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bwa mem options doc
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@nh13
nh13 committed Jan 16, 2025
1 parent 569c876 commit cfaf78c
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Showing 3 changed files with 183 additions and 31 deletions.
30 changes: 16 additions & 14 deletions pybwa/libbwaaln.pyi
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Original file line number Diff line number Diff line change
Expand Up @@ -7,20 +7,22 @@ from pysam import FastxRecord
from pybwa.libbwaindex import BwaIndex

class BwaAlnOptions:
def __init__(self,
max_mismatches: int | None = None,
max_gap_opens: int | None = None,
max_gap_extensions: int | None = None,
min_indel_to_end_distance: int | None = None,
max_occurrences_for_extending_long_deletion: int | None = None,
seed_length: int | None = None,
max_mismatches_in_seed: int | None = None,
mismatch_penalty: int | None = None,
gap_open_penalty: int | None = None,
gap_extension_penalty: int | None = None,
stop_at_max_best_hits: int | None = None,
max_hits: int | None = 3,
log_scaled_gap_penalty: bool | None = None) -> None: ...
def __init__(
self,
max_mismatches: int | None = None,
max_gap_opens: int | None = None,
max_gap_extensions: int | None = None,
min_indel_to_end_distance: int | None = None,
max_occurrences_for_extending_long_deletion: int | None = None,
seed_length: int | None = None,
max_mismatches_in_seed: int | None = None,
mismatch_penalty: int | None = None,
gap_open_penalty: int | None = None,
gap_extension_penalty: int | None = None,
stop_at_max_best_hits: int | None = None,
max_hits: int | None = 3,
log_scaled_gap_penalty: bool | None = None,
) -> None: ...
max_mismatches: int # -n <int>
# fnr:float # -n <float>
max_gap_opens: int # -o <int>
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35 changes: 34 additions & 1 deletion pybwa/libbwamem.pyi
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,40 @@ class BwaMemMode(enum.Enum):
INTRACTG = enum.auto()

class BwaMemOptions:
def __init__(self, finalize: bool = False) -> None: ...
def __init__(
self,
min_seed_len: int | None = None,
mode: BwaMemMode | None = None,
band_width: int | None = None,
match_score: int | None = None,
mismatch_penalty: int | None = None,
minimum_score: int | None = None,
unpaired_penalty: int | None = None,
n_threads: int | None = None,
skip_pairing: bool | None = None,
output_all_for_fragments: bool | None = None,
interleaved_paired_end: bool | None = None,
short_split_as_secondary: bool | None = None,
skip_mate_rescue: bool | None = None,
soft_clip_supplementary: bool | None = None,
with_xr_tag: bool | None = None,
query_coord_as_primary: bool | None = None,
keep_mapq_for_supplementary: bool | None = None,
with_xb_tag: bool | None = None,
max_occurrences: int | None = None,
off_diagonal_x_dropoff: float | None = None,
ignore_alternate_contigs: bool | None = None,
internal_seed_split_factor: float | None = None,
drop_chain_fraction: float | None = None,
max_mate_rescue_rounds: int | None = None,
min_seeded_bases_in_chain: int | None = None,
seed_occurrence_in_3rd_round: int | None = None,
xa_max_hits: int | tuple[int, int] | None = None,
xa_drop_ratio: float | None = None,
gap_open_penalty: int | tuple[int, int] | None = None,
gap_extension_penalty: int | tuple[int, int] | None = None,
clipping_penalty: int | tuple[int, int] | None = None,
) -> None: ...
_finalized: bool
_ignore_alt: bool
_mode: BwaMemMode | None
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149 changes: 133 additions & 16 deletions pybwa/libbwamem.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,41 @@ class BwaMemMode(enum.Enum):


cdef class BwaMemOptions:
"""The container for options for :class:`~pybwa.BwaMem`."""
"""The container for options for :class:`~pybwa.BwaMem`.
Args:
min_seed_len (int): :code:`bwa mem -k <int>`
mode (BwaMemMode): :code:`bwa mem -x <str>`
band_width (int): :code:`bwa mem -w <int>`
match_score (int): :code:`bwa mem -A <int>`
mismatch_penalty (int): :code:`bwa mem -A <int>`
minimum_score (int): :code:`bwa mem -T <int>`
unpaired_penalty (int): :code:`bwa mem -U <int>`
n_threads (int): :code:`bwa mem -t <int>`
skip_pairing (bool): :code:`bwa mem -P`
output_all_for_fragments (bool): :code:`bwa mem -a`
interleaved_paired_end (bool): :code:`bwa mem -p`
short_split_as_secondary (bool): :code:`bwa mem -M`
skip_mate_rescue (bool): :code:`bwa mem -S`
soft_clip_supplementary (bool): :code:`bwa mem -Y`
with_xr_tag (bool): :code:`bwa mem -V`
query_coord_as_primary (bool): :code:`bwa mem -5`
keep_mapq_for_supplementary (bool): :code:`bwa mem -q`
with_xb_tag (bool): :code:`bwa mem -u`
max_occurrences (int): :code:`bwa mem -c <int>`
off_diagonal_x_dropoff (float): :code:`bwa mem -d <float>`
ignore_alternate_contigs (bool): :code:`bwa mem -j`
internal_seed_split_factor (float): :code:`bwa mem -r <float>`
drop_chain_fraction (float): :code:`bwa mem -D <float>`
max_mate_rescue_rounds (int): :code:`bwa mem -m <int>`
min_seeded_bases_in_chain (int): :code:`bwa mem -W <int>`
seed_occurrence_in_3rd_round (int): :code:`bwa mem -y <int>`
xa_max_hits (int | tuple[int, int]): :code:`bwa mem -h <int<,int>>`
xa_drop_ratio (float): :code:`bwa mem -y <float>`
gap_open_penalty (int | tuple[int, int]): :code:`bwa mem -O <int<,int>>`
gap_extension_penalty (int | tuple[int, int]): :code:`bwa mem -E <int<,int>>`
clipping_penalty (int | tuple[int, int]): :code:`bwa mem -L <int<,int>>`
"""
_finalized: bool
_ignore_alt: bool
_mode: BwaMemMode | None
Expand All @@ -45,21 +79,104 @@ cdef class BwaMemOptions:
if self._finalized:
raise AttributeError(f"can't set attribute: {attr_name}")

def __init__(self, options: BwaMemOptions | None = None):
"""Builds a new `BwaMemOptions` instance.
Args:
options: initialize these options from the given options
"""
if options is None:
self._finalized = False
self._ignore_alt = False
self._mode = None
else:
self._finalized = options._finalized
self._ignore_alt = options._ignore_alt
self._mode = options._mode

def __init__(self,
min_seed_len: int | None = None,
mode: BwaMemMode | None = None,
band_width: int | None = None,
match_score: int | None = None,
mismatch_penalty: int | None = None,
minimum_score: int | None = None,
unpaired_penalty: int | None = None,
n_threads: int | None = None,
skip_pairing: bool | None = None,
output_all_for_fragments: bool | None = None,
interleaved_paired_end: bool | None = None,
short_split_as_secondary: bool | None = None,
skip_mate_rescue: bool | None = None,
soft_clip_supplementary: bool | None = None,
with_xr_tag: bool | None = None,
query_coord_as_primary: bool | None = None,
keep_mapq_for_supplementary: bool | None = None,
with_xb_tag: bool | None = None,
max_occurrences: int | None = None,
off_diagonal_x_dropoff: float | None = None,
ignore_alternate_contigs: bool | None = None,
internal_seed_split_factor: float | None = None,
drop_chain_fraction: float | None = None,
max_mate_rescue_rounds: int | None = None,
min_seeded_bases_in_chain: int | None = None,
seed_occurrence_in_3rd_round: int | None = None,
xa_max_hits: int | tuple[int, int] | None = None,
xa_drop_ratio: float | None = None,
gap_open_penalty: int | tuple[int, int] | None = None,
gap_extension_penalty: int | tuple[int, int] | None = None,
clipping_penalty: int | tuple[int, int] | None = None) -> None:
self._finalized = False
self._ignore_alt = False
self._mode = None
if min_seed_len is not None:
self.min_seed_len = min_seed_len
if mode is not None:
self.mode = mode
if band_width is not None:
self.band_width = band_width
if match_score is not None:
self.match_score = match_score
if mismatch_penalty is not None:
self.mismatch_penalty = mismatch_penalty
if minimum_score is not None:
self.minimum_score = minimum_score
if unpaired_penalty is not None:
self.unpaired_penalty = unpaired_penalty
if n_threads is not None:
self.n_threads = n_threads
if skip_pairing is not None:
self.skip_pairing = skip_pairing
if output_all_for_fragments is not None:
self.output_all_for_fragments = output_all_for_fragments
if interleaved_paired_end is not None:
self.interleaved_paired_end = interleaved_paired_end
if short_split_as_secondary is not None:
self.short_split_as_secondary = short_split_as_secondary
if skip_mate_rescue is not None:
self.skip_mate_rescue = skip_mate_rescue
if soft_clip_supplementary is not None:
self.soft_clip_supplementary = soft_clip_supplementary
if with_xr_tag is not None:
self.with_xr_tag = with_xr_tag
if query_coord_as_primary is not None:
self.query_coord_as_primary = query_coord_as_primary
if keep_mapq_for_supplementary is not None:
self.keep_mapq_for_supplementary = keep_mapq_for_supplementary
if with_xb_tag is not None:
self.with_xb_tag = with_xb_tag
if max_occurrences is not None:
self.max_occurrences = max_occurrences
if off_diagonal_x_dropoff is not None:
self.off_diagonal_x_dropoff = off_diagonal_x_dropoff
if ignore_alternate_contigs is not None:
self.ignore_alternate_contigs = ignore_alternate_contigs
if internal_seed_split_factor is not None:
self.internal_seed_split_factor = internal_seed_split_factor
if drop_chain_fraction is not None:
self.drop_chain_fraction = drop_chain_fraction
if max_mate_rescue_rounds is not None:
self.max_mate_rescue_rounds = max_mate_rescue_rounds
if min_seeded_bases_in_chain is not None:
self.min_seeded_bases_in_chain = min_seeded_bases_in_chain
if seed_occurrence_in_3rd_round is not None:
self.seed_occurrence_in_3rd_round = seed_occurrence_in_3rd_round
if xa_max_hits is not None:
self.xa_max_hits = xa_max_hits
if xa_drop_ratio is not None:
self.xa_drop_ratio = xa_drop_ratio
if gap_open_penalty is not None:
self.gap_open_penalty = gap_open_penalty
if gap_extension_penalty is not None:
self.gap_extension_penalty = gap_extension_penalty
if clipping_penalty is not None:
self.clipping_penalty = clipping_penalty

cdef _copy_options(self, dst: BwaMemOptions, src: BwaMemOptions):
memcpy(dst._options, src._options, sizeof(mem_opt_t))
memcpy(dst._options0, src._options0, sizeof(mem_opt_t))
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