class
HTS::Bam::Mpileup
- HTS::Bam::Mpileup
- Reference
- Object
Overview
High-level mpileup iterator over multiple BAM/CRAM inputs. Yields an Array of Pileup::Column (one per input) for each position.
Included Modules
- Enumerable(Array(HTS::Bam::Pileup::Column))
Defined in:
hts/bam/mpileup.crConstructors
-
.new(inputs : Array(Bam), maxcnt : Int32 | Nil = nil, overlaps : Bool = false, *, region : String | Nil = nil, regions : Array(String) | Nil = nil)
Accept Array(Bam).
Class Method Summary
-
.open(inputs : Array(Bam), maxcnt : Int32 | Nil = nil, overlaps : Bool = false, *, region : String | Nil = nil, regions : Array(String) | Nil = nil, &)
Open an Mpileup iterator with block (RAII style)
-
.open(inputs : Array(Bam), *, maxcnt : Int32 | Nil = nil, overlaps : Bool = false, region : String | Nil = nil, regions : Array(String) | Nil = nil, &)
Open an Mpileup iterator using keyword arguments.
Instance Method Summary
- #close : Nil
-
#each(&block : Array(HTS::Bam::Pileup::Column) -> ) : Nil
Iterate and yield per-position columns array (aligned by tid,pos across inputs)
- #finalize
Constructor Detail
def self.new(inputs : Array(Bam), maxcnt : Int32 | Nil = nil, overlaps : Bool = false, *, region : String | Nil = nil, regions : Array(String) | Nil = nil)
#
Accept Array(Bam). If region is set, it uses SAM-style 1-based inclusive coordinates and each input must already have an index loaded. If regions is set, htslib's multi-region iterator is used and overlapping records are returned once.
Class Method Detail
def self.open(inputs : Array(Bam), maxcnt : Int32 | Nil = nil, overlaps : Bool = false, *, region : String | Nil = nil, regions : Array(String) | Nil = nil, &)
#
Open an Mpileup iterator with block (RAII style)
def self.open(inputs : Array(Bam), *, maxcnt : Int32 | Nil = nil, overlaps : Bool = false, region : String | Nil = nil, regions : Array(String) | Nil = nil, &)
#
Open an Mpileup iterator using keyword arguments.
Instance Method Detail
def each(&block : Array(HTS::Bam::Pileup::Column) -> ) : Nil
#
Iterate and yield per-position columns array (aligned by tid,pos across inputs)