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. Columns contain the same Pileup::Alignment objects as single-input pileup; use Alignment#base, #base_qual, and #qname in hot paths before falling back to Alignment#record.

Included Modules

• Enumerable(Array(HTS::Bam::Pileup::Column))

Defined in:

hts/bam/mpileup.cr

Constructors

• .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(& : Array(HTS::Bam::Pileup::Column) -> ) : Nil

  Iterate and yield per-position columns array (aligned by tid,pos across inputs)

• #finalize

Constructor Detail

Class Method Detail

Instance Method Detail