diff --git a/tangermeme/tools/tomtom.py b/tangermeme/tools/tomtom.py index e2dea62..5c029be 100644 --- a/tangermeme/tools/tomtom.py +++ b/tangermeme/tools/tomtom.py @@ -11,8 +11,7 @@ from numpy import uint64 -@njit("float64(float64[:], float64[:, :], float64, float64, int64[:])", - cache=True) +@njit("float64(float64[:], float64[:, :], float64, float64, int64[:])") def _binned_median(x, bins, x_min, x_max, counts): """An internal function for calculating medians quickly. @@ -52,7 +51,7 @@ def _binned_median(x, bins, x_min, x_max, counts): @njit('''uint64(float64[:, :], float64[:, :], int32[:, :], float64[:, :], float64[:, :], float64[:], float64[:, :], float64[:], float64[:], int64[:], - int64, int64, int64)''', cache=True) + int64, int64, int64)''') def _integer_distances_and_histogram(X, Y, gamma, f, Z, medians, median_bins, X_norm, Y_norm, Y_counts, nq_csum, nq, n_bins): """An internal function for integerized scores and the histogram. @@ -114,7 +113,7 @@ def _integer_distances_and_histogram(X, Y, gamma, f, Z, medians, median_bins, return uint64(-i_min * bin_scale) -@njit('void(float64[:], float64[:], float64[:], float64[:], int64)', cache=True) +@njit('void(float64[:], float64[:], float64[:], float64[:], int64)') def _pairwise_max(x, y, y_csum, z, n): """An internal function for the pdf of the maximum of two pdfs. @@ -140,7 +139,7 @@ def _pairwise_max(x, y, y_csum, z, n): @njit('''void(float64[:, :], float64[:, :, :], float64[:, :], float64[:, :, :], - int64, int64, int64, uint64)''', cache=True) + int64, int64, int64, uint64)''') def _p_value_backgrounds(f, A, B, A_csum, nq, n_bins, t_max, offset): """An internal function that calculates the backgrounds for p-values. @@ -215,7 +214,7 @@ def _p_value_backgrounds(f, A, B, A_csum, nq, n_bins, t_max, offset): @njit('''void(int32[:, :], float64[:, :], uint64[:], int64[:], int64, uint64, - int64, float64[:, :])''', cache=True) + int64, float64[:, :])''') def _p_values(gamma, B_cdfs, rr_inv, T_lens, nq, offset, n_bins, results): """An internal function for calculating the best match and p-values. @@ -262,7 +261,7 @@ def _p_values(gamma, B_cdfs, rr_inv, T_lens, nq, offset, n_bins, results): total_offset += nt -@njit('void(float64[:, :])', cache=True) +@njit('void(float64[:, :])') def _merge_rc_results(results): """An internal method for taking the best across two strands."""