class HTS::Tabix

Defined in:

hts/tabix.cr
hts/tabix/errors.cr

Constructors

Class Method Summary

Instance Method Summary

Instance methods inherited from class HTS::Bgzf

<<(data) : self <<, bgzf? : Bool bgzf?, compression_level : Int32 compression_level, each_char(&) each_char, each_line(delimiter = '\n', &) each_line, each_line_view(delimiter = '\n', & : Bytes -> ) : self each_line_view, file_name : Path | String file_name, finalize finalize, flush : Int32 flush, getc : Char | Nil getc, gets(delimiter = '\n') : String | Nil gets, is_bgzf? : Bool is_bgzf?, mode : String mode, print(data : String) : Nil
print(data : Bytes) : Nil
print(data) : Nil
print(*objects) : Nil print, puts(data : String) : Int64
puts : Int64
puts(*objects) : Nil puts, read(size : Int32) : Bytes read, seek(offset) seek, tell tell, write(data : String) : Int64
write(data : Bytes) : Int64 write

Constructor methods inherited from class HTS::Bgzf

new(file_name : Path | String, mode = "r", threads = 0) new

Class methods inherited from class HTS::Bgzf

open(file_name : Path | String, mode = "r", threads = 0)
open(file_name : Path | String, mode = "r", threads = 0, &) open

Instance methods inherited from class HTS::Hts

close close, closed? closed?, file_format file_format, file_format_version file_format_version, rewind rewind, seek(offset) seek, set_threads(n) set_threads, tell tell, threads=(n) threads=, to_unsafe to_unsafe

Macros inherited from class HTS::Hts

define_getter(name) define_getter, define_iterator(name) define_iterator

Constructor Detail

def self.new(file_name : Path | String, mode = "r", index : String = "", threads = 0, build_index = false, preset = :vcf) #

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Class Method Detail

def self.build_index(file_name : Path | String, index_name = "", min_shift = 0, threads = 0, verbose = true, preset = :vcf) #

Build a tabix index for file_name on disk. Uses the VCF preset by default.

Supported presets are :vcf, :bed, :gff, :sam, and :psltbl.


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def self.open(file_name : Path | String, mode = "r", index = "", threads = 0, build_index = false, preset = :vcf) #

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def self.open(file_name : Path | String, mode = "r", index = "", threads = 0, build_index = false, preset = :vcf, &) #

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Instance Method Detail

def build_index(index_name = "", min_shift = 0, verbose = true, preset = :vcf) #

Build a tabix index for this file. Delegates to the class method.


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def close #

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def each_fields(region : String, & : Array(String) -> ) : self #

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def each_line(region : String, & : String -> ) : self #

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def each_line_view(region : String, & : Bytes -> ) : self #

The borrowed line is valid only during the block.

EXPERIMENTAL


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def each_selected_fields(region : String, *field_indices, & : Array(Bytes) -> ) : self #

The values and their backing array are reused after each block call.

EXPERIMENTAL


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def file_name : Path | String #

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def finalize #

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def index_loaded? #

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def load_index(index_name = @index_name) #

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def mode : String #

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def name2id(name : String) : Int32 #

Return the sequence (chromosome) ID for name, or -1 if not found.


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def query(chrom : String, start : Int, end_ : Int, &) #

Query by chromosome name and 0-based half-open coordinates [start, end_). Yields each matching record as an Array(String) of tab-split fields.


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def query(region : String, &) #

Query by region string using htslib's native parser. Yields each matching record as an Array(String) of tab-split fields.


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def seqnames : Array(String) #

Return the list of sequence names stored in the index.


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