class HTS::Bam::Pileup

• HTS::Bam::Pileup
• Reference
• Object

Overview

High-level pileup iterator over a single BAM/CRAM input. Yields a zero-copy Column view (tid, pos, and per-read Alignment access) at each position. Iterating a Column allocates nothing per read; see Column's borrowing contract for the validity rules.

Defined in:

hts/bam/pileup.cr

Constructors

• .new(bam : Bam, region : String | Nil = nil, maxcnt : Int32 | Nil = nil, *, filter : Filter = Filter.new)

  Create a Pileup iterator @param bam [HTS::Bam] @param region [String, nil] Optional region string (e.g., "chr1:1000-2000", requires index) @param maxcnt [Int32, nil] Max per-position depth (capped) @param filter [Filter] Read-level filter applied before pileup (see Filter)

Class Method Summary

• .open(bam : Bam, region : String | Nil = nil, maxcnt : Int32 | Nil = nil, *, filter : Filter = Filter.new, &)

  Open a Pileup iterator with block (RAII style)

• .open(bam : Bam, *, region : String | Nil = nil, maxcnt : Int32 | Nil = nil, filter : Filter = Filter.new, &)

  Open a Pileup iterator using keyword arguments, matching Mpileup.

Instance Method Summary

• #close : Nil

  Release native resources

• #count : Int32

  Count pileup columns by consuming this iterator.

• #count(& : Column -> Bool) : Int32

  Count pileup columns matching the block by consuming this iterator.

• #each(& : Column -> ) : Nil

  Iterate over pileup columns.

• #finalize
• #reset : Nil

  Reset internal state, if needed by the caller

Constructor Detail

Class Method Detail

Instance Method Detail