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Inspect native minibwa alignment batches

Source: R/native.R
mb_align_n.Rd

mb_align_col() returns ALTREP views over native alignment columns. These views do not copy columns unless R forces materialization. mb_align_read_col() returns ALTREP views over the read-level sidecar with one row per input read, including reads without hits. C consumers should prefer the installed Rminibwa.h API.

Usage

mb_align_n(x)

mb_align_read_n(x)

mb_align_col(x, name)

mb_align_read_col(x, name)

mb_align_cigar_words(x)

Arguments

x

Native alignment batch returned by mb_map() or mb_map_batch().

name

Column name. Alignment columns include read_id, tid, qlen, qs, qe, tlen, ts, te, strand, mapq, score, matches, blen, flags, n_sub, cigar_offset, and cigar_n. Read-sidecar columns include read_id, length, fragment_id, mate, hit_offset, and hit_count.

Value

mb_align_n() returns the number of alignment records. mb_align_read_n() returns the number of input reads represented in the batch. mb_align_col() and mb_align_read_col() return ALTREP integer or real vectors. mb_align_cigar_words() returns a raw debug copy of packed minibwa CIGAR words.