/dports/biology/py-macs2/MACS-2.2.7.1/MACS2/IO/ |
H A D | PeakIO.c | 5662 __Pyx_XDECREF(__pyx_v_peaks); in __pyx_pf_5MACS2_2IO_6PeakIO_6PeakIO_12filter_pscore() 5926 __Pyx_XDECREF(__pyx_v_peaks); in __pyx_pf_5MACS2_2IO_6PeakIO_6PeakIO_14filter_qscore() 6371 __Pyx_XDECREF(__pyx_v_peaks); in __pyx_pf_5MACS2_2IO_6PeakIO_6PeakIO_16filter_fc() 6551 __Pyx_XDECREF(__pyx_v_peaks); in __pyx_pf_5MACS2_2IO_6PeakIO_6PeakIO_18total() 7997 __Pyx_XDECREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_6PeakIO_6PeakIO__to_xls() 8958 __Pyx_XDECREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_6PeakIO_6PeakIO__to_bed() 9931 __Pyx_XDECREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_6PeakIO_6PeakIO__to_summits_bed() 18881 PyObject *__pyx_v_peaks = 0; in __pyx_pf_5MACS2_2IO_6PeakIO_11BroadPeakIO_4filter_pscore() local 19146 PyObject *__pyx_v_peaks = 0; in __pyx_pf_5MACS2_2IO_6PeakIO_11BroadPeakIO_6filter_qscore() local 19454 PyObject *__pyx_v_peaks = 0; in __pyx_pf_5MACS2_2IO_6PeakIO_11BroadPeakIO_8filter_fc() local [all …]
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H A D | CallPeakUnitPrecompiled.c | 12396 __pyx_v_peaks = __pyx_t_1; in __pyx_f_5MACS2_2IO_23CallPeakUnitPrecompiled_28CallerFromPrecompiledPileups_call_peaks() 13035 __Pyx_INCREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_23CallPeakUnitPrecompiled_28CallerFromPrecompiledPileups_call_peaks() 13036 __pyx_r = __pyx_v_peaks; in __pyx_f_5MACS2_2IO_23CallPeakUnitPrecompiled_28CallerFromPrecompiledPileups_call_peaks() 13061 __Pyx_XDECREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_23CallPeakUnitPrecompiled_28CallerFromPrecompiledPileups_call_peaks() 13895 __Pyx_INCREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_23CallPeakUnitPrecompiled_28CallerFromPrecompiledPileups___chrom_call_peak_using_certain_criteria() 13896 __pyx_r = __pyx_v_peaks; in __pyx_f_5MACS2_2IO_23CallPeakUnitPrecompiled_28CallerFromPrecompiledPileups___chrom_call_peak_using_certain_criteria() 14398 __pyx_r = __pyx_v_peaks; in __pyx_f_5MACS2_2IO_23CallPeakUnitPrecompiled_28CallerFromPrecompiledPileups___chrom_call_peak_using_certain_criteria() 14469 __Pyx_INCREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_23CallPeakUnitPrecompiled_28CallerFromPrecompiledPileups___chrom_call_peak_using_certain_criteria() 14470 __pyx_r = __pyx_v_peaks; in __pyx_f_5MACS2_2IO_23CallPeakUnitPrecompiled_28CallerFromPrecompiledPileups___chrom_call_peak_using_certain_criteria() 24992 PyObject *__pyx_v_peaks = 0; in __pyx_pw_5MACS2_2IO_23CallPeakUnitPrecompiled_28CallerFromPrecompiledPileups_13refine_peak_from_tags_distribution() local [all …]
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H A D | FixWidthTrack.c | 12253 __Pyx_INCREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_compute_region_tags_from_peaks() 12254 __Pyx_GIVEREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_compute_region_tags_from_peaks() 12255 PyTuple_SET_ITEM(__pyx_t_8, 0+__pyx_t_7, __pyx_v_peaks); in __pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_compute_region_tags_from_peaks() 13260 PyObject *__pyx_v_peaks = 0; in __pyx_pw_5MACS2_2IO_13FixWidthTrack_7FWTrack_33compute_region_tags_from_peaks() local 13324 __pyx_v_peaks = values[0]; in __pyx_pw_5MACS2_2IO_13FixWidthTrack_7FWTrack_33compute_region_tags_from_peaks() 13537 PyObject *__pyx_temp[4] = {__pyx_t_6, __pyx_v_peaks, __pyx_t_3, __pyx_t_4}; in __pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_refine_peak_from_tags_distribution() 13561 __Pyx_INCREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_refine_peak_from_tags_distribution() 13562 __Pyx_GIVEREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_refine_peak_from_tags_distribution() 13563 PyTuple_SET_ITEM(__pyx_t_8, 0+__pyx_t_7, __pyx_v_peaks); in __pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_refine_peak_from_tags_distribution() 14818 PyObject *__pyx_v_peaks = 0; in __pyx_pw_5MACS2_2IO_13FixWidthTrack_7FWTrack_35refine_peak_from_tags_distribution() local [all …]
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H A D | CallPeakUnit.c | 13259 PyObject *__pyx_v_peaks = NULL; in __pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_peaks() local 13424 __pyx_v_peaks = __pyx_t_1; in __pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_peaks() 14080 __Pyx_INCREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_peaks() 14081 __pyx_r = __pyx_v_peaks; in __pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_peaks() 14106 __Pyx_XDECREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_peaks() 24872 PyObject *__pyx_temp[4] = {__pyx_t_6, __pyx_v_peaks, __pyx_t_3, __pyx_t_4}; in __pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine_peak_from_tags_distribution() 24896 __Pyx_INCREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine_peak_from_tags_distribution() 24897 __Pyx_GIVEREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine_peak_from_tags_distribution() 24898 PyTuple_SET_ITEM(__pyx_t_8, 0+__pyx_t_7, __pyx_v_peaks); in __pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine_peak_from_tags_distribution() 26111 PyObject *__pyx_v_peaks = 0; in __pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_13refine_peak_from_tags_distribution() local [all …]
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H A D | BedGraph.c | 7567 PyObject *__pyx_v_peaks = NULL; in __pyx_pf_5MACS2_2IO_8BedGraph_14bedGraphTrackI_24call_peaks() local 7648 __pyx_v_peaks = __pyx_t_1; in __pyx_pf_5MACS2_2IO_8BedGraph_14bedGraphTrackI_24call_peaks() 8295 __Pyx_INCREF(__pyx_v_peaks); in __pyx_pf_5MACS2_2IO_8BedGraph_14bedGraphTrackI_24call_peaks() 8296 __Pyx_GIVEREF(__pyx_v_peaks); in __pyx_pf_5MACS2_2IO_8BedGraph_14bedGraphTrackI_24call_peaks() 8434 __Pyx_INCREF(__pyx_v_peaks); in __pyx_pf_5MACS2_2IO_8BedGraph_14bedGraphTrackI_24call_peaks() 8435 __Pyx_GIVEREF(__pyx_v_peaks); in __pyx_pf_5MACS2_2IO_8BedGraph_14bedGraphTrackI_24call_peaks() 8461 __Pyx_INCREF(__pyx_v_peaks); in __pyx_pf_5MACS2_2IO_8BedGraph_14bedGraphTrackI_24call_peaks() 8462 __pyx_r = __pyx_v_peaks; in __pyx_pf_5MACS2_2IO_8BedGraph_14bedGraphTrackI_24call_peaks() 8487 __Pyx_XDECREF(__pyx_v_peaks); in __pyx_pf_5MACS2_2IO_8BedGraph_14bedGraphTrackI_24call_peaks() 8511 PyObject *__pyx_v_peaks = 0; in __pyx_pw_5MACS2_2IO_8BedGraph_14bedGraphTrackI_27__close_peak() local [all …]
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H A D | ScoreTrack.c | 16635 PyObject *__pyx_v_peaks = NULL; in __pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_peaks() local 16805 __pyx_v_peaks = __pyx_t_1; in __pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_peaks() 17441 __Pyx_INCREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_peaks() 17442 __pyx_r = __pyx_v_peaks; in __pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_peaks() 17478 __Pyx_XDECREF(__pyx_v_peaks); in __pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_peaks() 18077 …__pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_add); if (unlikely(!__pyx_t_3)) __P… in __pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak() 18924 …->__pyx_vtab)->__pyx___close_peak(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_l… in __pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak2() 19213 …->__pyx_vtab)->__pyx___close_peak(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_l… in __pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak2() 19527 …__pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_add); if (unlikely(!__pyx_t_6)) __P… in __pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak2() 28600 …__pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_add); if (unlikely(!__pyx_t_9)) __P… in __pyx_f_5MACS2_2IO_10ScoreTrack_18TwoConditionScores___add_a_peak() [all …]
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/dports/biology/py-macs2/MACS-2.2.7.1/MACS2/ |
H A D | PeakDetect.c | 4262 __pyx_v_peaks = __pyx_t_2; in __pyx_pf_5MACS2_10PeakDetect_10PeakDetect_4__call_peaks_w_control() 4640 __pyx_v_peaks = __pyx_t_2; in __pyx_pf_5MACS2_10PeakDetect_10PeakDetect_4__call_peaks_w_control() 4746 __pyx_v_peaks = __pyx_t_6; in __pyx_pf_5MACS2_10PeakDetect_10PeakDetect_4__call_peaks_w_control() 4796 __Pyx_INCREF(__pyx_v_peaks); in __pyx_pf_5MACS2_10PeakDetect_10PeakDetect_4__call_peaks_w_control() 4797 __pyx_r = __pyx_v_peaks; in __pyx_pf_5MACS2_10PeakDetect_10PeakDetect_4__call_peaks_w_control() 4823 __Pyx_XDECREF(__pyx_v_peaks); in __pyx_pf_5MACS2_10PeakDetect_10PeakDetect_4__call_peaks_w_control() 5677 __pyx_v_peaks = __pyx_t_5; in __pyx_pf_5MACS2_10PeakDetect_10PeakDetect_6__call_peaks_wo_control() 5815 __pyx_v_peaks = __pyx_t_1; in __pyx_pf_5MACS2_10PeakDetect_10PeakDetect_6__call_peaks_wo_control() 6211 __Pyx_INCREF(__pyx_v_peaks); in __pyx_pf_5MACS2_10PeakDetect_10PeakDetect_6__call_peaks_wo_control() 6212 __pyx_r = __pyx_v_peaks; in __pyx_pf_5MACS2_10PeakDetect_10PeakDetect_6__call_peaks_wo_control() [all …]
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/dports/science/py-dipy/dipy-1.4.1/dipy/tracking/ |
H A D | propspeed.c | 2858 …double *__pyx_v_dx, double *__pyx_v_qa, double *__pyx_v_ind, npy_intp __pyx_v_peaks, double *__pyx… in __pyx_f_4dipy_8tracking_9propspeed__nearest_direction() argument 2933 __pyx_t_2 = __pyx_v_peaks; in __pyx_f_4dipy_8tracking_9propspeed__nearest_direction() 3218 npy_intp __pyx_v_peaks; in __pyx_f_4dipy_8tracking_9propspeed__propagation_direction() local 3250 __pyx_v_peaks = (__pyx_v_qa_shape[3]); in __pyx_f_4dipy_8tracking_9propspeed__propagation_direction() 3352 __pyx_t_3 = __pyx_v_peaks; in __pyx_f_4dipy_8tracking_9propspeed__propagation_direction() 3399 …speed__nearest_direction(__pyx_v_dx, __pyx_v_qa_tmp, __pyx_v_ind_tmp, __pyx_v_peaks, __pyx_v_odf_v… in __pyx_f_4dipy_8tracking_9propspeed__propagation_direction()
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/dports/science/py-dipy/dipy-1.4.1/dipy/direction/ |
H A D | bootstrap_direction_getter.c | 3351 PyArrayObject *__pyx_v_peaks = 0; in __pyx_f_4dipy_9direction_26bootstrap_direction_getter_19BootDirectionGetter_get_direction_c() local 3444 …ferAndValidate(&__pyx_pybuffernd_peaks.rcbuffer->pybuffer, (PyObject*)__pyx_v_peaks, &__Pyx_TypeIn… in __pyx_f_4dipy_9direction_26bootstrap_direction_getter_19BootDirectionGetter_get_direction_c() 3456 __Pyx_XDECREF_SET(__pyx_v_peaks, ((PyArrayObject *)__pyx_t_4)); in __pyx_f_4dipy_9direction_26bootstrap_direction_getter_19BootDirectionGetter_get_direction_c() 3466 …__pyx_t_14 = PyObject_Length(((PyObject *)__pyx_v_peaks)); if (unlikely(__pyx_t_14 == ((Py_ssize_t… in __pyx_f_4dipy_9direction_26bootstrap_direction_getter_19BootDirectionGetter_get_direction_c() 3476 …ection_29closest_peak_direction_getter_closest_peak(((PyArrayObject *)__pyx_v_peaks), __pyx_v_dire… in __pyx_f_4dipy_9direction_26bootstrap_direction_getter_19BootDirectionGetter_get_direction_c() 3525 __Pyx_XDECREF((PyObject *)__pyx_v_peaks); in __pyx_f_4dipy_9direction_26bootstrap_direction_getter_19BootDirectionGetter_get_direction_c()
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H A D | closest_peak_direction_getter.c | 5336 PyArrayObject *__pyx_v_peaks = 0; in __pyx_f_4dipy_9direction_29closest_peak_direction_getter_26ClosestPeakDirectionGetter_get_direction_c() local 5412 …ferAndValidate(&__pyx_pybuffernd_peaks.rcbuffer->pybuffer, (PyObject*)__pyx_v_peaks, &__Pyx_TypeIn… in __pyx_f_4dipy_9direction_29closest_peak_direction_getter_26ClosestPeakDirectionGetter_get_direction_c() 5424 __pyx_v_peaks = ((PyArrayObject *)__pyx_t_1); in __pyx_f_4dipy_9direction_29closest_peak_direction_getter_26ClosestPeakDirectionGetter_get_direction_c() 5434 …__pyx_t_11 = PyObject_Length(((PyObject *)__pyx_v_peaks)); if (unlikely(__pyx_t_11 == ((Py_ssize_t… in __pyx_f_4dipy_9direction_29closest_peak_direction_getter_26ClosestPeakDirectionGetter_get_direction_c() 5461 …ection_29closest_peak_direction_getter_closest_peak(((PyArrayObject *)__pyx_v_peaks), __pyx_v_dire… in __pyx_f_4dipy_9direction_29closest_peak_direction_getter_26ClosestPeakDirectionGetter_get_direction_c() 5492 __Pyx_XDECREF((PyObject *)__pyx_v_peaks); in __pyx_f_4dipy_9direction_29closest_peak_direction_getter_26ClosestPeakDirectionGetter_get_direction_c()
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