smftools 0.3.1__py3-none-any.whl → 0.3.2__py3-none-any.whl

smftools/tools/sequence_alignment.py

@@ -0,0 +1,140 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from typing import Literal
+
+
+@dataclass(frozen=True)
+class AlignmentMismatch:
+    """Record a mismatch or gap between two aligned sequences."""
+
+    event: Literal["substitution", "insertion", "deletion"]
+    seq1_pos: int | None
+    seq1_base: str | None
+    seq2_pos: int | None
+    seq2_base: str | None
+
+
+def align_sequences_with_mismatches(
+    seq1: str,
+    seq2: str,
+    match_score: int = 1,
+    mismatch_score: int = -1,
+    gap_score: int = -1,
+    ignore_n: bool = True,
+) -> tuple[str, str, list[AlignmentMismatch]]:
+    """Globally align two sequences and return mismatch positions/bases.
+
+    The alignment uses a simple Needleman-Wunsch dynamic programming approach
+    with configurable scores. Mismatch reporting is based on the aligned
+    sequences and returns 0-based coordinates in each sequence. Gap events
+    are represented with a ``None`` coordinate for the gapped sequence.
+
+    Args:
+        seq1: First sequence (treated as reference for positions).
+        seq2: Second sequence.
+        match_score: Score for matching bases.
+        mismatch_score: Score for mismatching bases.
+        gap_score: Score for introducing a gap.
+        ignore_n: Whether to ignore mismatches involving the base ``N``.
+
+    Returns:
+        Tuple of (aligned_seq1, aligned_seq2, mismatches).
+    """
+    seq1 = seq1.upper()
+    seq2 = seq2.upper()
+    n, m = len(seq1), len(seq2)
+
+    scores = [[0] * (m + 1) for _ in range(n + 1)]
+    traceback = [[None] * (m + 1) for _ in range(n + 1)]
+
+    for i in range(1, n + 1):
+        scores[i][0] = scores[i - 1][0] + gap_score
+        traceback[i][0] = "up"
+    for j in range(1, m + 1):
+        scores[0][j] = scores[0][j - 1] + gap_score
+        traceback[0][j] = "left"
+
+    for i in range(1, n + 1):
+        for j in range(1, m + 1):
+            diag_score = scores[i - 1][j - 1] + (
+                match_score if seq1[i - 1] == seq2[j - 1] else mismatch_score
+            )
+            up_score = scores[i - 1][j] + gap_score
+            left_score = scores[i][j - 1] + gap_score
+
+            best_score = max(diag_score, up_score, left_score)
+            scores[i][j] = best_score
+            if best_score == diag_score:
+                traceback[i][j] = "diag"
+            elif best_score == up_score:
+                traceback[i][j] = "up"
+            else:
+                traceback[i][j] = "left"
+
+    aligned1: list[str] = []
+    aligned2: list[str] = []
+    i, j = n, m
+    while i > 0 or j > 0:
+        direction = traceback[i][j]
+        if direction == "diag":
+            aligned1.append(seq1[i - 1])
+            aligned2.append(seq2[j - 1])
+            i -= 1
+            j -= 1
+        elif direction == "up":
+            aligned1.append(seq1[i - 1])
+            aligned2.append("-")
+            i -= 1
+        else:
+            aligned1.append("-")
+            aligned2.append(seq2[j - 1])
+            j -= 1
+
+    aligned_seq1 = "".join(reversed(aligned1))
+    aligned_seq2 = "".join(reversed(aligned2))
+
+    mismatches: list[AlignmentMismatch] = []
+    seq1_index = 0
+    seq2_index = 0
+    for base1, base2 in zip(aligned_seq1, aligned_seq2, strict=True):
+        if base1 == "-":
+            if not (ignore_n and base2 == "N"):
+                mismatches.append(
+                    AlignmentMismatch(
+                        event="insertion",
+                        seq1_pos=None,
+                        seq1_base=None,
+                        seq2_pos=seq2_index,
+                        seq2_base=base2,
+                    )
+                )
+            seq2_index += 1
+            continue
+        if base2 == "-":
+            if not (ignore_n and base1 == "N"):
+                mismatches.append(
+                    AlignmentMismatch(
+                        event="deletion",
+                        seq1_pos=seq1_index,
+                        seq1_base=base1,
+                        seq2_pos=None,
+                        seq2_base=None,
+                    )
+                )
+            seq1_index += 1
+            continue
+        if base1 != base2 and not (ignore_n and "N" in (base1, base2)):
+            mismatches.append(
+                AlignmentMismatch(
+                    event="substitution",
+                    seq1_pos=seq1_index,
+                    seq1_base=base1,
+                    seq2_pos=seq2_index,
+                    seq2_base=base2,
+                )
+            )
+        seq1_index += 1
+        seq2_index += 1
+
+    return aligned_seq1, aligned_seq2, mismatches

smftools/tools/tensor_factorization.py

@@ -60,6 +60,8 @@ def calculate_sequence_cp_decomposition(
     adata: "ad.AnnData",
     *,
     layer: str,
+    var_mask: np.ndarray | None = None,
+    var_mask_name: str | None = None,
     rank: int = 5,
     n_iter_max: int = 100,
     random_state: int = 0,
@@ -71,12 +73,15 @@ def calculate_sequence_cp_decomposition(
     backend: str = "pytorch",
     show_progress: bool = False,
     init: str = "random",
+    non_negative: bool = False,
 ) -> "ad.AnnData":
     """Compute CP decomposition on one-hot encoded sequence data with masking.
 
     Args:
         adata: AnnData object to update.
         layer: Layer name containing integer-encoded sequences.
+        var_mask: Optional boolean mask over variables to include in the CP fit.
+        var_mask_name: Optional label describing the provided ``var_mask``.
         rank: CP rank.
         n_iter_max: Maximum number of iterations for the solver.
         random_state: Random seed for initialization.
@@ -87,6 +92,7 @@ def calculate_sequence_cp_decomposition(
         bases: Bases to one-hot encode (in order).
         backend: Tensorly backend to use (``numpy`` or ``pytorch``).
         show_progress: Whether to display progress during factorization if supported.
+        non_negative: Whether to request a non-negative CP decomposition.
 
     Returns:
         Updated AnnData object containing the CP decomposition outputs.
@@ -101,12 +107,31 @@ def calculate_sequence_cp_decomposition(
     tensorly = require("tensorly", extra="ml-base", purpose="CP decomposition")
     from tensorly.decomposition import parafac
 
+    try:
+        from tensorly.decomposition import non_negative_parafac
+    except ImportError:
+        non_negative_parafac = None
+
     tensorly.set_backend(backend)
 
     if layer not in adata.layers:
         raise KeyError(f"Layer '{layer}' not found in adata.layers.")
 
-    one_hot, mask = build_sequence_one_hot_and_mask(adata.layers[layer], bases=tuple(bases))
+    layer_data = adata.layers[layer]
+    mask_indices = None
+    if var_mask is not None:
+        var_mask_array = np.asarray(var_mask, dtype=bool)
+        if var_mask_array.shape[0] != adata.n_vars:
+            raise ValueError(
+                "var_mask must match adata.n_vars; "
+                f"got {var_mask_array.shape[0]} vs {adata.n_vars}."
+            )
+        if not var_mask_array.any():
+            raise ValueError("var_mask must include at least one variable.")
+        mask_indices = var_mask_array
+        layer_data = layer_data[:, var_mask_array]
+
+    one_hot, mask = build_sequence_one_hot_and_mask(layer_data, bases=tuple(bases))
     mask_tensor = np.repeat(mask[:, :, None], one_hot.shape[2], axis=2)
 
     device = "numpy"
@@ -131,10 +156,21 @@ def calculate_sequence_cp_decomposition(
     }
     import inspect
 
-    if "verbose" in inspect.signature(parafac).parameters:
+    decomposition_fn = parafac
+    if non_negative:
+        if non_negative_parafac is not None:
+            decomposition_fn = non_negative_parafac
+        elif "non_negative" in inspect.signature(parafac).parameters:
+            parafac_kwargs["non_negative"] = True
+        else:
+            raise ValueError(
+                "Non-negative CP decomposition requested but tensorly does not support it."
+            )
+
+    if "verbose" in inspect.signature(decomposition_fn).parameters:
         parafac_kwargs["verbose"] = show_progress
 
-    cp = parafac(one_hot, **parafac_kwargs)
+    cp = decomposition_fn(one_hot, **parafac_kwargs)
 
     if backend == "pytorch":
         weights = cp.weights.detach().cpu().numpy()
@@ -146,7 +182,16 @@ def calculate_sequence_cp_decomposition(
         read_factors, position_factors, base_factors = [np.asarray(f) for f in cp.factors]
 
     adata.obsm[embedding_key] = read_factors
-    adata.varm[components_key] = position_factors
+    if mask_indices is None:
+        adata.varm[components_key] = position_factors
+    else:
+        full_components = np.full(
+            (adata.n_vars, position_factors.shape[1]),
+            np.nan,
+            dtype=position_factors.dtype,
+        )
+        full_components[mask_indices] = position_factors
+        adata.varm[components_key] = full_components
     adata.uns[uns_key] = {
         "rank": rank,
         "n_iter_max": n_iter_max,
@@ -158,6 +203,9 @@ def calculate_sequence_cp_decomposition(
         "base_labels": list(bases),
         "backend": backend,
         "device": str(device),
+        "non_negative": non_negative,
+        "var_mask_name": var_mask_name,
+        "var_mask_count": int(np.sum(mask_indices)) if mask_indices is not None else None,
     }
 
     logger.info(

{smftools-0.3.1.dist-info → smftools-0.3.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: smftools
-Version: 0.3.1
+Version: 0.3.2
 Summary: Single Molecule Footprinting Analysis in Python.
 Project-URL: Source, https://github.com/jkmckenna/smftools
 Project-URL: Documentation, https://smftools.readthedocs.io/
@@ -55,6 +55,7 @@ Provides-Extra: all
 Requires-Dist: captum; extra == 'all'
 Requires-Dist: fastcluster; extra == 'all'
 Requires-Dist: hydra-core; extra == 'all'
+Requires-Dist: igraph; extra == 'all'
 Requires-Dist: leidenalg; extra == 'all'
 Requires-Dist: lightning; extra == 'all'
 Requires-Dist: matplotlib>=3.6.2; extra == 'all'
@@ -69,6 +70,7 @@ Requires-Dist: pysam>=0.19.1; extra == 'all'
 Requires-Dist: scikit-learn>=1.0.2; extra == 'all'
 Requires-Dist: seaborn>=0.11; extra == 'all'
 Requires-Dist: shap; extra == 'all'
+Requires-Dist: tensorly; extra == 'all'
 Requires-Dist: torch>=1.9.0; extra == 'all'
 Requires-Dist: umap-learn>=0.5.5; extra == 'all'
 Requires-Dist: upsetplot; extra == 'all'

{smftools-0.3.1.dist-info → smftools-0.3.2.dist-info}/RECORD

@@ -1,27 +1,30 @@
 smftools/__init__.py,sha256=Wun5eO3FHy7sAelTLlLdFj3NurqZFQxfO3U5YHJ3KcY,1247
 smftools/_settings.py,sha256=QqZzjz6Y_-gZH4VJAPRCL68HRlGjzl3hXU7d-dMi8-M,418
-smftools/_version.py,sha256=e9cd8nKFi-8fyxRlTRJYWgSHyt1C_r_TE3kQS7NeJv0,58
-smftools/cli_entry.py,sha256=Mfhg8GWqER0AHYqKB2McocljX3OWcaYFOEfDrR3WGbQ,10808
-smftools/constants.py,sha256=atMoOE3wM803ixhE_PdklOYbNhJvh-37gNkOyg9Jtnw,4007
+smftools/_version.py,sha256=xm1u7RHIf6fYv7ou5-vxQ9OiaAwZ0vJK7AngPQ7IBek,58
+smftools/cli_entry.py,sha256=rFd_rSY8KA28LdHGS5wnSY1nCaiSZMSlhG4bm2Dn1w0,11675
+smftools/constants.py,sha256=NZjUgTD57StBaktxPIpUGoAmNjNB6D68Yr6ueAQJ8KY,4111
 smftools/logging_utils.py,sha256=OpDul2P5FCWhjJqunYK2MrSaYtbKEPGFE0Z7vZhSX0Y,2193
 smftools/metadata.py,sha256=-U8jVzjBsXbZ2SKRcyPHMCDPnsQQRR4djzerjpeQvzU,14917
 smftools/optional_imports.py,sha256=PpjWa-H-rlxwXJjkPLSHkiuim922xwDVsqlgFY8wWqw,1039
-smftools/readwrite.py,sha256=ZOy54ABP4fcSe37-bGyhhd8kKOaVXPMCB-WFn_rrOwg,53665
+smftools/readwrite.py,sha256=fvCJsIZ6Idjp0QIzbxXTPSXmQOb6ggx8idRaTbDck7w,54876
 smftools/cli/__init__.py,sha256=U4S_2y3zgLZVfMenHRaJFBW8yqh2mUBuI291LGQVOJ8,35
-smftools/cli/helpers.py,sha256=Oj5wrdjrZHNqyPrmwaaPoQ_QvuM-b7e_A4osyrYsf-A,2432
-smftools/cli/hmm_adata.py,sha256=068V4qBCodW6xCZEkTWOkz0QHZ3UuixhTKAipFLimxE,48284
-smftools/cli/latent_adata.py,sha256=O9CPbm0ru4pFOENQmvTDzUINKLiSYeTOR671vJnyxJU,10431
-smftools/cli/load_adata.py,sha256=7-wsYIRs-axh2U4LYm0JtgpCNpWQntxkU-9X4nuz9Fc,31606
-smftools/cli/preprocess_adata.py,sha256=A7P5JvBhlUtl2Pepu5yHigzgRDmhDp7uwJS8DWyBZEk,28294
-smftools/cli/spatial_adata.py,sha256=xRoYYGtGI4msiZVy68fISLjMlbWDhKQYFe6l1n0zKtM,34273
+smftools/cli/chimeric_adata.py,sha256=roX2qpIg_84lpRFCHgD9MPLTh_Qv8XQU0250_RLyhtI,73758
+smftools/cli/helpers.py,sha256=LGiQyJfqB8mTQ6BhJWG1vc4hkZv0BmxBCbCzY7vAE2A,2932
+smftools/cli/hmm_adata.py,sha256=ZGzU9cfLaYUrUTtGFzUvmgFNQHHzBTkN1jXsGMEpZzE,49363
+smftools/cli/latent_adata.py,sha256=q4PupWWPR8ZY-Qsmj6Ug2WoTRf8SUA4-caNq5Vie2-M,26523
+smftools/cli/load_adata.py,sha256=RSgX1kvEcqSx3JRXL055m2u4hro8uM-sNvA5jVVxOr8,31539
+smftools/cli/preprocess_adata.py,sha256=D2LGNto2aeAvPjMwSPKR9CzxTIewhTtBUL3n47gE5Pw,25161
+smftools/cli/recipes.py,sha256=v3CnuNOyizD_tdNlHF2Qv9LsUkNMYDIVlqr_I3275QA,735
+smftools/cli/spatial_adata.py,sha256=MLsCo8PTYw1jxxXh9bdUG1Ftjuk2bp36oSGmnw7GvF8,30149
+smftools/cli/variant_adata.py,sha256=RNV0WyLVOdJhFAaM6XjUVh__kLMD7kv1BTSym7HIezY,16889
 smftools/cli/archived/cli_flows.py,sha256=w1rPHSH8WzZn7owz0ra7WOUGlJSEsaRw_W3x-9Ra42k,4977
 smftools/config/__init__.py,sha256=rcI3qG1DGfRcvQzh8bffiHuRPcmPsas5T8MN6uhScxA,106
-smftools/config/conversion.yaml,sha256=ih5qu1gMSOFmjHU1JLqgQ9CzekWD5vKQQREWnIm0HX0,1498
-smftools/config/deaminase.yaml,sha256=JCE1nF39AX436-3RyvuZN24gdJfriDijNv5XNHrMT8I,1357
-smftools/config/default.yaml,sha256=yyATffMZbyLuiTQ6dpq4pNFvAgYp1CTntAdGA30R4wM,14976
+smftools/config/conversion.yaml,sha256=djZTJ1EwHc1Ax_fIsZo1UnERDpyER15rgo8APrOtAwE,1243
+smftools/config/deaminase.yaml,sha256=uZZzWeNc3TcBGY7o58lqQb3XOMAi3kIpHsUBqWUuM9g,1388
+smftools/config/default.yaml,sha256=gCWhoemO97zyaNTrt0A40RWnaHJ6R65mJJ4gEMUjgC4,16242
 smftools/config/direct.yaml,sha256=Jw8Nj3QKQrCfJpVl8sGgCKdRvjk5cV66dzRlNfoDOzI,2269
 smftools/config/discover_input_files.py,sha256=NcOqNYoXggLDieam8UMJAc2sWmoYOZ_Wqp2mApnlBfs,4015
-smftools/config/experiment_config.py,sha256=7KoibibpZxz_rRuOj8QiU9gvuMhwMtlF2sbw6EZeszE,70415
+smftools/config/experiment_config.py,sha256=soaTSwVbZELCDS1D5EQa2MF5RvPFP3lNQAaDhYMIbjM,75729
 smftools/datasets/F1_hybrid_NKG2A_enhander_promoter_GpC_conversion_SMF.h5ad.gz,sha256=q6wJtgFRDln0o20XNCx1qad3lwcdCoylqPN7wskTfI8,2926497
 smftools/datasets/F1_sample_sheet.csv,sha256=9PodIIOXK2eamYPbC6DGnXdzgi9bRDovf296j1aM0ak,259
 smftools/datasets/__init__.py,sha256=_G08ZAMlA9zpY5UjWTVlpAbW2YPS4PLCmz5g1pZdcCw,157
@@ -29,7 +32,7 @@ smftools/datasets/dCas9_m6A_invitro_kinetics.h5ad.gz,sha256=niOcVHaYY7h3XyvwSkN-
 smftools/datasets/datasets.py,sha256=-VOdONP-K_ftLDtLktRKbq3S6vSB4pzRQ6VYBxAy_4A,1074
 smftools/hmm/HMM.py,sha256=Yq7awVwCtTPb4HET1UIx2VTHVvgiwu_2pjEgZTTkTP4,85660
 smftools/hmm/__init__.py,sha256=vs-fjo-v9y8EwdoErK6KDBm-YzD_XmTtflsdTJlRgTg,746
-smftools/hmm/call_hmm_peaks.py,sha256=CzTEz3EP_LNLirIVYzRxbV7_5fCBpLa9azLPSEt6s7s,13529
+smftools/hmm/call_hmm_peaks.py,sha256=jfmo-zzmA57d3pNG1RM1FqjsHue3IErgjOWIf3EuXtQ,13533
 smftools/hmm/display_hmm.py,sha256=N94hmEKZGehPdsB9yLyY7U1_tTWDk2NTMU-PuWnEQqA,1321
 smftools/hmm/hmm_readwrite.py,sha256=n-ok3wH1-anSn90vEA91jWKRbtq0bxM66hp2eYoWk34,687
 smftools/hmm/nucleosome_hmm_refinement.py,sha256=lHB6XVJWhwN-jR1TjBOMIOBQ5soncAJbv3djbkyH1NU,6882
@@ -41,12 +44,12 @@ smftools/informatics/__init__.py,sha256=Q2l7iGOEuZXtGmqWG3NwF-_vNwl4VmJPsElg7-eA
 smftools/informatics/bam_functions.py,sha256=b_Vb08HmOl8-hXLbkVNBw-zl-1loXqw-yQJkklJUvyY,73636
 smftools/informatics/basecalling.py,sha256=PgjWoOgfQaUOCoKpyaKO8m8sauMW3el6wdEtzGlvy4s,3699
 smftools/informatics/bed_functions.py,sha256=9y3XNNl6QivqkWEfoH5XszP3Qsj0P-rCopgfd0HpFgs,21268
-smftools/informatics/binarize_converted_base_identities.py,sha256=KRL-KT8MYADadHgRbTgoOFD30LlZazKHe10Hz9nO6Z4,7850
+smftools/informatics/binarize_converted_base_identities.py,sha256=2vncAGQ84GD-yvZpvnbBLj_ex9ABNACOzYAeX9yOPB4,4023
 smftools/informatics/complement_base_list.py,sha256=6DInlD4cdjKJmmUv4Cp4UU9HHLe60Pm8RF9AoBfBfF0,571
-smftools/informatics/converted_BAM_to_adata.py,sha256=CIIrJVQHFpc2gg7K1W99kpmG5IUVBVqQIRBPKuR4EHk,42759
+smftools/informatics/converted_BAM_to_adata.py,sha256=qDdY5S7oCkH9Ov6a0BADnt2ytZYtcXSU1K2RyoNZxoo,44986
 smftools/informatics/fasta_functions.py,sha256=MD-fL0BkExiDXMUSPkHaHrkOK7aqzOozWREGr5Gzw8w,14111
-smftools/informatics/h5ad_functions.py,sha256=wGsvk51FhrByNPI-TCgZEh0nKyW6jd1t_mHR6957IAo,17577
-smftools/informatics/modkit_extract_to_adata.py,sha256=oL1dxcNLCsGqFngZd3HYW63tBzkGKQx9kbCWOAzwwfc,84454
+smftools/informatics/h5ad_functions.py,sha256=V-lLmrff4Yv02PiKp9ePjYK7dHZALJInHID3_bSabTY,21178
+smftools/informatics/modkit_extract_to_adata.py,sha256=YF0zeg6k0FiPRCzLLrTcZQ5Q97fI8tZRnzNWco5Jwa0,84581
 smftools/informatics/modkit_functions.py,sha256=BvWd_qulVOQKZJFMd4pLTVD3ruo1dT48BmvQsdHB0_E,6103
 smftools/informatics/ohe.py,sha256=fdMEdXG45hiCsHtmYkPsXJKLJ-SBaZktdGx-bmfI3a0,5997
 smftools/informatics/pod5_functions.py,sha256=6_EA2StpslOe0phSwR9TDB_U-Tmx4ykuBcTAiOL0LPU,10327
@@ -123,17 +126,25 @@ smftools/machine_learning/training/train_sklearn_model.py,sha256=zQ5SQpu_sl7IVcZ
 smftools/machine_learning/utils/__init__.py,sha256=aiCNpHD08ENEBtz8jzDfVZ8cB7ef9uOE7YaOPDkQUYg,99
 smftools/machine_learning/utils/device.py,sha256=2D5TF6DQIZKTcyNqIcJ7UMFeiWS_kCAvZUBK6XngCXk,432
 smftools/machine_learning/utils/grl.py,sha256=ptr-08dRKAGBZ1cySy_B90GgMn5kXtNXlcUC4PJ5mNA,485
-smftools/plotting/__init__.py,sha256=GA-fyueJMOgQYe3EH6juWZ3wNYo0ugUqKyoBlubWOoc,2100
-smftools/plotting/autocorrelation_plotting.py,sha256=gc3iyGgFEvMcyHXE2K8S956Nx6IfduglOOeJj3te8nU,30590
-smftools/plotting/classifiers.py,sha256=9Qt0eixvgE3WXl6jcwPm7O3ATA7Q6mfqRh_B_9M2qTQ,16749
-smftools/plotting/general_plotting.py,sha256=TZeIJOCLuNzeUDktee2HP9LJO-o1clNPcPaZ64WHFLk,134703
-smftools/plotting/hmm_plotting.py,sha256=3UkhfbZYM0hXvSoQJ94F2GR70cTPjpfm9w2nOo8itL0,14964
-smftools/plotting/position_stats.py,sha256=yxZx0Hjx4MsKINe9kkq-R7TkjODBGaDrbH9y0mrrTWs,19351
-smftools/plotting/qc_plotting.py,sha256=ODK8UrjVrAJeG8Qfu09DmAJ_o9GJaXRxGwN0pEgbHAU,10358
-smftools/preprocessing/__init__.py,sha256=x-QTdVOYbVPpHqO2cBPhmsO-6AliemcBb2Qo78cQrqw,1952
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 smftools/preprocessing/append_binary_layer_by_base_context.py,sha256=7mFG7xjAPgm_60AcdCnnjJZK5gJe4VuLohopkrAHmvQ,7640
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 smftools/preprocessing/binarize.py,sha256=eDFLybKKIF2wcrtN3JWVjeGXSUayezxLhX76UllAhVc,888
 smftools/preprocessing/binarize_on_Youden.py,sha256=JTHosTDy9-gJ0bPrHkGnz_Ao_AeE8IiutqFA6MksdM8,4887
 smftools/preprocessing/binary_layers_to_ohe.py,sha256=nYvAefdIKGj-JyNtBqHcekJKI4BI2CM9pN-Mq1BT-28,1931
@@ -149,8 +160,8 @@ smftools/preprocessing/clean_NaN.py,sha256=hrPhbKfqDpSiXLXXJxvcmtwqFhOecJVC29Z7P
 smftools/preprocessing/filter_adata_by_nan_proportion.py,sha256=5V1PNJISYm92QtEGmS9XSqx456Ult8RY8LMBclNylno,1490
 smftools/preprocessing/filter_reads_on_length_quality_mapping.py,sha256=83G8ovetiAmh8EbikqAUhNnzaX_KnWe0rZ7vfrgeye4,8018
 smftools/preprocessing/filter_reads_on_modification_thresholds.py,sha256=yxYZB9Ran1ZxuZm9iHi5bpLo6xcro5zKyv9rnYUtT6g,21688
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-smftools/preprocessing/invert_adata.py,sha256=-aiidr_PXSf8IIpC4PMRm2RlLAWi-dtZDpr0iSOY-PY,1367
+smftools/preprocessing/flag_duplicate_reads.py,sha256=Khauxw8_stBLmmkM1z4HVVuXpcWIhgTjJwoH-WfOoko,75436
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 smftools/preprocessing/load_sample_sheet.py,sha256=rzY76rCYVf3idu2ZRw4pEjVRBB5AyUkSYY-UzpmE_aw,2193
 smftools/preprocessing/make_dirs.py,sha256=SjeiXoWsy_SldM-RoQbpfo2mXdnP78xhHVHywTD7IZI,662
 smftools/preprocessing/min_non_diagonal.py,sha256=2sOWl7zKWltNmv-Jv-ZXb099dYBX28suAOE6DUlUO-U,749
@@ -164,26 +175,29 @@ smftools/preprocessing/archived/preprocessing.py,sha256=l0Im9O45kaMYxipyFiPFBA8M
 smftools/preprocessing/archived/remove_duplicates.py,sha256=W1Y2ufD2nE9Tnx3NXpEPxso08tiV50iRy77_X3RZkyQ,735
 smftools/schema/__init__.py,sha256=0chkz2Zc3UKSJO4m0MUemfs-WjGUSSghiuuFM28UvsY,293
 smftools/schema/anndata_schema_v1.yaml,sha256=FCMjYIqgt-YxQxehcgkdwWBzqk1k-aSZ3fUcksX1bH4,8310
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 smftools/tools/calculate_leiden.py,sha256=48Y72NIzGb6yxtnUund7gS_2jIFro5lwJC0ycNOoAJI,1867
-smftools/tools/calculate_nmf.py,sha256=O5IC9G5CrWdhefHaOPOkyx0Jiro_DZ4mvF75psEP4Q8,4192
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 smftools/tools/cluster_adata_on_methylation.py,sha256=NsU11zFyBB_TZFdVZxjqeSZsiVZgb8iCXaOBY54FA9U,7684
 smftools/tools/general_tools.py,sha256=XO8em-clV4onfbYEH6JTfNj3svLQnwBZ1Tja7s8qsXg,3260
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 smftools/tools/read_stats.py,sha256=8rV2BXymdPuPihh0Ev-HqPT40lobyt5WExoYjbmrbcI,6534
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 smftools/tools/spatial_autocorrelation.py,sha256=euunec6Mmkm5iBDN7TM4q4NXLl9n8UP77-6GSGYCVOk,25473
 smftools/tools/subset_adata.py,sha256=6xPf6hyKcYwg4L2n0iCnz-Pl84fS4jLgxmD47J-OEco,1012
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 smftools/tools/archived/apply_hmm.py,sha256=b1DKT_02weiPgkfQ0_Zfk7wN8FRZAMeYvBe74H3QuDU,9357
 smftools/tools/archived/classifiers.py,sha256=iKkK9UyEwEdNwLx-t_r52CURkP3iZ-pFwmQtXF_lnLY,42191
 smftools/tools/archived/classify_methylated_features.py,sha256=uXWXl4t9cP4inRiSvL4MxGbwC2MxT5uT-D1FFdex8oE,2933
 smftools/tools/archived/classify_non_methylated_features.py,sha256=vhfLbR5fqALps5HXxQ91x3lUTGLcfciaEsQkSFeLOgM,3292
 smftools/tools/archived/subset_adata_v1.py,sha256=CBTbHolOil7m4eR0bwIzxS7ZPvo3hmDsPVZGUBzWYrs,1361
 smftools/tools/archived/subset_adata_v2.py,sha256=npic7cuFIOeUiyRjATVrP4A0O7cV0EgHvRXi9aMMOcI,2311
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