Utility class to enable for-each style iteration in the VariantReader class.
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#include <variant_iterator.h>
Utility class to enable for-each style iteration in the VariantReader class.
| gamgee::VariantIterator::VariantIterator |
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default |
creates an empty iterator (used for the end() method)
| gamgee::VariantIterator::VariantIterator |
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const std::shared_ptr< htsFile > & |
variant_file_ptr, |
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const std::shared_ptr< bcf_hdr_t > & |
variant_header_ptr |
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initializes a new iterator based on an input stream (e.g. a vcf/bcf file, stdin, ...)
- Parameters
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| variant_file_ptr | shared pointer to a vcf/bcf file opened via the bcf_open() macro from htslib |
| variant_header_ptr | shared pointer to a vcf/bcf file header created with the bcf_hdr_read() macro from htslib |
a VariantIterator move constructor guarantees all objects will have the same state.
| bool gamgee::VariantIterator::empty |
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const |
returns whether the iterator has no additional records
- Returns
- true if the the iterator has no additional records
| void gamgee::VariantIterator::fetch_next_record |
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protectedvirtual |
fetches next Variant record into existing htslib memory without making a copy
pre-fetches the next variant record
- Warning
- we're reusing the existing htslib memory, so users should be aware that all objects from the previous iteration are now stale unless a deep copy has been performed
Reimplemented in gamgee::IndexedVariantIterator.
| bool gamgee::VariantIterator::operator!= |
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const VariantIterator & |
rhs | ) |
const |
inequality operator (needed by for-each loop)
- Parameters
-
- Returns
- whether or not the two iterators are the same (e.g. have the same input stream on the same status)
| Variant & gamgee::VariantIterator::operator* |
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dereference operator (needed by for-each loop)
- Returns
- a persistent Variant object independent from the iterator (a copy of the iterator's object)
| Variant & gamgee::VariantIterator::operator++ |
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pre-fetches the next record and tests for end of file
- Returns
- a reference to the object (it can be const& because this return value should only be used by the for-each loop to check for the eof)
a VariantIterator move assignment operator guarantees all objects will have the same state.
| std::shared_ptr<htsFile> gamgee::VariantIterator::m_variant_file_ptr |
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protected |
pointer to the vcf/bcf file
| std::shared_ptr<bcf_hdr_t> gamgee::VariantIterator::m_variant_header_ptr |
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protected |
pointer to the variant header
| Variant gamgee::VariantIterator::m_variant_record |
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protected |
temporary record to hold between fetch (operator++) and serve (operator*)
| std::shared_ptr<bcf1_t> gamgee::VariantIterator::m_variant_record_ptr |
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protected |
pointer to the internal structure of the variant record. Useful to only allocate it once.
The documentation for this class was generated from the following files:
1.8.8