struct HTS::Bam::Pileup::Alignment

• HTS::Bam::Pileup::Alignment
• Struct
• Value
• Object

Overview

Thin value-type view over a single bam_pileup1_t entry. Small scalars (query_pos, indel, bitfields, base, base_qual) are copied at construction so they remain valid after the iterator moves on; record()/qname() reach back into the live htslib record and must be called during iteration. qname()/record() memoization is per captured Alignment value; repeated column[0].record calls construct fresh Alignment values and duplicate the record each time. Store alignment = column[0] when reusing them. A struct so that iterating a Column allocates no per-read heap object.

Defined in:

hts/bam/pileup.cr

Constructors

• .new(entry : Pointer(LibHTS::BamPileup1T), header : Bam::Header)

Instance Method Summary

• #base : Char | Nil
• #base_qual : UInt8 | Nil
• #bitfields : UInt32
• #del? : Bool

  Bitfield helpers

• #head? : Bool
• #indel : Int32
• #qname : String

  Query name for the underlying read without duplicating the full record.

• #query_pos : Int32
• #record : Bam::Record

  Lazily duplicates the underlying bam1_t.

• #refskip? : Bool
• #tail? : Bool

Constructor Detail

Instance Method Detail