gsMap 1.73.2__py3-none-any.whl → 1.73.4__py3-none-any.whl

gsMap/utils/generate_r2_matrix.py

@@ -1,67 +1,27 @@
+"""
+Module for reading and processing PLINK genotype data and calculating LD scores.
+
+Note:
+This code is adapted and modified from:
+https://github.com/bulik/ldsc/blob/master/ldsc/ldscore.py
+"""
+
+import logging
+
 import bitarray as ba
 import numpy as np
 import pandas as pd
+import pyranges as pr
 from tqdm import tqdm
 
-
-# Define the reading functions
-def ID_List_Factory(colnames, keepcol, fname_end, header=None, usecols=None):
-    # -
-    class IDContainer:
-        """
-        A class to read data from a file, store it as a DataFrame, and provide a method for a left outer join operation.
-        """
-
-        def __init__(self, fname):
-            """
-            Initialize the IDContainer with the given filename and reading options.
-            """
-            self.usecols = usecols
-            self.colnames = colnames
-            self.keepcol = keepcol
-            self.fname_end = fname_end
-            self.header = header
-            self.read(fname)
-            self.n = len(self.df)
-
-        # -
-        def read(self, fname):
-            """
-            Read data from the given file and store it as a DataFrame.
-            """
-            end = self.fname_end
-            if end and not fname.endswith(end):
-                raise ValueError(f"{end} filename must end in {end}")
-            self.df = pd.read_csv(
-                fname,
-                header=self.header,
-                usecols=self.usecols,
-                sep=r"\s+",
-            )
-            if self.colnames:
-                self.df.columns = self.colnames
-            if self.keepcol is not None:
-                self.IDList = self.df.iloc[:, [self.keepcol]].astype("object")
-
-    return IDContainer
+# Configure logger
+logger = logging.getLogger("gsMap.utils.plink_ldscore_tool")
 
 
 def getBlockLefts(coords, max_dist):
     """
-    Converts coordinates + max block length to the a list of coordinates of the leftmost
+    Converts coordinates + max block length to a list of coordinates of the leftmost
     SNPs to be included in blocks.
-
-    Parameters
-    ----------
-    coords : array
-        Array of coordinates. Must be sorted.
-    max_dist : float
-        Maximum distance between SNPs included in the same window.
-
-    Returns
-    -------
-    block_left : 1D np.ndarray with same length as block_left
-        block_left[j] :=  min{k | dist(j, k) < max_dist}.
     """
     M = len(coords)
     j = 0
@@ -77,16 +37,6 @@ def getBlockLefts(coords, max_dist):
 def block_left_to_right(block_left):
     """
     Converts block lefts to block rights.
-
-    Parameters
-    ----------
-    block_left : array
-        Array of block lefts.
-
-    Returns
-    -------
-    block_right : 1D np.ndarray with same length as block_left
-        block_right[j] := max {k | block_left[k] <= j}
     """
     M = len(block_left)
     j = 0
@@ -99,223 +49,149 @@ def block_left_to_right(block_left):
     return block_right
 
 
-class GenotypeArrayInMemory:
+class PlinkBEDFile:
     """
-    Parent class for various classes containing interfaces for files with genotype
-    matrices, e.g., plink .bed files, etc
+    Interface for Plink .bed format for reading and processing genotype data.
     """
 
-    def __init__(self, fname, n, snp_list, keep_snps=None, keep_indivs=None, mafMin=None):
-        self.m = len(snp_list.IDList)
-        self.n = n
-        self.keep_snps = keep_snps
-        self.keep_indivs = keep_indivs
-        self.df = np.array(snp_list.df[["CHR", "SNP", "BP", "CM"]])
-        self.colnames = ["CHR", "SNP", "BP", "CM"]
-        self.mafMin = mafMin if mafMin is not None else 0
-        self._currentSNP = 0
-        (self.nru, self.geno) = self.__read__(fname, self.m, n)
-        # filter individuals
-        if keep_indivs is not None:
-            keep_indivs = np.array(keep_indivs, dtype="int")
-            if np.any(keep_indivs > self.n):
-                raise ValueError("keep_indivs indices out of bounds")
-            # -
-            (self.geno, self.m, self.n) = self.__filter_indivs__(
-                self.geno, keep_indivs, self.m, self.n
-            )
-            # -
-            if self.n > 0:
-                print(f"After filtering, {self.n} individuals remain")
-            else:
-                raise ValueError("After filtering, no individuals remain")
-        # -
-        # filter SNPs
-        if keep_snps is not None:
-            keep_snps = np.array(keep_snps, dtype="int")
-            if np.any(keep_snps > self.m):  # if keep_snps is None, this returns False
-                raise ValueError("keep_snps indices out of bounds")
-        # -
-        (self.geno, self.m, self.n, self.kept_snps, self.freq) = self.__filter_snps_maf__(
-            self.geno, self.m, self.n, self.mafMin, keep_snps
+    def __init__(self, bfile_prefix):
+        """
+        Initialize the PlinkBEDFile from a PLINK file prefix.
+
+        Parameters
+        ----------
+        bfile_prefix : str
+            PLINK file prefix (without .bed/.bim/.fam extension)
+        """
+        # Initialize bitarray for bed code mapping
+        self._bedcode = {
+            2: ba.bitarray("11"),
+            9: ba.bitarray("10"),
+            1: ba.bitarray("01"),
+            0: ba.bitarray("00"),
+        }
+
+        # Load BIM file
+        self.bim_df = self.load_bim(f"{bfile_prefix}.bim")
+
+        # Load FAM file
+        self.fam_df = self.load_fam(f"{bfile_prefix}.fam")
+
+        # Set up initial parameters
+        self.m_original = len(self.bim_df)
+        self.n_original = len(self.fam_df)
+
+        # Read the bed file
+        logger.info(f"Loading Plink genotype data from {bfile_prefix}.bed")
+        (self.nru_original, self.geno_original) = self._read(
+            f"{bfile_prefix}.bed", self.m_original, self.n_original
         )
-        # -
-        if self.m > 0:
-            print(f"After filtering, {self.m} SNPs remain")
+
+        # Pre-calculate MAF for all SNPs
+        logger.info("Calculating MAF and QC for all SNPs")
+        self.all_snp_info = self._calculate_all_snp_info()
+
+        # Filter out invalid SNPs
+        valid_mask = self.all_snp_info["valid_snp"]
+        if num_invalid := np.sum(~valid_mask):
+            logger.warning(f"Filtering out {num_invalid} bad quality SNPs")
         else:
-            raise ValueError("After filtering, no SNPs remain")
-        # -
-        self.df = self.df[self.kept_snps, :]
-        self.maf = np.minimum(self.freq, np.ones(self.m) - self.freq)
-        self.sqrtpq = np.sqrt(self.freq * (np.ones(self.m) - self.freq))
-        self.df = np.c_[self.df, self.maf]
-        self.colnames.append("MAF")
-
-    # -
-    def __read__(self, fname, m, n):
-        raise NotImplementedError
-
-    def __restart__(self):
-        self._currentSNP = 0
+            logger.info("All SNPs passed the basic quality check")
 
-    # -
-    def __filter_indivs__(geno, keep_indivs, m, n):
-        raise NotImplementedError
+        # Only keep valid SNPs
+        self.kept_snps = np.arange(self.m_original)[valid_mask]
 
-    # -
-    def __filter_maf_(geno, m, n, maf):
-        raise NotImplementedError
+        # Update bim_df to only include valid SNPs and reset index
+        self.bim_df = self.bim_df.loc[valid_mask].reset_index(drop=True)
 
-    # -
-    def ldScoreVarBlocks(self, block_left, c, annot=None):
-        """Computes an unbiased estimate of L2(j) for j=1,..,M."""
+        # Create new genotype data with only the valid SNPs
+        new_geno = ba.bitarray()
+        for j in self.kept_snps:
+            new_geno += self.geno_original[
+                2 * self.nru_original * j : 2 * self.nru_original * (j + 1)
+            ]
 
-        def func(x):
-            return self.__l2_unbiased__(x, self.n)
+        # Update original data to only include valid SNPs
+        self.geno_original = new_geno
+        self.m_original = len(self.kept_snps)
 
-        snp_getter = self.nextSNPs
-        return self.__corSumVarBlocks__(block_left, c, func, snp_getter, annot)
+        # Initialize current state variables
+        self._currentSNP = 0
+        self.m = self.m_original
+        self.n = self.n_original
+        self.nru = self.nru_original
+        self.geno = self.geno_original.copy()
 
-    # -
-    # In small samples, the observed r^2 tends to be higher than the true r^2 due to sampling variability.
-    # The bias correction term (1-sq) / denom adjusts for this bias by subtracting a small value that depends on the sample size and the observed r^2.
-    def __l2_unbiased__(self, x, n):
-        denom = n - 2 if n > 2 else n  # allow n<2 for testing purposes
-        sq = np.square(x)
-        return sq - (1 - sq) / denom
+        # Update frequency info based on valid SNPs
+        self.freq = self.all_snp_info["freq"][valid_mask]
+        self.maf = np.minimum(self.freq, 1 - self.freq)
+        self.sqrtpq = np.sqrt(self.freq * (1 - self.freq))
 
-    # -
-    # Methods for calculating sums of Pearson correlation coefficients (i.e.,ld-score)
-    # c stands for the chunk size (default = 50)
-    def __corSumVarBlocks__(self, block_left, c, func, snp_getter, annot=None):
+        # Add MAF to the BIM dataframe
+        self.bim_df["MAF"] = self.maf
+
+        logger.info(f"Loaded genotype data with {self.m} SNPs and {self.n} individuals")
+
+    @staticmethod
+    def load_bim(bim_file):
         """
+        Load a BIM file into a pandas DataFrame.
+
         Parameters
         ----------
-        block_left : np.ndarray with shape (M, )
-            block_left[i] = index of leftmost SNP included in LD Score of SNP i.
-            if c > 1, then only entries that are multiples of c are examined, and it is
-            assumed that block_left[a*c+i] = block_left[a*c], except at
-            the beginning of the chromosome where the 0th SNP is included in the window.
-        c : int
-            Chunk size.
-        func : function
-            Function to be applied to the genotype correlation matrix. Before dotting with
-            annot. Examples: for biased L2, np.square. For biased L4,
-            lambda x: np.square(np.square(x)). For L1, lambda x: x.
-        snp_getter : function(int)
-            The method to be used to get the next SNPs
-        annot: numpy array with shape (m,n_a)
-            SNP annotations.
+        bim_file : str
+            Path to the BIM file
 
         Returns
         -------
-        cor_sum : np.ndarray with shape (M, num_annots)
-            Estimates.
+        pd.DataFrame
+            DataFrame containing BIM data
         """
-        m, n = self.m, self.n
-        block_sizes = np.array(np.arange(m) - block_left)
-        block_sizes = np.ceil(block_sizes / c) * c
-        if annot is None:
-            annot = np.ones((m, 1))
-        else:
-            annot_m = annot.shape[0]
-            if annot_m != self.m:
-                raise ValueError("Incorrect number of SNPs in annot")
-        # -
-        n_a = annot.shape[1]  # number of annotations
-        cor_sum = np.zeros((m, n_a))
-        # b = index of first SNP for which SNP 0 is not included in LD Score
-        b = np.nonzero(block_left > 0)
-        if np.any(b):
-            b = b[0][0]
-        else:
-            b = m
-        b = int(np.ceil(b / c) * c)  # round up to a multiple of c
-        if b > m:
-            c = 1
-            b = m
+        df = pd.read_csv(
+            bim_file, sep="\t", header=None, names=["CHR", "SNP", "CM", "BP", "A1", "A2"]
+        )
+        return df
 
-        l_A = 0  # l_A := index of leftmost SNP in matrix A
-        A = snp_getter(b)
-        rfuncAB = np.zeros((b, c))
-        rfuncBB = np.zeros((c, c))
-        # chunk inside of block
-        for l_B in np.arange(0, b, c):  # l_B := index of leftmost SNP in matrix B
-            B = A[:, l_B : l_B + c]
-            # ld matrix
-            np.dot(A.T, B / n, out=rfuncAB)
-            # ld matrix square
-            rfuncAB = func(rfuncAB)
-            cor_sum[l_A : l_A + b, :] += np.dot(rfuncAB, annot[l_B : l_B + c, :])
+    @staticmethod
+    def convert_bim_to_pyrange(bim_df) -> pr.PyRanges:
+        bim_pr = bim_df.copy()
+        bim_pr.drop(columns=["MAF"], inplace=True)
+        bim_pr.columns = ["Chromosome", "SNP", "CM", "Start", "A1", "A2"]
+        bim_pr.Chromosome = "chr" + bim_pr["Chromosome"].astype(str)
 
-        # chunk to right of block
-        b0 = b
-        md = int(c * np.floor(m / c))
-        end = md + 1 if md != m else md
-        for l_B in tqdm(np.arange(b0, end, c), desc="Compute SNP Gene Weight"):
-            # check if the annot matrix is all zeros for this block + chunk
-            # this happens w/ sparse categories (i.e., pathways)
-            # update the block
-            old_b = b
-            b = int(block_sizes[l_B])
-            if l_B > b0 and b > 0:
-                # block_size can't increase more than c
-                # block_size can't be less than c unless it is zero
-                # both of these things make sense
-                A = np.hstack((A[:, old_b - b + c : old_b], B))
-                l_A += old_b - b + c
-            elif l_B == b0 and b > 0:
-                A = A[:, b0 - b : b0]
-                l_A = b0 - b
-            elif b == 0:  # no SNPs to left in window, e.g., after a sequence gap
-                A = np.array(()).reshape((n, 0))
-                l_A = l_B
-            if l_B == md:
-                c = m - md
-                rfuncAB = np.zeros((b, c))
-                rfuncBB = np.zeros((c, c))
-            if b != old_b:
-                rfuncAB = np.zeros((b, c))
-            # -
-            B = snp_getter(c)
-            p1 = np.all(annot[l_A : l_A + b, :] == 0)
-            p2 = np.all(annot[l_B : l_B + c, :] == 0)
-            if p1 and p2:
-                continue
-            # -
-            np.dot(A.T, B / n, out=rfuncAB)
-            rfuncAB = func(rfuncAB)
-            cor_sum[l_A : l_A + b, :] += np.dot(rfuncAB, annot[l_B : l_B + c, :])
-            cor_sum[l_B : l_B + c, :] += np.dot(annot[l_A : l_A + b, :].T, rfuncAB).T
-            np.dot(B.T, B / n, out=rfuncBB)
-            rfuncBB = func(rfuncBB)
-            cor_sum[l_B : l_B + c, :] += np.dot(rfuncBB, annot[l_B : l_B + c, :])
-        # -
-        return cor_sum
+        # Adjust coordinates (BIM is 1-based, PyRanges uses 0-based)
+        bim_pr["End"] = bim_pr["Start"].copy()
+        bim_pr["Start"] = bim_pr["Start"] - 1
 
+        bim_pr = pr.PyRanges(bim_pr)
 
-class PlinkBEDFile(GenotypeArrayInMemory):
-    """
-    Interface for Plink .bed format
-    """
+        return bim_pr
 
-    def __init__(self, fname, n, snp_list, keep_snps=None, keep_indivs=None, mafMin=None):
-        self._bedcode = {
-            2: ba.bitarray("11"),
-            9: ba.bitarray("10"),
-            1: ba.bitarray("01"),
-            0: ba.bitarray("00"),
-        }
-        # -
-        GenotypeArrayInMemory.__init__(
-            self, fname, n, snp_list, keep_snps=keep_snps, keep_indivs=keep_indivs, mafMin=mafMin
-        )
+    @staticmethod
+    def load_fam(fam_file):
+        """
+        Load a FAM file into a pandas DataFrame.
+
+        Parameters
+        ----------
+        fam_file : str
+            Path to the FAM file
+
+        Returns
+        -------
+        pd.DataFrame
+            DataFrame containing FAM data
+        """
+        df = pd.read_csv(fam_file, sep=r"\s+", header=None, usecols=[1], names=["IID"])
+        return df
 
-    # -
-    def __read__(self, fname, m, n):
+    def _read(self, fname, m, n):
+        """
+        Read the bed file and return the genotype data.
+        """
         if not fname.endswith(".bed"):
             raise ValueError(".bed filename must end in .bed")
-        # -
+
         fh = open(fname, "rb")
         magicNumber = ba.bitarray(endian="little")
         magicNumber.fromfile(fh, 2)
@@ -323,29 +199,150 @@ class PlinkBEDFile(GenotypeArrayInMemory):
         bedMode.fromfile(fh, 1)
         e = (4 - n % 4) if n % 4 != 0 else 0
         nru = n + e
-        self.nru = nru
-        # check magic number
+
+        # Check magic number
         if magicNumber != ba.bitarray("0011011011011000"):
             raise OSError("Magic number from Plink .bed file not recognized")
-        # -
+
         if bedMode != ba.bitarray("10000000"):
             raise OSError("Plink .bed file must be in default SNP-major mode")
-        # check file length
-        self.geno = ba.bitarray(endian="little")
-        self.geno.fromfile(fh)
-        self.__test_length__(self.geno, self.m, self.nru)
-        return (self.nru, self.geno)
-
-    # -
-    def __test_length__(self, geno, m, nru):
+
+        # Check file length
+        geno = ba.bitarray(endian="little")
+        geno.fromfile(fh)
+        self._test_length(geno, m, nru)
+        return (nru, geno)
+
+    def _test_length(self, geno, m, nru):
+        """
+        Test if the genotype data has the expected length.
+        """
         exp_len = 2 * m * nru
         real_len = len(geno)
         if real_len != exp_len:
             s = "Plink .bed file has {n1} bits, expected {n2}"
             raise OSError(s.format(n1=real_len, n2=exp_len))
 
-    # -
-    def __filter_indivs__(self, geno, keep_indivs, m, n):
+    def _calculate_all_snp_info(self):
+        """
+        Pre-calculate MAF and other information for all SNPs.
+
+        Returns
+        -------
+        dict
+            Dictionary containing information for all SNPs
+        """
+        nru = self.nru_original
+        n = self.n_original
+        m = self.m_original
+        geno = self.geno_original
+
+        snp_info = {
+            "freq": np.zeros(m),  # Allele frequencies
+            "het_miss_count": np.zeros(m),  # Count of het or missing genotypes
+            "valid_snp": np.zeros(m, dtype=bool),  # Whether SNP passes basic criteria
+        }
+
+        # For each SNP, calculate statistics
+        for j in range(m):
+            z = geno[2 * nru * j : 2 * nru * (j + 1)]
+            A = z[0::2]
+            a = A.count()
+            B = z[1::2]
+            b = B.count()
+            c = (A & B).count()
+            major_ct = b + c  # number of copies of the major allele
+            n_nomiss = n - a + c  # number of individuals with nonmissing genotypes
+            f = major_ct / (2 * n_nomiss) if n_nomiss > 0 else 0
+            het_miss_ct = a + b - 2 * c  # count of SNPs that are het or missing
+
+            snp_info["freq"][j] = f
+            snp_info["het_miss_count"][j] = het_miss_ct
+            snp_info["valid_snp"][j] = het_miss_ct < n  # Basic validity check
+
+        return snp_info
+
+    def apply_filters(self, keep_snps=None, keep_indivs=None, mafMin=None):
+        """
+        Apply filters to the genotype data without reloading the bed file.
+
+        Parameters
+        ----------
+        keep_snps : array-like, optional
+            Indices of SNPs to keep.
+        keep_indivs : array-like, optional
+            Indices of individuals to keep.
+        mafMin : float, optional
+            Minimum minor allele frequency.
+
+        Returns
+        -------
+        self
+            Returns self for method chaining.
+        """
+        # Reset to original state first
+        self.geno = self.geno_original.copy()
+        self.m = self.m_original
+        self.n = self.n_original
+        self.nru = self.nru_original
+        self._currentSNP = 0
+
+        # Initialize with all SNPs
+        kept_snps = np.arange(self.m_original)
+
+        # Apply MAF filter using pre-calculated values
+        if mafMin is not None and mafMin > 0:
+            maf_values = np.minimum(self.all_snp_info["freq"], 1 - self.all_snp_info["freq"])
+            maf_mask = (maf_values > mafMin) & self.all_snp_info["valid_snp"]
+            kept_snps = kept_snps[maf_mask]
+            logger.info(f"After MAF filtering (>{mafMin}), {len(kept_snps)} SNPs remain")
+
+        # Apply SNP filter if specified
+        if keep_snps is not None:
+            keep_snps = np.array(keep_snps, dtype="int")
+            if np.any(keep_snps > self.m_original):
+                raise ValueError("keep_snps indices out of bounds")
+
+            # Intersect with current kept_snps
+            kept_snps = np.intersect1d(kept_snps, keep_snps)
+            logger.info(f"After keep_snps filtering, {len(kept_snps)} SNPs remain")
+
+        # Filter SNPs in the genotype data
+        if len(kept_snps) < self.m_original:
+            # Create new genotype data with only the kept SNPs
+            new_geno = ba.bitarray()
+            for j in kept_snps:
+                new_geno += self.geno_original[2 * self.nru * j : 2 * self.nru * (j + 1)]
+            self.geno = new_geno
+            self.m = len(kept_snps)
+
+        # Filter individuals if specified
+        if keep_indivs is not None:
+            keep_indivs = np.array(keep_indivs, dtype="int")
+            if np.any(keep_indivs > self.n):
+                raise ValueError("keep_indivs indices out of bounds")
+
+            (self.geno, self.m, self.n) = self._filter_indivs(
+                self.geno, keep_indivs, self.m, self.n
+            )
+
+            if self.n > 0:
+                logger.info(f"After filtering, {self.n} individuals remain")
+            else:
+                raise ValueError("After filtering, no individuals remain")
+
+        # Update kept_snps and other attributes
+        self.kept_snps = kept_snps
+        self.freq = self.all_snp_info["freq"][kept_snps]
+        self.maf = np.minimum(self.freq, 1 - self.freq)
+        self.sqrtpq = np.sqrt(self.freq * (1 - self.freq))
+
+        return self
+
+    def _filter_indivs(self, geno, keep_indivs, m, n):
+        """
+        Filter individuals based on the keep_indivs parameter.
+        """
         n_new = len(keep_indivs)
         e = (4 - n_new % 4) if n_new % 4 != 0 else 0
         nru_new = n_new + e
@@ -358,95 +355,120 @@ class PlinkBEDFile(GenotypeArrayInMemory):
         self.nru = nru_new
         return (z, m, n_new)
 
-    # -
-    def __filter_snps_maf__(self, geno, m, n, mafMin, keep_snps):
+    def get_snps_by_maf(self, mafMin):
         """
-        Credit to Chris Chang and the Plink2 developers for this algorithm
-        Modified from plink_filter.c
-        https://github.com/chrchang/plink-ng/blob/master/plink_filter.c
-        Genotypes are read forwards (since we are cheating and using endian="little")
-        A := (genotype) & 1010...
-        B := (genotype) & 0101...
-        C := (A >> 1) & B
-        Then
-        a := A.count() = missing ct + hom major ct
-        b := B.count() = het ct + hom major ct
-        c := C.count() = hom major ct
-        Which implies that
-        missing ct = a - c
-        # of indivs with nonmissing genotype = n - a + c
-        major allele ct = b + c
-        major allele frequency = (b+c)/(2*(n-a+c))
-        het ct + missing ct = a + b - 2*c
-        Why does bitarray not have >> ????
+        Get the list of SNPs that pass the MAF threshold.
+
+        Parameters
+        ----------
+        mafMin : float
+            Minimum MAF threshold
+
+        Returns
+        -------
+        list
+            List of SNP IDs that pass the MAF threshold
         """
-        nru = self.nru
-        m_poly = 0
-        y = ba.bitarray()
-        if keep_snps is None:
-            keep_snps = range(m)
-        kept_snps = []
-        freq = []
-        for e, j in enumerate(keep_snps):
-            z = geno[2 * nru * j : 2 * nru * (j + 1)]
-            A = z[0::2]
-            a = A.count()
-            B = z[1::2]
-            b = B.count()
-            c = (A & B).count()
-            major_ct = b + c  # number of copies of the major allele
-            n_nomiss = n - a + c  # number of individuals with nonmissing genotypes
-            f = major_ct / (2 * n_nomiss) if n_nomiss > 0 else 0
-            het_miss_ct = a + b - 2 * c  # remove SNPs that are only either het or missing
-            if np.minimum(f, 1 - f) > mafMin and het_miss_ct < n:
-                freq.append(f)
-                y += z
-                m_poly += 1
-                kept_snps.append(j)
-        # -
-        return (y, m_poly, n, kept_snps, freq)
-
-    # -
-    def nextSNPs(self, b, minorRef=None):
+        # Use the pre-calculated MAF values
+        maf_values = np.minimum(self.all_snp_info["freq"], 1 - self.all_snp_info["freq"])
+        maf_mask = (maf_values > mafMin) & self.all_snp_info["valid_snp"]
+
+        # Get SNP names from the BIM dataframe
+        snp_pass_maf = self.bim_df.loc[maf_mask, "SNP"].tolist()
+
+        logger.info(f"{len(snp_pass_maf)} SNPs with MAF > f{mafMin}")
+
+        return snp_pass_maf
+
+    def get_ldscore(self, annot_matrix=None, ld_wind=1.0, ld_unit="CM", keep_snps_index=None):
         """
-        Unpacks the binary array of genotypes and returns an n x b matrix of floats of
-        normalized genotypes for the next b SNPs, where n := number of samples.
+        Calculate LD scores using an annotation matrix.
 
         Parameters
         ----------
-        b : int
-            Number of SNPs to return.
-        minorRef: bool, default None
-            Should we flip reference alleles so that the minor allele is the reference?
-            (This is useful for computing l1 w.r.t. minor allele).
+        annot_matrix : np.ndarray, optional
+            Annotation matrix. If None, uses a matrix of all ones.
+        ld_wind : float, optional
+            LD window size, by default 1.0
+        ld_unit : str, optional
+            Unit for the LD window, by default "CM"
+        keep_snps_index : list[int], optional
+            Indices of SNPs to keep, by default None
 
         Returns
         -------
-        X : np.array with dtype float64 with shape (n, b), where n := number of samples
-            Matrix of genotypes normalized to mean zero and variance one. If minorRef is
-            not None, then the minor allele will be the positive allele (i.e., two copies
-            of the minor allele --> a positive number).
+        np.ndarray
+            Array with calculated LD scores
+        """
+        # Apply filters if needed
+        if keep_snps_index is not None:
+            original_kept_snps = self.kept_snps.copy()
+            self.apply_filters(keep_snps=keep_snps_index)
+
+        # Configure LD window based on specified unit
+        if ld_unit == "SNP":
+            max_dist = ld_wind
+            coords = np.array(range(self.m))
+        elif ld_unit == "KB":
+            max_dist = ld_wind * 1000
+            coords = np.array(self.bim_df.loc[self.kept_snps, "BP"])
+        elif ld_unit == "CM":
+            max_dist = ld_wind
+            coords = np.array(self.bim_df.loc[self.kept_snps, "CM"])
+            # Check if the CM is all 0
+            if np.all(coords == 0):
+                logger.warning(
+                    "All CM values are 0. Using 1MB window size for LD score calculation."
+                )
+                max_dist = 1_000_000
+                coords = np.array(self.bim_df.loc[self.kept_snps, "BP"])
+        else:
+            raise ValueError(f"Invalid ld_wind_unit: {ld_unit}. Must be one of: SNP, KB, CM")
+
+        # Calculate blocks for LD computation
+        block_left = getBlockLefts(coords, max_dist)
+        assert block_left.sum() > 0, "Invalid window size, please check the ld_wind parameter."
+
+        # Calculate LD scores
+        ld_scores = self.ldScoreVarBlocks(block_left, 100, annot=annot_matrix)
+
+        # Restore original state if filters were applied
+        if keep_snps_index is not None:
+            self.apply_filters(keep_snps=original_kept_snps)
+
+        return ld_scores
+
+    def restart(self):
+        """
+        Reset the current SNP index to 0.
+        """
+        self._currentSNP = 0
+
+    def nextSNPs(self, b, minorRef=None):
+        """
+        Unpacks the binary array of genotypes and returns an n x b matrix of floats of
+        normalized genotypes for the next b SNPs.
         """
-        # -
         try:
             b = int(b)
             if b <= 0:
                 raise ValueError("b must be > 0")
         except TypeError as e:
             raise TypeError("b must be an integer") from e
-        # -
+
         if self._currentSNP + b > self.m:
             s = "{b} SNPs requested, {k} SNPs remain"
             raise ValueError(s.format(b=b, k=(self.m - self._currentSNP)))
-        # -
+
         c = self._currentSNP
         n = self.n
         nru = self.nru
         slice = self.geno[2 * c * nru : 2 * (c + b) * nru]
-        X = np.array(slice.decode(self._bedcode), dtype="float64").reshape((b, nru)).T
+        X = np.array(slice.decode(self._bedcode), dtype="float32").reshape((b, nru)).T
         X = X[0:n, :]
-        Y = np.zeros(X.shape)
-        # normalize the SNPs and impute the missing one with the mean
+        Y = np.zeros(X.shape, dtype="float32")
+
+        # Normalize the SNPs and impute the missing ones with the mean
         for j in range(0, b):
             newsnp = X[:, j]
             ii = newsnp != 9
@@ -455,35 +477,116 @@ class PlinkBEDFile(GenotypeArrayInMemory):
             denom = np.std(newsnp)
             if denom == 0:
                 denom = 1
-            # -
+
             if minorRef is not None and self.freq[self._currentSNP + j] > 0.5:
                 denom = denom * -1
-            # -
+
             Y[:, j] = (newsnp - avg) / denom
-        # -
+
         self._currentSNP += b
         return Y
 
+    def _l2_unbiased(self, x, n):
+        """
+        Calculate the unbiased estimate of L2.
+        """
+        denom = n - 2 if n > 2 else n  # allow n<2 for testing purposes
+        sq = np.square(x)
+        return sq - (1 - sq) / denom
+
+    def ldScoreVarBlocks(self, block_left, c, annot=None):
+        """
+        Computes an unbiased estimate of L2(j) for j=1,..,M.
+        """
 
-def load_bfile(bfile_chr_prefix, keep_snps=None, keep_indivs=None, mafMin=None):
-    PlinkBIMFile = ID_List_Factory(
-        ["CHR", "SNP", "CM", "BP", "A1", "A2"], 1, ".bim", usecols=[0, 1, 2, 3, 4, 5]
-    )
-    PlinkFAMFile = ID_List_Factory(["IID"], 0, ".fam", usecols=[1])
+        def func(x):
+            return self._l2_unbiased(x, self.n)
 
-    snp_file = bfile_chr_prefix + ".bim"
-    array_snps = PlinkBIMFile(snp_file)
+        snp_getter = self.nextSNPs
+        return self._corSumVarBlocks(block_left, c, func, snp_getter, annot)
 
-    # Load fam
-    ind_file = bfile_chr_prefix + ".fam"
-    array_indivs = PlinkFAMFile(ind_file)
+    def _corSumVarBlocks(self, block_left, c, func, snp_getter, annot=None):
+        """
+        Calculate the sum of correlation coefficients.
+        """
+        m, n = self.m, self.n
+        block_sizes = np.array(np.arange(m) - block_left)
+        block_sizes = np.ceil(block_sizes / c) * c
+        if annot is None:
+            annot = np.ones((m, 1), dtype="float32")
+        else:
+            # annot = annot.astype("float32")  # Ensure annot is float32
+            annot_m = annot.shape[0]
+            if annot_m != self.m:
+                raise ValueError("Incorrect number of SNPs in annot")
 
-    n = len(array_indivs.IDList)
+        n_a = annot.shape[1]  # number of annotations
+        cor_sum = np.zeros((m, n_a), dtype="float32")
+        # b = index of first SNP for which SNP 0 is not included in LD Score
+        b = np.nonzero(block_left > 0)
+        if np.any(b):
+            b = b[0][0]
+        else:
+            b = m
+        b = int(np.ceil(b / c) * c)  # round up to a multiple of c
+        if b > m:
+            c = 1
+            b = m
 
-    # Load genotype array
-    array_file = bfile_chr_prefix + ".bed"
-    geno_array = PlinkBEDFile(
-        array_file, n, array_snps, keep_snps=keep_snps, keep_indivs=keep_indivs, mafMin=mafMin
-    )
+        l_A = 0  # l_A := index of leftmost SNP in matrix A
+        A = snp_getter(b)  # This now returns float32 data
+        rfuncAB = np.zeros((b, c), dtype="float32")
+        rfuncBB = np.zeros((c, c), dtype="float32")
+        # chunk inside of block
+        for l_B in np.arange(0, b, c):  # l_B := index of leftmost SNP in matrix B
+            B = A[:, l_B : l_B + c]
+            # ld matrix
+            np.dot(A.T, B / n, out=rfuncAB)
+            # ld matrix square
+            rfuncAB = func(rfuncAB)
+            cor_sum[l_A : l_A + b, :] += np.dot(rfuncAB, annot[l_B : l_B + c, :])
 
-    return array_snps, array_indivs, geno_array
+        # chunk to right of block
+        b0 = b
+        md = int(c * np.floor(m / c))
+        end = md + 1 if md != m else md
+        for l_B in tqdm(np.arange(b0, end, c), desc="Compute SNP Gene Weight"):
+            # check if the annot matrix is all zeros for this block + chunk
+            # this happens w/ sparse categories (i.e., pathways)
+            # update the block
+            old_b = b
+            b = int(block_sizes[l_B])
+            if l_B > b0 and b > 0:
+                # block_size can't increase more than c
+                # block_size can't be less than c unless it is zero
+                # both of these things make sense
+                A = np.hstack((A[:, old_b - b + c : old_b], B))
+                l_A += old_b - b + c
+            elif l_B == b0 and b > 0:
+                A = A[:, b0 - b : b0]
+                l_A = b0 - b
+            elif b == 0:  # no SNPs to left in window, e.g., after a sequence gap
+                A = np.array((), dtype="float32").reshape((n, 0))
+                l_A = l_B
+            if l_B == md:
+                c = m - md
+                rfuncAB = np.zeros((b, c), dtype="float32")
+                rfuncBB = np.zeros((c, c), dtype="float32")
+            if b != old_b:
+                rfuncAB = np.zeros((b, c), dtype="float32")
+
+            B = snp_getter(c)  # This now returns float32 data
+            p1 = np.all(annot[l_A : l_A + b, :] == 0)
+            p2 = np.all(annot[l_B : l_B + c, :] == 0)
+            if p1 and p2:
+                continue
+
+            np.dot(A.T, B / n, out=rfuncAB)
+            rfuncAB = func(rfuncAB)
+            cor_sum[l_A : l_A + b, :] += np.dot(rfuncAB, annot[l_B : l_B + c, :])
+            cor_sum[l_B : l_B + c, :] += np.dot(annot[l_A : l_A + b, :].T, rfuncAB).T
+            np.dot(B.T, B / n, out=rfuncBB)
+            rfuncBB = func(rfuncBB)
+            cor_sum[l_B : l_B + c, :] += np.dot(rfuncBB, annot[l_B : l_B + c, :])
+
+        return cor_sum