Utility class to manipulate a Variant record.
More...
#include <variant.h>
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| | Variant ()=default |
| | initializes a null Variant More...
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| | Variant (const std::shared_ptr< bcf_hdr_t > &header, const std::shared_ptr< bcf1_t > &body) noexcept |
| | creates a Variant given htslib objects. More...
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| | Variant (const Variant &other) |
| | makes a deep copy of a Variant and it's header. Shared pointers maintain state to all other associated objects correctly. More...
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| | Variant (Variant &&other) noexcept |
| | moves Variant and it's header accordingly. Shared pointers maintain state to all other associated objects correctly. More...
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| Variant & | operator= (const Variant &other) |
| | deep copy assignment of a Variant and it's header. Shared pointers maintain state to all other associated objects correctly. More...
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| Variant & | operator= (Variant &&other) noexcept |
| | move assignment of a Variant and it's header. Shared pointers maintain state to all other associated objects correctly. More...
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| VariantHeader | header () const |
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| uint32_t | chromosome () const |
| | returns the integer representation of the chromosome. Notice that chromosomes are listed in index order with regards to the header (so a 0-based number). Similar to Picards getReferenceIndex() More...
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| uint32_t | alignment_start () const |
| | returns a 1-based alignment start position (as you would see in a VCF file). More...
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| uint32_t | qual () const |
| | returns the Phred scaled site qual (probability that the site is not reference). See VCF spec. More...
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| uint32_t | n_samples () const |
| | returns the number of samples in this Variant record More...
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| uint32_t | n_alleles () const |
| | returns the number of alleles in this Variant record More...
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| std::vector< uint8_t > | genotype_quals () const |
| | returns a vector with a copy of all the GQ values for all samples contiguously in memory. More...
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Utility class to manipulate a Variant record.
| gamgee::Variant::Variant |
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default |
initializes a null Variant
- Note
- this is only used internally by the iterators
- Warning
- if you need to create a Variant from scratch, use the builder instead
| gamgee::Variant::Variant |
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const std::shared_ptr< bcf_hdr_t > & |
header, |
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const std::shared_ptr< bcf1_t > & |
body |
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) |
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explicitnoexcept |
creates a Variant given htslib objects.
creates a variant record that points to htslib memory already allocated
- Note
- used by all iterators
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the resulting Variant shares ownership of the pre-allocated memory via shared_ptr reference counting
| gamgee::Variant::Variant |
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const Variant & |
other | ) |
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makes a deep copy of a Variant and it's header. Shared pointers maintain state to all other associated objects correctly.
creates a deep copy of a variant record and header
| gamgee::Variant::Variant |
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Variant && |
other | ) |
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noexcept |
moves Variant and it's header accordingly. Shared pointers maintain state to all other associated objects correctly.
moves a variant record and header, transferring ownership of the underlying htslib memory
| uint32_t gamgee::Variant::alignment_start |
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const |
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inline |
returns a 1-based alignment start position (as you would see in a VCF file).
- Note
- the internal encoding is 0-based to mimic that of the BCF files.
| uint32_t gamgee::Variant::chromosome |
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const |
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inline |
returns the integer representation of the chromosome. Notice that chromosomes are listed in index order with regards to the header (so a 0-based number). Similar to Picards getReferenceIndex()
| vector< uint8_t > gamgee::Variant::genotype_quals |
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const |
returns a vector with a copy of all the GQ values for all samples contiguously in memory.
< if the format is missing or the GQ tag is missing, return an empty vector
| uint32_t gamgee::Variant::n_alleles |
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const |
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inline |
returns the number of alleles in this Variant record
| uint32_t gamgee::Variant::n_samples |
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const |
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inline |
returns the number of samples in this Variant record
deep copy assignment of a Variant and it's header. Shared pointers maintain state to all other associated objects correctly.
creates a deep copy of a variant record
- Parameters
-
- Note
- the parameter is passed by copy so we can maintain the strong exception safety guarantee
< shared_ptr assignment will take care of deallocating old record if necessary
< shared_ptr assignment will take care of deallocating old record if necessary
move assignment of a Variant and it's header. Shared pointers maintain state to all other associated objects correctly.
moves a variant record, transferring ownership of the underlying htslib memory
| uint32_t gamgee::Variant::qual |
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const |
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inline |
returns the Phred scaled site qual (probability that the site is not reference). See VCF spec.
The documentation for this class was generated from the following files:
1.8.7
