Index

A

align() (pybwa.BwaAln method) (pybwa.BwaMem method)

AUTO (pybwa.BwaIndexBuildMethod attribute) AuxHit (class in pybwa)

B

band_width (pybwa.BwaMemOptions attribute) BwaAln (class in pybwa) BwaAlnOptions (class in pybwa)

BwaIndex (class in pybwa) BwaMem (class in pybwa) BwaMemOptions (class in pybwa) BWTSW (pybwa.BwaIndexBuildMethod attribute)

C

chunk_size (pybwa.BwaMemOptions attribute)

cigar (pybwa.AuxHit attribute) clipping_penalty (pybwa.BwaMemOptions attribute)

D

DEBUG (pybwa.BwaVerbosity attribute)

drop_chain_fraction (pybwa.BwaMemOptions attribute)

E

edits (pybwa.AuxHit attribute)

end (pybwa.AuxHit property) ERROR (pybwa.BwaVerbosity attribute)

F

finalize() (pybwa.BwaMemOptions method)

finalized (pybwa.BwaMemOptions attribute) find_all_hits (pybwa.BwaAlnOptions attribute)

G

gap_extension_penalty (pybwa.BwaAlnOptions attribute) (pybwa.BwaMemOptions attribute)

gap_open_penalty (pybwa.BwaAlnOptions attribute) (pybwa.BwaMemOptions attribute)

H

header (pybwa.BwaIndex attribute)

I

ignore_alternate_contigs (pybwa.BwaMemOptions attribute) index() (pybwa.BwaIndex class method) INFO (pybwa.BwaVerbosity attribute)

interleaved_paired_end (pybwa.BwaMemOptions attribute) internal_seed_split_factor (pybwa.BwaMemOptions attribute) INTRACTG (pybwa.BwaMemMode attribute) IS (pybwa.BwaIndexBuildMethod attribute)

K

keep_mapq_for_supplementary (pybwa.BwaMemOptions attribute)

L

log_scaled_gap_penalty (pybwa.BwaAlnOptions attribute)

M

match_score (pybwa.BwaMemOptions attribute) max_entries (pybwa.BwaAlnOptions attribute) max_gap_extensions (pybwa.BwaAlnOptions attribute) max_gap_opens (pybwa.BwaAlnOptions attribute) max_hits (pybwa.BwaAlnOptions attribute) max_mate_rescue_rounds (pybwa.BwaMemOptions attribute) max_mismatches (pybwa.BwaAlnOptions attribute) max_mismatches_in_seed (pybwa.BwaAlnOptions attribute) max_occurrences (pybwa.BwaMemOptions attribute)

max_occurrences_for_extending_long_deletion (pybwa.BwaAlnOptions attribute) md (pybwa.AuxHit attribute) min_indel_to_end_distance (pybwa.BwaAlnOptions attribute) min_seed_len (pybwa.BwaMemOptions attribute) min_seeded_bases_in_chain (pybwa.BwaMemOptions attribute) minimum_score (pybwa.BwaMemOptions attribute) mismatch_penalty (pybwa.BwaAlnOptions attribute) (pybwa.BwaMemOptions attribute) mismatches (pybwa.AuxHit property) mode (pybwa.BwaMemOptions attribute)

N

negative (pybwa.AuxHit attribute)

O

off_diagonal_x_dropoff (pybwa.BwaMemOptions attribute)

ONT2D (pybwa.BwaMemMode attribute) output_all_for_fragments (pybwa.BwaMemOptions attribute)

P

PACBIO (pybwa.BwaMemMode attribute)

Q

query_coord_as_primary (pybwa.BwaMemOptions attribute)

QUIET (pybwa.BwaVerbosity attribute)

R

RB2 (pybwa.BwaIndexBuildMethod attribute) refname (pybwa.AuxHit attribute)

reinitialize_seed() (pybwa.BwaAln method) rest (pybwa.AuxHit attribute)

S

seed_length (pybwa.BwaAlnOptions attribute) seed_occurrence_in_3rd_round (pybwa.BwaMemOptions attribute) set_bwa_verbosity() (in module pybwa) short_split_as_secondary (pybwa.BwaMemOptions attribute)

skip_mate_rescue (pybwa.BwaMemOptions attribute) skip_pairing (pybwa.BwaMemOptions attribute) soft_clip_supplementary (pybwa.BwaMemOptions attribute) start (pybwa.AuxHit attribute) stop_at_max_best_hits (pybwa.BwaAlnOptions attribute)

T

threads (pybwa.BwaAlnOptions attribute) (pybwa.BwaMemOptions attribute)

to_xa_hits() (in module pybwa)

U

unpaired_penalty (pybwa.BwaMemOptions attribute)

V

validate() (pybwa.BwaAlnOptions method) (pybwa.BwaMemOptions method)

W

WARNING (pybwa.BwaVerbosity attribute) with_md (pybwa.BwaAlnOptions attribute)

with_xb_tag (pybwa.BwaMemOptions attribute) with_xr_tag (pybwa.BwaMemOptions attribute)

X

xa_drop_ratio (pybwa.BwaMemOptions attribute)

xa_max_hits (pybwa.BwaMemOptions attribute)