* ial, int* jal): Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
bcf_ij2G auto bcf_ij2G(T0 i, T1 j): bcf_ij2G() - common task: allele indexes to Number=G index (diploid) @i,j: allele indexes, 0-based, i<=j
bcf_int2acgt auto bcf_int2acgt(T i): Undocumented in source. Be warned that the author may not have intended to support it.
bcf_remove_allele_set int bcf_remove_allele_set(const(bcf_hdr_t)* header, bcf1_t* line, const(kbitset_t)* rm_set): bcf_remove_allele_set() - remove ALT alleles according to bitset @rm_set @header: for access to BCF_DT_ID dictionary @line: VCF line obtained from vcf_parse1 @rm_set: pointer to kbitset_t object with bits set for allele indexes to remove
bcf_remove_alleles int bcf_remove_alleles(const(bcf_hdr_t)* header, bcf1_t* line, int mask): bcf_remove_alleles() - remove ALT alleles according to bitmask @mask @header: for access to BCF_DT_ID dictionary @line: VCF line obtained from vcf_parse1 @mask: alleles to remove
bcf_trim_alleles int bcf_trim_alleles(const(bcf_hdr_t)* header, bcf1_t* line): bcf_trim_alleles() - remove ALT alleles unused in genotype fields @header: for access to BCF_DT_ID dictionary @line: VCF line obtain from vcf_parse1

Manifest constants

GT_HAPL_A enum GT_HAPL_A;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
GT_HAPL_R enum GT_HAPL_R;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
GT_HET_AA enum GT_HET_AA;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
GT_HET_RA enum GT_HET_RA;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
GT_HOM_AA enum GT_HOM_AA;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.
GT_HOM_RR enum GT_HOM_RR;: bcf_gt_type() - determines type of the genotype @fmt_ptr: the GT format field as set for example by set_fmt_ptr @isample: sample index (starting from 0) @ial: index of the 1st non-reference allele (starting from 1) @jal: index of the 2nd non-reference allele (starting from 1)
GT_UNKN enum GT_UNKN;: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

Structs

kbitset_t struct kbitset_t: Undocumented in source but is binding to C. You might be able to learn more by searching the web for its name.

htslib.vcfutils

Members

Functions

Manifest constants

Structs

Meta

Source