bcf_hdr_set_samples() - for more efficient VCF parsing when only one/few samples are needed
@samples: samples to include or exclude from file or as a comma-separated string.
LIST|FILE .. select samples in list/file
^LIST|FILE .. exclude samples from list/file
- .. include all samples
NULL .. exclude all samples
@is_file: @samples is a file (1) or a comma-separated list (0)
The bottleneck of VCF reading is parsing of genotype fields. If the
reader knows in advance that only subset of samples is needed (possibly
no samples at all), the performance of bcf_read() can be significantly
improved by calling bcf_hdr_set_samples after bcf_hdr_read().
The function bcf_read() will subset the VCF/BCF records automatically
with the notable exception when reading records via bcf_itr_next().
In this case, bcf_subset_format() must be called explicitly, because
bcf_readrec() does not see the header.
Returns 0 on success, -1 on error or a positive integer if the list
contains samples not present in the VCF header. In such a case, the
return value is the index of the offending sample.
bcf_hdr_set_samples() - for more efficient VCF parsing when only one/few samples are needed @samples: samples to include or exclude from file or as a comma-separated string. LIST|FILE .. select samples in list/file ^LIST|FILE .. exclude samples from list/file - .. include all samples NULL .. exclude all samples @is_file: @samples is a file (1) or a comma-separated list (0)
The bottleneck of VCF reading is parsing of genotype fields. If the reader knows in advance that only subset of samples is needed (possibly no samples at all), the performance of bcf_read() can be significantly improved by calling bcf_hdr_set_samples after bcf_hdr_read(). The function bcf_read() will subset the VCF/BCF records automatically with the notable exception when reading records via bcf_itr_next(). In this case, bcf_subset_format() must be called explicitly, because bcf_readrec() does not see the header.
Returns 0 on success, -1 on error or a positive integer if the list contains samples not present in the VCF header. In such a case, the return value is the index of the offending sample.