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Add query to ref coord mapping #120

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Add query to ref coord mapping #120

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5b55e6b
add query to ref coord mapping
chilampoon Oct 10, 2023
3c807bb
rm redundant interpolation
chilampoon Oct 11, 2023
804fb9b
change N ref ops to false
chilampoon Oct 12, 2023
a62f46d
intron aware extract_ref_reg
chilampoon Oct 15, 2023
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change N ref ops to false
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@chilampoon
chilampoon committed Oct 12, 2023
commit 804fb9b7e82fa5636d0f39abb8e94f99ae7d2b7b
22 changes: 2 additions & 20 deletions src/remora/data_chunks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,7 @@
[True, False, False, False, False, False, False, True, True]
)
QUERY_OPS = np.array([True, True, False, False, True, False, False, True, True])
REF_OPS = np.array([True, False, True, True, False, False, False, True, True])
REFCOORD_OPS = np.array([True, False, True, False, False, False, False, True, True])
REF_OPS = np.array([True, False, True, False, False, False, False, True, True])
CIGAR_CODES = ["M", "I", "D", "N", "S", "H", "P", "=", "X"]
CODE_TO_OP = {
"M": 0,
Expand Down Expand Up @@ -99,28 +98,11 @@ def make_sequence_coordinate_mapping(cigar):
query_knots = np.concatenate(
[[0], (query_knots[is_match] - offsets).T.flatten(), [query_knots[-1]]]
)
ref_coords = get_ref_coords(ops, lens)
knots = np.interp(np.concatenate([[0], ref_coords]), ref_knots, query_knots)
knots = np.interp(np.arange(ref_knots[-1] + 1), ref_knots, query_knots)

return knots


def get_ref_coords(ops, lens):
'''
Map query base to reference coordinates (1-based).
Returns
array shape (ref_len,); ref_len = len(aln.get_reference_sequences())
'''
starts = np.cumsum(np.where(REF_OPS[ops], lens, 0)) - np.where(REF_OPS[ops], lens, 0)
ranges = [
np.arange(start, start + l)
for op, start, l in zip(ops, starts, lens)
if REFCOORD_OPS[op]
]
ref_coords = np.concatenate(ranges) + 1
return ref_coords


def compute_ref_to_signal(query_to_signal, cigar):
ref_to_read_knots = make_sequence_coordinate_mapping(cigar)
assert query_to_signal.size == ref_to_read_knots[-1].astype(int) + 1, (
Expand Down