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A library for working with phylogenetic and population genetic data.
v0.27.0
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Go to the documentation of this file. 1 #ifndef GENESIS_POPULATION_FORMATS_SAM_VARIANT_INPUT_ITERATOR_H_
2 #define GENESIS_POPULATION_FORMATS_SAM_VARIANT_INPUT_ITERATOR_H_
46 #include <unordered_map>
47 #include <unordered_set>
68 namespace population {
141 struct SamFileHandle;
194 return ¤t_variant_;
199 return ¤t_variant_;
204 return current_variant_;
209 return current_variant_;
238 return parent_ == it.parent_;
243 return !(*
this == it);
282 std::vector<std::string>
rg_tags(
bool all_header_tags =
false )
const;
308 void process_base_( bam_pileup1_t
const* p );
317 size_t get_sample_index_( bam_pileup1_t
const* p )
const;
328 std::shared_ptr<SamFileHandle> handle_;
380 throw std::runtime_error(
"Input sam/bam/cram file not found: " + input_file_ );
418 return flags_include_all_;
441 flags_include_all_ = value;
447 return flags_include_any_;
470 flags_include_any_ = value;
476 return flags_exclude_all_;
500 flags_exclude_all_ = value;
506 return flags_exclude_any_;
529 flags_exclude_any_ = value;
539 return min_map_qual_;
551 min_map_qual_ = value;
557 return min_base_qual_;
568 min_base_qual_ = value;
611 return max_acc_depth_;
626 max_acc_depth_ = value;
649 split_by_rg_ = value;
655 return with_unaccounted_rg_;
673 with_unaccounted_rg_ = value;
679 return rg_tag_filter_;
701 rg_tag_filter_ = value;
707 return inverse_rg_tag_filter_;
717 inverse_rg_tag_filter_ = value;
739 std::string input_file_;
744 uint32_t flags_include_all_ = 0;
745 uint32_t flags_include_any_ = 0;
746 uint32_t flags_exclude_all_ = 0;
747 uint32_t flags_exclude_any_ = 0;
750 int min_map_qual_ = 0;
751 int min_base_qual_ = 0;
756 int max_acc_depth_ = 0;
758 bool split_by_rg_ =
false;
759 bool with_unaccounted_rg_ =
false;
760 std::unordered_set<std::string> rg_tag_filter_;
761 bool inverse_rg_tag_filter_ =
false;
773 #endif // htslib guard
774 #endif // include guard
Provides functions for accessing the file system.
A single variant at a position in a chromosome, along with BaseCounts for a set of samples.
Container namespace for all symbols of genesis in order to keep them separate when used as a library.
bool is_file(std::string const &path)
Return true iff the provided path is a file.