struct HTS::Bam::Pileup::Column

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

Overview

A pileup column at a genomic position, as a zero-copy view over htslib's current pileup buffer. It holds only pointers and constructs Alignment values lazily, so iterating (#each / #[]) allocates nothing per read and matches the C mpileup hot-path cost.

BORROWING CONTRACT: a Column and any Alignment obtained from it are valid ONLY during the current iteration step (the current block invocation). To retain data across positions, read the copied-out scalars (Alignment#base, #base_qual, #query_pos) or call Alignment#record. Do not deref a Column after the iterator advances or the Pileup is closed.

This borrowed view intentionally does not include Enumerable: methods such as to_a or map would make short-lived C-backed entries look like ordinary retained Crystal values.

Defined in:

hts/bam/pileup.cr

Constructors

• .new(tid : Int32, pos : Int64, base : Pointer(LibHTS::BamPileup1T), count : Int32, header : Bam::Header)

Instance Method Summary

• #[](index : Int32) : Alignment
• #chrom : String

  Reference (chromosome) name for this position Returns empty string if tid is -1 (unmapped)

• #count : Int32

  Number of reads covering this position.

• #count(& : Alignment -> Bool) : Int32

  Count reads matching the block without materializing an Array.

• #depth : Int32

  Depth equals number of alignments covering this position

• #each(& : Alignment -> ) : Nil

  Iterate the reads covering this position without allocating an Array.

• #pos : Int64
• #tid : Int32

Constructor Detail

Instance Method Detail