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A library for working with phylogenetic and population genetic data.
v0.32.0
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Go to the documentation of this file. 1 #ifndef GENESIS_POPULATION_FILTER_VARIANT_FILTER_H_
2 #define GENESIS_POPULATION_FILTER_VARIANT_FILTER_H_
45 namespace population {
405 #endif // include guard
@ kAboveSnpMaxCount
Sum of nucleotides is above VariantFilterNumericalParams::snp_max_count.
@ kMaskedPosition
Position has been masked out from processing.
@ kNumeric
Any of the numeric variant filters failed.
@ kBelowMinAlleleFreq
Did not reach minimum allele frequency.
@ kSamplesFailed
Either all or some of the samples failed their respetive filters.
@ kInvalid
Generic indicator that the Variant is invalid.
@ kNotPassed
Generic indicator that the Variant has not passed a filter.
VariantFilterTagCategory
List of filter categories for a Variant.
@ kNotBiallelicSnp
SNP position, but not biallelic, i.e., has more than one alternative.
VariantFilterCategoryStats variant_filter_stats_category_counts(VariantFilterStats const &stats)
Generate summary counts for a VariantFilterStats counter.
@ kInvariant
Postion is not a SNP according to the SNP filters.
@ kMaskedRegion
Position is part of a masked region.
@ kEmpty
All counts across all samples are zero.
@ kMissingInvalid
Position is missing or otherwise invalid.
@ kPassed
Variant has passed all filters.
@ kNotSnp
Invariant position, not a SNP.
@ kEnd
End of the enum values.
Container namespace for all symbols of genesis in order to keep them separate when used as a library.
@ kBelowMinReadDepth
Sum of counts across all samples is below the min read depth threshold.
@ kAboveDeletionsCountLimit
Too many deletions at the position.
@ kNoSamplePassed
None of the SampleCounts of the Variant passed their filters.
VariantFilterTag
List of filters that we apply to a Variant, to indicate whether the Variant passed or not.
@ kMissing
Position is missing in the input data.
@ kEnd
End of the enum values.
@ kMasked
Position is masked.
std::ostream & print_variant_filter_category_stats(std::ostream &os, VariantFilterCategoryStats const &stats, bool verbose)
@ kNotAllSamplesPassed
Some of the SampleCounts of the Variant did not pass their filters.
std::ostream & print_variant_filter_stats(std::ostream &os, VariantFilterStats const &stats, bool verbose)
Print a textual representation of the counts collected.
Counts of how many entries with a particular Filter Tag occured in some data.
VariantFilterTagCategory variant_filter_tag_to_category(VariantFilterTag tag)
For a given tag, return its category tag.
@ kBelowSnpMinCount
Sum of nucleotides is below VariantFilterNumericalParams::snp_min_count.
@ kAboveMaxReadDepth
Sum of counts across all samples is above the max read depth threshold.
@ kPassed
Variant has passed all filters.