class

Minimap2::BSeqFile

Inherits Reference < Object

FASTA/FASTQ file reader — pure Crystal replacement for bseq.c / kseq.h. Supports plain text and gzip-compressed files (via Crystal's Compress::Gzip).

Constants

CHECK_PAIR_THRES = 1000000

Constructors

new(io : IO)

Source

open(fn : String) : BSeqFile

Source

Instance methods

Source

eof?

Source

read_seqs(chunk_size : Int64, with_qual : Bool = false, with_comment : Bool = false, frag_mode : Bool = false) : Array(BSeq1)

Read a mini-batch of sequences up to chunk_size total bases. Returns an empty array at EOF. with_qual — keep quality string (FASTQ only) with_comment — keep FASTQ/FASTA comment field frag_mode — keep paired reads together even if chunk overflows

Source