class HTS::Bam::Pileup::Alignment

Overview

Thin wrapper around a single bam_pileup1_t entry. Small fields are copied so they remain valid after the iterator moves on.

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

def self.new(entry : Pointer(LibHTS::BamPileup1T), header : Bam::Header) #

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Instance Method Detail

def base : Char | Nil #

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def base_qual : UInt8 | Nil #

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def bitfields : UInt32 #

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def del? : Bool #

Bitfield helpers

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def head? : Bool #

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def indel : Int32 #

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def qname : String #

Query name for the underlying read without duplicating the full record. Call this before the pileup iterator advances or closes.

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def query_pos : Int32 #

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def record : Bam::Record #

Lazily duplicates the underlying bam1_t. This is convenient but relatively expensive in pileup hot paths; prefer direct accessors such as #base, #base_qual, and #qname when possible. Call this before the pileup iterator advances or closes.

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def refskip? : Bool #

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def tail? : Bool #

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