class HTS::Bam
Included Modules
- Enumerable(HTS::Bam::Record)
Defined in:
hts/bam.crhts/bam/cigar.cr
hts/bam/flag.cr
hts/bam/header.cr
hts/bam/record.cr
Constructors
Class Method Summary
- .open(file_name : Path | String, mode = "r", index = "", fai = "", threads = 0, build_index = false)
- .open(file_name : Path | String, mode = "r", index = "", fai = "", threads = 0, build_index = false, &)
Instance Method Summary
- #<<(record)
- #build_index(index_name, min_shift = 0)
- #chrom
- #cigar
- #close
-
#each(copy = false, &)
Must yield this collection's elements to the block.
- #each_chrom(&)
- #each_cigar(&)
- #each_flag(&)
- #each_insert_size(&)
- #each_mapq(&)
- #each_mate_chrom(&)
- #each_mate_pos(&)
- #each_pos(&)
- #each_qname(&)
- #each_qual(&)
- #each_seq(&)
- #fai=(fai)
- #file_name : String
- #finalize
- #flag
- #header : HTS::Bam::Header
- #header=(header)
- #index_loaded?
- #insert_size
- #isize
- #load_index(index_name = "")
- #mapq
- #mate_chrom
- #mate_pos
- #mode : String
- #mpos
- #nthreads : Int32
- #pos
- #qname
- #qual
- #query(region, &)
- #seq
- #write(record)
- #write_header(header)
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,
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 : String = "r", index = "", fai = "", threads : Int32 = 0, build_index = false)
#
Class Method Detail
def self.open(file_name : Path | String, mode = "r", index = "", fai = "", threads = 0, build_index = false)
#
def self.open(file_name : Path | String, mode = "r", index = "", fai = "", threads = 0, build_index = false, &)
#
Instance Method Detail
def each(copy = false, &)
#
Description copied from module Enumerable(HTS::Bam::Record)
Must yield this collection's elements to the block.