[med-svn] [macs] 01/03: Imported Upstream version 2.1.0.20151222
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Feb 2 08:42:31 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository macs.
commit 9c2e14a3c8be86b6354a69ac99f349b03d054e1b
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Mon Feb 1 09:48:38 2016 -0800
Imported Upstream version 2.1.0.20151222
---
ChangeLog | 18 +
MACS2.egg-info/PKG-INFO | 2 +-
MACS2/Constants.py | 2 +-
MACS2/IO/CallPeakUnit.c | 5584 ++++++++++++++++++++++---------------------
MACS2/IO/CallPeakUnit.pyx | 41 +-
MACS2/IO/FixWidthTrack.c | 1472 ++++++------
MACS2/IO/FixWidthTrack.pyx | 20 +-
MACS2/IO/PairedEndTrack.c | 439 ++--
MACS2/IO/PairedEndTrack.pyx | 10 +-
MACS2/IO/Parser.c | 793 +++---
MACS2/IO/Parser.pyx | 6 +-
MACS2/callpeak_cmd.py | 6 +-
PKG-INFO | 2 +-
setup.py | 4 +-
setup_w_cython.py | 4 +-
15 files changed, 4272 insertions(+), 4131 deletions(-)
diff --git a/ChangeLog b/ChangeLog
index 09fe6b1..3757a5c 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,21 @@
+2015-12-22 Tao Liu <vladimir.liu at gmail.com>
+ MACS version 2.1.0 20151222 (tag:rc Dongzhi)
+
+ * Bug fixes
+
+ 1) Fix a bug while dealing with some chromosomes only containing
+ one read (pair). The size of dup_plus/dup_minus arrays after
+ filtering dups should +1.
+
+ 2) Fix a bug related to the broad peak calling function in
+ previous versions. The gaps were miscalculated, so segmented weak
+ broad calls may be reported, and sometimes you would see peaks
+ with lower than cutoff values in the output files.
+
+ 3) "Potentially" Fixed issue #105 on temporary cache files, need
+ further followup.
+
+
2015-07-31 Tao Liu <vladimir.liu at gmail.com>
MACS version 2.1.0 20150731 (tag:rc)
diff --git a/MACS2.egg-info/PKG-INFO b/MACS2.egg-info/PKG-INFO
index 7875ec9..af49a01 100644
--- a/MACS2.egg-info/PKG-INFO
+++ b/MACS2.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: MACS2
-Version: 2.1.0.20150731
+Version: 2.1.0.20151222
Summary: Model Based Analysis for ChIP-Seq data
Home-page: http://github.com/taoliu/MACS/
Author: Tao Liu
diff --git a/MACS2/Constants.py b/MACS2/Constants.py
index b7596ec..de57fab 100644
--- a/MACS2/Constants.py
+++ b/MACS2/Constants.py
@@ -1,4 +1,4 @@
-MACS_VERSION = "2.1.0.20150731"
+MACS_VERSION = "2.1.0.20151222"
#MACSDIFF_VERSION = "1.0.4 20110212 (tag:alpha)"
FILTERDUP_VERSION = "1.0.0 20140616"
RANDSAMPLE_VERSION = "1.0.0 20120703"
diff --git a/MACS2/IO/CallPeakUnit.c b/MACS2/IO/CallPeakUnit.c
index 2d1ab86..040da78 100644
--- a/MACS2/IO/CallPeakUnit.c
+++ b/MACS2/IO/CallPeakUnit.c
@@ -761,7 +761,7 @@ struct __pyx_opt_args_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_broa
struct __pyx_opt_args_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___close_peak_for_broad_region;
struct __pyx_opt_args_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine_peak_from_tags_distribution;
-/* "MACS2/IO/CallPeakUnit.pyx":705
+/* "MACS2/IO/CallPeakUnit.pyx":706
*
*
* cdef object __pre_computes ( self, int max_gap = 50, int min_length = 200 ): # <<<<<<<<<<<<<<
@@ -774,7 +774,7 @@ struct __pyx_opt_args_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_com
int min_length;
};
-/* "MACS2/IO/CallPeakUnit.pyx":857
+/* "MACS2/IO/CallPeakUnit.pyx":858
*
*
* cpdef call_peaks ( self, list scoring_function_symbols, list score_cutoff_s, int min_length = 200, # <<<<<<<<<<<<<<
@@ -789,7 +789,7 @@ struct __pyx_opt_args_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_peak
PyBoolObject *auto_cutoff;
};
-/* "MACS2/IO/CallPeakUnit.pyx":1062
+/* "MACS2/IO/CallPeakUnit.pyx":1063
* return peaks
*
* cdef bool __close_peak_wo_subpeaks (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<<
@@ -801,7 +801,7 @@ struct __pyx_opt_args_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___close_p
PyObject *score_cutoff_s;
};
-/* "MACS2/IO/CallPeakUnit.pyx":1122
+/* "MACS2/IO/CallPeakUnit.pyx":1123
* return True
*
* cdef bool __close_peak_with_subpeaks (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<<
@@ -814,7 +814,7 @@ struct __pyx_opt_args_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___close_p
float min_valley;
};
-/* "MACS2/IO/CallPeakUnit.pyx":1427
+/* "MACS2/IO/CallPeakUnit.pyx":1428
* return True
*
* cpdef call_broadpeaks (self, list scoring_function_symbols, list lvl1_cutoff_s, list lvl2_cutoff_s, int min_length=200, int lvl1_max_gap=50, int lvl2_max_gap=400, bool auto_cutoff = False): # <<<<<<<<<<<<<<
@@ -829,7 +829,7 @@ struct __pyx_opt_args_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_broa
PyBoolObject *auto_cutoff;
};
-/* "MACS2/IO/CallPeakUnit.pyx":1701
+/* "MACS2/IO/CallPeakUnit.pyx":1712
* return
*
* cdef bool __close_peak_for_broad_region (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<<
@@ -841,7 +841,7 @@ struct __pyx_opt_args_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___close_p
PyObject *score_cutoff_s;
};
-/* "MACS2/IO/CallPeakUnit.pyx":1805
+/* "MACS2/IO/CallPeakUnit.pyx":1818
* return bpeaks
*
* cpdef refine_peak_from_tags_distribution ( self, peaks, int window_size = 100, float cutoff = 5 ): # <<<<<<<<<<<<<<
@@ -1547,7 +1547,6 @@ static PyObject *__pyx_builtin_sum;
static PyObject *__pyx_builtin_zip;
static PyObject *__pyx_builtin_Exception;
static PyObject *__pyx_builtin_file;
-static PyObject *__pyx_builtin_IOError;
static PyObject *__pyx_builtin_sorted;
static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_ValueError;
@@ -1599,6 +1598,7 @@ static char __pyx_k_doc[] = "__doc__";
static char __pyx_k_end[] = "end";
static char __pyx_k_get[] = "get";
static char __pyx_k_map[] = "map";
+static char __pyx_k_pop[] = "pop";
static char __pyx_k_sum[] = "sum";
static char __pyx_k_zip[] = "zip";
static char __pyx_k_args[] = "args";
@@ -1660,7 +1660,6 @@ static char __pyx_k_values[] = "values";
static char __pyx_k_vstack[] = "vstack";
static char __pyx_k_Counter[] = "Counter";
static char __pyx_k_FWTrack[] = "FWTrack";
-static char __pyx_k_IOError[] = "IOError";
static char __pyx_k_LOG10_E[] = "LOG10_E";
static char __pyx_k_TMP_txt[] = "TMP.txt";
static char __pyx_k_cPickle[] = "cPickle";
@@ -1773,7 +1772,7 @@ static char __pyx_k_3_Pre_compute_pvalue_qvalue_tab[] = "#3 Pre-compute pvalue-q
static char __pyx_k_3_SPMR_is_requested_so_pileup_w[] = "#3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.";
static char __pyx_k_3_Write_bedGraph_files_for_cont[] = "#3 Write bedGraph files for control lambda (after scaling if necessary)... %s";
static char __pyx_k_3_Write_bedGraph_files_for_trea[] = "#3 Write bedGraph files for treatment pileup (after scaling if necessary)... %s";
-static char __pyx_k_Users_taoliu_Dropbox_projects_m[] = "/Users/taoliu/Dropbox/projects/macs2/MACS/MACS2/IO/CallPeakUnit.pyx";
+static char __pyx_k_Users_taoliu_Dropbox_Projects_M[] = "/Users/taoliu/Dropbox/Projects/MACS2/MACS/MACS2/IO/CallPeakUnit.pyx";
static char __pyx_k_number_of_functions_and_cutoffs[] = "number of functions and cutoffs should be the same!";
static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd";
@@ -1814,7 +1813,6 @@ static PyObject *__pyx_n_s_FWTrack;
static PyObject *__pyx_n_s_Float64HashTable;
static PyObject *__pyx_kp_u_Format_string_allocated_too_shor;
static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2;
-static PyObject *__pyx_n_s_IOError;
static PyObject *__pyx_n_s_LOG10_E;
static PyObject *__pyx_n_s_LogLR_Asym;
static PyObject *__pyx_n_s_MACS2_IO_CallPeakUnit;
@@ -1837,7 +1835,7 @@ static PyObject *__pyx_n_s_T;
static PyObject *__pyx_kp_s_TMP_txt;
static PyObject *__pyx_kp_s_TREAT_bdg;
static PyObject *__pyx_kp_s_Tao_Liu_vladimir_liu_gmail_com;
-static PyObject *__pyx_kp_s_Users_taoliu_Dropbox_projects_m;
+static PyObject *__pyx_kp_s_Users_taoliu_Dropbox_Projects_M;
static PyObject *__pyx_n_s_ValueError;
static PyObject *__pyx_kp_s__32;
static PyObject *__pyx_kp_s_access_pq_hash_for_d_times;
@@ -1941,6 +1939,7 @@ static PyObject *__pyx_n_s_peaks;
static PyObject *__pyx_n_s_pileup;
static PyObject *__pyx_n_s_pileup_a_chromosome;
static PyObject *__pyx_n_s_pileup_a_chromosome_c;
+static PyObject *__pyx_n_s_pop;
static PyObject *__pyx_n_s_protocol;
static PyObject *__pyx_n_s_pscore;
static PyObject *__pyx_kp_s_pscore_qscore_npeaks_lpeaks_avel;
@@ -6345,11 +6344,10 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
PyObject *__pyx_t_7 = NULL;
PyObject *__pyx_t_8 = NULL;
PyObject *__pyx_t_9 = NULL;
- int __pyx_t_10;
+ PyObject *__pyx_t_10 = NULL;
PyObject *__pyx_t_11 = NULL;
PyObject *__pyx_t_12 = NULL;
- PyObject *__pyx_t_13 = NULL;
- PyObject *(*__pyx_t_14)(PyObject *);
+ PyObject *(*__pyx_t_13)(PyObject *);
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -6480,7 +6478,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
* self.chr_pos_treat_ctrl = cPickle.load( f )
* f.close() # <<<<<<<<<<<<<<
* return
- * except IOError:
+ * except:
*/
__pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_close); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_8);
@@ -6508,7 +6506,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
* self.chr_pos_treat_ctrl = cPickle.load( f )
* f.close()
* return # <<<<<<<<<<<<<<
- * except IOError:
+ * except:
* temp_fd, temp_filename = mkstemp()
*/
__Pyx_XDECREF(__pyx_r);
@@ -6524,12 +6522,11 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
/* "MACS2/IO/CallPeakUnit.pyx":464
* f.close()
* return
- * except IOError: # <<<<<<<<<<<<<<
+ * except: # <<<<<<<<<<<<<<
* temp_fd, temp_filename = mkstemp()
* os.close(temp_fd)
*/
- __pyx_t_10 = PyErr_ExceptionMatches(__pyx_builtin_IOError);
- if (__pyx_t_10) {
+ /*except:*/ {
__Pyx_AddTraceback("MACS2.IO.CallPeakUnit.CallerFromAlignments.__pileup_treat_ctrl_a_chromosome", __pyx_clineno, __pyx_lineno, __pyx_filename);
if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_8, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -6538,31 +6535,31 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
/* "MACS2/IO/CallPeakUnit.pyx":465
* return
- * except IOError:
+ * except:
* temp_fd, temp_filename = mkstemp() # <<<<<<<<<<<<<<
* os.close(temp_fd)
* self.pileup_data_files[ chrom ] = temp_filename
*/
- __pyx_t_11 = __Pyx_GetModuleGlobalName(__pyx_n_s_mkstemp); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
- __Pyx_GOTREF(__pyx_t_11);
- __pyx_t_12 = NULL;
- if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_11))) {
- __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_11);
- if (likely(__pyx_t_12)) {
- PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11);
- __Pyx_INCREF(__pyx_t_12);
+ __pyx_t_10 = __Pyx_GetModuleGlobalName(__pyx_n_s_mkstemp); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_11 = NULL;
+ if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_10))) {
+ __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_10);
+ if (likely(__pyx_t_11)) {
+ PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_10);
+ __Pyx_INCREF(__pyx_t_11);
__Pyx_INCREF(function);
- __Pyx_DECREF_SET(__pyx_t_11, function);
+ __Pyx_DECREF_SET(__pyx_t_10, function);
}
}
- if (__pyx_t_12) {
- __pyx_t_7 = __Pyx_PyObject_CallOneArg(__pyx_t_11, __pyx_t_12); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
- __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
+ if (__pyx_t_11) {
+ __pyx_t_7 = __Pyx_PyObject_CallOneArg(__pyx_t_10, __pyx_t_11); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
} else {
- __pyx_t_7 = __Pyx_PyObject_CallNoArg(__pyx_t_11); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_7 = __Pyx_PyObject_CallNoArg(__pyx_t_10); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
PyObject* sequence = __pyx_t_7;
#if CYTHON_COMPILING_IN_CPYTHON
@@ -6577,84 +6574,84 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
}
#if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- __pyx_t_11 = PyTuple_GET_ITEM(sequence, 0);
- __pyx_t_12 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_10 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_11 = PyTuple_GET_ITEM(sequence, 1);
} else {
- __pyx_t_11 = PyList_GET_ITEM(sequence, 0);
- __pyx_t_12 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_10 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_11 = PyList_GET_ITEM(sequence, 1);
}
+ __Pyx_INCREF(__pyx_t_10);
__Pyx_INCREF(__pyx_t_11);
- __Pyx_INCREF(__pyx_t_12);
#else
- __pyx_t_11 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_10 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_11 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_12 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
- __Pyx_GOTREF(__pyx_t_12);
#endif
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
} else {
Py_ssize_t index = -1;
- __pyx_t_13 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
- __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_12 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_GOTREF(__pyx_t_12);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_14 = Py_TYPE(__pyx_t_13)->tp_iternext;
- index = 0; __pyx_t_11 = __pyx_t_14(__pyx_t_13); if (unlikely(!__pyx_t_11)) goto __pyx_L14_unpacking_failed;
+ __pyx_t_13 = Py_TYPE(__pyx_t_12)->tp_iternext;
+ index = 0; __pyx_t_10 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_10)) goto __pyx_L14_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_10);
+ index = 1; __pyx_t_11 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_11)) goto __pyx_L14_unpacking_failed;
__Pyx_GOTREF(__pyx_t_11);
- index = 1; __pyx_t_12 = __pyx_t_14(__pyx_t_13); if (unlikely(!__pyx_t_12)) goto __pyx_L14_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_12);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_13), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
- __pyx_t_14 = NULL;
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_13 = NULL;
+ __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
goto __pyx_L15_unpacking_done;
__pyx_L14_unpacking_failed:;
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_t_14 = NULL;
+ __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
+ __pyx_t_13 = NULL;
if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__pyx_L15_unpacking_done:;
}
- __pyx_v_temp_fd = __pyx_t_11;
+ __pyx_v_temp_fd = __pyx_t_10;
+ __pyx_t_10 = 0;
+ __pyx_v_temp_filename = __pyx_t_11;
__pyx_t_11 = 0;
- __pyx_v_temp_filename = __pyx_t_12;
- __pyx_t_12 = 0;
/* "MACS2/IO/CallPeakUnit.pyx":466
- * except IOError:
+ * except:
* temp_fd, temp_filename = mkstemp()
* os.close(temp_fd) # <<<<<<<<<<<<<<
* self.pileup_data_files[ chrom ] = temp_filename
* else:
*/
- __pyx_t_12 = __Pyx_GetModuleGlobalName(__pyx_n_s_os); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
- __Pyx_GOTREF(__pyx_t_12);
- __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_t_12, __pyx_n_s_close); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_11 = __Pyx_GetModuleGlobalName(__pyx_n_s_os); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_11);
- __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- __pyx_t_12 = NULL;
- if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_11))) {
- __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_11);
- if (likely(__pyx_t_12)) {
- PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11);
- __Pyx_INCREF(__pyx_t_12);
+ __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_t_11, __pyx_n_s_close); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __pyx_t_11 = NULL;
+ if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_10))) {
+ __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_10);
+ if (likely(__pyx_t_11)) {
+ PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_10);
+ __Pyx_INCREF(__pyx_t_11);
__Pyx_INCREF(function);
- __Pyx_DECREF_SET(__pyx_t_11, function);
+ __Pyx_DECREF_SET(__pyx_t_10, function);
}
}
- if (!__pyx_t_12) {
- __pyx_t_7 = __Pyx_PyObject_CallOneArg(__pyx_t_11, __pyx_v_temp_fd); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ if (!__pyx_t_11) {
+ __pyx_t_7 = __Pyx_PyObject_CallOneArg(__pyx_t_10, __pyx_v_temp_fd); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_7);
} else {
- __pyx_t_13 = PyTuple_New(1+1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
- __Pyx_GOTREF(__pyx_t_13);
- PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_t_12); __Pyx_GIVEREF(__pyx_t_12); __pyx_t_12 = NULL;
+ __pyx_t_12 = PyTuple_New(1+1); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_GOTREF(__pyx_t_12);
+ PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_t_11); __Pyx_GIVEREF(__pyx_t_11); __pyx_t_11 = NULL;
__Pyx_INCREF(__pyx_v_temp_fd);
- PyTuple_SET_ITEM(__pyx_t_13, 0+1, __pyx_v_temp_fd);
+ PyTuple_SET_ITEM(__pyx_t_12, 0+1, __pyx_v_temp_fd);
__Pyx_GIVEREF(__pyx_v_temp_fd);
- __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_13, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_10, __pyx_t_12, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
}
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
/* "MACS2/IO/CallPeakUnit.pyx":467
@@ -6674,7 +6671,6 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
goto __pyx_L5_exception_handled;
}
- goto __pyx_L6_except_error;
__pyx_L6_except_error:;
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_5);
@@ -6758,18 +6754,18 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
__pyx_t_7 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_14 = Py_TYPE(__pyx_t_7)->tp_iternext;
- index = 0; __pyx_t_8 = __pyx_t_14(__pyx_t_7); if (unlikely(!__pyx_t_8)) goto __pyx_L16_unpacking_failed;
+ __pyx_t_13 = Py_TYPE(__pyx_t_7)->tp_iternext;
+ index = 0; __pyx_t_8 = __pyx_t_13(__pyx_t_7); if (unlikely(!__pyx_t_8)) goto __pyx_L16_unpacking_failed;
__Pyx_GOTREF(__pyx_t_8);
- index = 1; __pyx_t_2 = __pyx_t_14(__pyx_t_7); if (unlikely(!__pyx_t_2)) goto __pyx_L16_unpacking_failed;
+ index = 1; __pyx_t_2 = __pyx_t_13(__pyx_t_7); if (unlikely(!__pyx_t_2)) goto __pyx_L16_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_14(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_14 = NULL;
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = NULL;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L17_unpacking_done;
__pyx_L16_unpacking_failed:;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_14 = NULL;
+ __pyx_t_13 = NULL;
if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L17_unpacking_done:;
@@ -7282,8 +7278,8 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
__pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 497; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 497; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = __Pyx_PyObject_Call(__pyx_t_7, __pyx_t_8, __pyx_t_2); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 497; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_10 = __Pyx_PyObject_Call(__pyx_t_7, __pyx_t_8, __pyx_t_2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 497; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -7291,10 +7287,10 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
__Pyx_GOTREF(__pyx_t_2);
PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
- PyList_SET_ITEM(__pyx_t_2, 1, __pyx_t_11);
- __Pyx_GIVEREF(__pyx_t_11);
+ PyList_SET_ITEM(__pyx_t_2, 1, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
__pyx_t_9 = 0;
- __pyx_t_11 = 0;
+ __pyx_t_10 = 0;
__pyx_v_ctrl_pv = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
}
@@ -7366,17 +7362,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
}
__pyx_t_2 = __Pyx_PyDict_GetItem(__pyx_v_self->pileup_data_files, __pyx_v_chrom); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L22_error;};
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_11 = PyTuple_New(2); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
- __Pyx_GOTREF(__pyx_t_11);
- PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_2);
+ __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_n_s_wb);
- PyTuple_SET_ITEM(__pyx_t_11, 1, __pyx_n_s_wb);
+ PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_n_s_wb);
__Pyx_GIVEREF(__pyx_n_s_wb);
__pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_file, __pyx_t_11, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_file, __pyx_t_10, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF_SET(__pyx_v_f, __pyx_t_2);
__pyx_t_2 = 0;
@@ -7385,12 +7381,12 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
* f = file(self.pileup_data_files[ chrom ],"wb")
* cPickle.dump( self.chr_pos_treat_ctrl, f , protocol=2 ) # <<<<<<<<<<<<<<
* f.close()
- * except IOError:
+ * except:
*/
__pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_cPickle); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_dump); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
- __Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_10 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_dump); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -7403,9 +7399,9 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
__pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_GOTREF(__pyx_t_9);
if (PyDict_SetItem(__pyx_t_9, __pyx_n_s_protocol, __pyx_int_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
- __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_2, __pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_10, __pyx_t_2, __pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
@@ -7414,8 +7410,8 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
* f = file(self.pileup_data_files[ chrom ],"wb")
* cPickle.dump( self.chr_pos_treat_ctrl, f , protocol=2 )
* f.close() # <<<<<<<<<<<<<<
- * except IOError:
- * pass
+ * except:
+ * # fail to write then remove the key in pileup_data_files
*/
__pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_f, __pyx_n_s_close); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_GOTREF(__pyx_t_9);
@@ -7444,10 +7440,10 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
goto __pyx_L29_try_end;
__pyx_L22_error:;
+ __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
- __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
__Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
@@ -7455,16 +7451,57 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
/* "MACS2/IO/CallPeakUnit.pyx":510
* cPickle.dump( self.chr_pos_treat_ctrl, f , protocol=2 )
* f.close()
- * except IOError: # <<<<<<<<<<<<<<
- * pass
+ * except: # <<<<<<<<<<<<<<
+ * # fail to write then remove the key in pileup_data_files
+ * self.pileup_data_files.pop(chrom)
+ */
+ /*except:*/ {
+ __Pyx_AddTraceback("MACS2.IO.CallPeakUnit.CallerFromAlignments.__pileup_treat_ctrl_a_chromosome", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_8, &__pyx_t_9, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(__pyx_t_2);
+
+ /* "MACS2/IO/CallPeakUnit.pyx":512
+ * except:
+ * # fail to write then remove the key in pileup_data_files
+ * self.pileup_data_files.pop(chrom) # <<<<<<<<<<<<<<
* return
+ *
*/
- __pyx_t_10 = PyErr_ExceptionMatches(__pyx_builtin_IOError);
- if (__pyx_t_10) {
- PyErr_Restore(0,0,0);
+ __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->pileup_data_files, __pyx_n_s_pop); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_12 = NULL;
+ if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_7))) {
+ __pyx_t_12 = PyMethod_GET_SELF(__pyx_t_7);
+ if (likely(__pyx_t_12)) {
+ PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_7);
+ __Pyx_INCREF(__pyx_t_12);
+ __Pyx_INCREF(function);
+ __Pyx_DECREF_SET(__pyx_t_7, function);
+ }
+ }
+ if (!__pyx_t_12) {
+ __pyx_t_10 = __Pyx_PyObject_CallOneArg(__pyx_t_7, __pyx_v_chrom); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ } else {
+ __pyx_t_11 = PyTuple_New(1+1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_12); __Pyx_GIVEREF(__pyx_t_12); __pyx_t_12 = NULL;
+ __Pyx_INCREF(__pyx_v_chrom);
+ PyTuple_SET_ITEM(__pyx_t_11, 0+1, __pyx_v_chrom);
+ __Pyx_GIVEREF(__pyx_v_chrom);
+ __pyx_t_10 = __Pyx_PyObject_Call(__pyx_t_7, __pyx_t_11, NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ }
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
goto __pyx_L23_exception_handled;
}
- goto __pyx_L24_except_error;
__pyx_L24_except_error:;
__Pyx_XGIVEREF(__pyx_t_6);
__Pyx_XGIVEREF(__pyx_t_5);
@@ -7479,9 +7516,9 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
__pyx_L29_try_end:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":512
- * except IOError:
- * pass
+ /* "MACS2/IO/CallPeakUnit.pyx":513
+ * # fail to write then remove the key in pileup_data_files
+ * self.pileup_data_files.pop(chrom)
* return # <<<<<<<<<<<<<<
*
* cdef list __chrom_pair_treat_ctrl ( self, treat_pv, ctrl_pv ):
@@ -7504,9 +7541,9 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
+ __Pyx_XDECREF(__pyx_t_10);
__Pyx_XDECREF(__pyx_t_11);
__Pyx_XDECREF(__pyx_t_12);
- __Pyx_XDECREF(__pyx_t_13);
__Pyx_AddTraceback("MACS2.IO.CallPeakUnit.CallerFromAlignments.__pileup_treat_ctrl_a_chromosome", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
@@ -7520,7 +7557,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pile
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":514
+/* "MACS2/IO/CallPeakUnit.pyx":515
* return
*
* cdef list __chrom_pair_treat_ctrl ( self, treat_pv, ctrl_pv ): # <<<<<<<<<<<<<<
@@ -7612,7 +7649,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_pybuffernd_ret_c.data = NULL;
__pyx_pybuffernd_ret_c.rcbuffer = &__pyx_pybuffer_ret_c;
- /* "MACS2/IO/CallPeakUnit.pyx":536
+ /* "MACS2/IO/CallPeakUnit.pyx":537
* float32_t * ret_c_ptr
*
* [ t_p, t_v ] = treat_pv # <<<<<<<<<<<<<<
@@ -7629,7 +7666,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
if (unlikely(size != 2)) {
if (size > 2) __Pyx_RaiseTooManyValuesError(2);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
@@ -7642,21 +7679,21 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_2);
#else
- __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
#endif
} else {
Py_ssize_t index = -1;
- __pyx_t_3 = PyObject_GetIter(__pyx_v_treat_pv); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetIter(__pyx_v_treat_pv); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_4 = Py_TYPE(__pyx_t_3)->tp_iternext;
index = 0; __pyx_t_1 = __pyx_t_4(__pyx_t_3); if (unlikely(!__pyx_t_1)) goto __pyx_L3_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
index = 1; __pyx_t_2 = __pyx_t_4(__pyx_t_3); if (unlikely(!__pyx_t_2)) goto __pyx_L3_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_4(__pyx_t_3), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_4(__pyx_t_3), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = NULL;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L4_unpacking_done;
@@ -7664,11 +7701,11 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_4 = NULL;
if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L4_unpacking_done:;
}
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = ((PyArrayObject *)__pyx_t_1);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -7684,7 +7721,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
__pyx_pybuffernd_t_p.diminfo[0].strides = __pyx_pybuffernd_t_p.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_t_p.diminfo[0].shape = __pyx_pybuffernd_t_p.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = 0;
__pyx_v_t_p = ((PyArrayObject *)__pyx_t_1);
@@ -7704,13 +7741,13 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
__pyx_pybuffernd_t_v.diminfo[0].strides = __pyx_pybuffernd_t_v.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_t_v.diminfo[0].shape = __pyx_pybuffernd_t_v.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_10 = 0;
__pyx_v_t_v = ((PyArrayObject *)__pyx_t_2);
__pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":537
+ /* "MACS2/IO/CallPeakUnit.pyx":538
*
* [ t_p, t_v ] = treat_pv
* [ c_p, c_v ] = ctrl_pv # <<<<<<<<<<<<<<
@@ -7727,7 +7764,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
if (unlikely(size != 2)) {
if (size > 2) __Pyx_RaiseTooManyValuesError(2);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
@@ -7740,21 +7777,21 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__Pyx_INCREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_1);
#else
- __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
#endif
} else {
Py_ssize_t index = -1;
- __pyx_t_3 = PyObject_GetIter(__pyx_v_ctrl_pv); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetIter(__pyx_v_ctrl_pv); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_4 = Py_TYPE(__pyx_t_3)->tp_iternext;
index = 0; __pyx_t_2 = __pyx_t_4(__pyx_t_3); if (unlikely(!__pyx_t_2)) goto __pyx_L5_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
index = 1; __pyx_t_1 = __pyx_t_4(__pyx_t_3); if (unlikely(!__pyx_t_1)) goto __pyx_L5_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_4(__pyx_t_3), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_4(__pyx_t_3), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = NULL;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L6_unpacking_done;
@@ -7762,11 +7799,11 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_4 = NULL;
if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L6_unpacking_done:;
}
- if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = ((PyArrayObject *)__pyx_t_2);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -7782,7 +7819,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
__pyx_pybuffernd_c_p.diminfo[0].strides = __pyx_pybuffernd_c_p.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_c_p.diminfo[0].shape = __pyx_pybuffernd_c_p.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = 0;
__pyx_v_c_p = ((PyArrayObject *)__pyx_t_2);
@@ -7802,13 +7839,13 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
__pyx_pybuffernd_c_v.diminfo[0].strides = __pyx_pybuffernd_c_v.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_c_v.diminfo[0].shape = __pyx_pybuffernd_c_v.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_10 = 0;
__pyx_v_c_v = ((PyArrayObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":539
+ /* "MACS2/IO/CallPeakUnit.pyx":540
* [ c_p, c_v ] = ctrl_pv
*
* lt = t_p.shape[0] # <<<<<<<<<<<<<<
@@ -7817,7 +7854,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_lt = (__pyx_v_t_p->dimensions[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":540
+ /* "MACS2/IO/CallPeakUnit.pyx":541
*
* lt = t_p.shape[0]
* lc = c_p.shape[0] # <<<<<<<<<<<<<<
@@ -7826,7 +7863,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_lc = (__pyx_v_c_p->dimensions[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":542
+ /* "MACS2/IO/CallPeakUnit.pyx":543
* lc = c_p.shape[0]
*
* chrom_max_len = lt + lc # <<<<<<<<<<<<<<
@@ -7835,34 +7872,34 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_chrom_max_len = (__pyx_v_lt + __pyx_v_lc);
- /* "MACS2/IO/CallPeakUnit.pyx":544
+ /* "MACS2/IO/CallPeakUnit.pyx":545
* chrom_max_len = lt + lc
*
* ret_p = np.zeros( chrom_max_len, dtype="int32" ) # position # <<<<<<<<<<<<<<
* ret_t = np.zeros( chrom_max_len, dtype="float32" ) # value from treatment
* ret_c = np.zeros( chrom_max_len, dtype="float32" ) # value from control
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v_chrom_max_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v_chrom_max_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(((__pyx_t_11) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_11, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_11) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_11, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = ((PyArrayObject *)__pyx_t_11);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -7878,40 +7915,40 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
__pyx_pybuffernd_ret_p.diminfo[0].strides = __pyx_pybuffernd_ret_p.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_ret_p.diminfo[0].shape = __pyx_pybuffernd_ret_p.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = 0;
__pyx_v_ret_p = ((PyArrayObject *)__pyx_t_11);
__pyx_t_11 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":545
+ /* "MACS2/IO/CallPeakUnit.pyx":546
*
* ret_p = np.zeros( chrom_max_len, dtype="int32" ) # position
* ret_t = np.zeros( chrom_max_len, dtype="float32" ) # value from treatment # <<<<<<<<<<<<<<
* ret_c = np.zeros( chrom_max_len, dtype="float32" ) # value from control
*
*/
- __pyx_t_11 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_11, __pyx_n_s_zeros); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_11, __pyx_n_s_zeros); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __pyx_t_11 = __Pyx_PyInt_From_long(__pyx_v_chrom_max_len); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyInt_From_long(__pyx_v_chrom_max_len); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_11);
__Pyx_GIVEREF(__pyx_t_11);
__pyx_t_11 = 0;
- __pyx_t_11 = PyDict_New(); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyDict_New(); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- if (PyDict_SetItem(__pyx_t_11, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_3, __pyx_t_11); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_11, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_3, __pyx_t_11); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_10 = ((PyArrayObject *)__pyx_t_2);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -7927,40 +7964,40 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
__pyx_pybuffernd_ret_t.diminfo[0].strides = __pyx_pybuffernd_ret_t.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_ret_t.diminfo[0].shape = __pyx_pybuffernd_ret_t.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_10 = 0;
__pyx_v_ret_t = ((PyArrayObject *)__pyx_t_2);
__pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":546
+ /* "MACS2/IO/CallPeakUnit.pyx":547
* ret_p = np.zeros( chrom_max_len, dtype="int32" ) # position
* ret_t = np.zeros( chrom_max_len, dtype="float32" ) # value from treatment
* ret_c = np.zeros( chrom_max_len, dtype="float32" ) # value from control # <<<<<<<<<<<<<<
*
* t_p_ptr = <int32_t *> t_p.data
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_zeros); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_zeros); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_PyInt_From_long(__pyx_v_chrom_max_len); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_From_long(__pyx_v_chrom_max_len); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_10 = ((PyArrayObject *)__pyx_t_1);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -7976,13 +8013,13 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
__pyx_pybuffernd_ret_c.diminfo[0].strides = __pyx_pybuffernd_ret_c.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_ret_c.diminfo[0].shape = __pyx_pybuffernd_ret_c.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_10 = 0;
__pyx_v_ret_c = ((PyArrayObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":548
+ /* "MACS2/IO/CallPeakUnit.pyx":549
* ret_c = np.zeros( chrom_max_len, dtype="float32" ) # value from control
*
* t_p_ptr = <int32_t *> t_p.data # <<<<<<<<<<<<<<
@@ -7991,7 +8028,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_t_p_ptr = ((int32_t *)__pyx_v_t_p->data);
- /* "MACS2/IO/CallPeakUnit.pyx":549
+ /* "MACS2/IO/CallPeakUnit.pyx":550
*
* t_p_ptr = <int32_t *> t_p.data
* t_v_ptr = <float32_t *> t_v.data # <<<<<<<<<<<<<<
@@ -8000,7 +8037,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_t_v_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_t_v->data);
- /* "MACS2/IO/CallPeakUnit.pyx":550
+ /* "MACS2/IO/CallPeakUnit.pyx":551
* t_p_ptr = <int32_t *> t_p.data
* t_v_ptr = <float32_t *> t_v.data
* c_p_ptr = <int32_t *> c_p.data # <<<<<<<<<<<<<<
@@ -8009,7 +8046,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_c_p_ptr = ((int32_t *)__pyx_v_c_p->data);
- /* "MACS2/IO/CallPeakUnit.pyx":551
+ /* "MACS2/IO/CallPeakUnit.pyx":552
* t_v_ptr = <float32_t *> t_v.data
* c_p_ptr = <int32_t *> c_p.data
* c_v_ptr = <float32_t *> c_v.data # <<<<<<<<<<<<<<
@@ -8018,7 +8055,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_c_v_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_c_v->data);
- /* "MACS2/IO/CallPeakUnit.pyx":552
+ /* "MACS2/IO/CallPeakUnit.pyx":553
* c_p_ptr = <int32_t *> c_p.data
* c_v_ptr = <float32_t *> c_v.data
* ret_p_ptr = <int32_t *> ret_p.data # <<<<<<<<<<<<<<
@@ -8027,7 +8064,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ret_p_ptr = ((int32_t *)__pyx_v_ret_p->data);
- /* "MACS2/IO/CallPeakUnit.pyx":553
+ /* "MACS2/IO/CallPeakUnit.pyx":554
* c_v_ptr = <float32_t *> c_v.data
* ret_p_ptr = <int32_t *> ret_p.data
* ret_t_ptr = <float32_t *>ret_t.data # <<<<<<<<<<<<<<
@@ -8036,7 +8073,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ret_t_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_ret_t->data);
- /* "MACS2/IO/CallPeakUnit.pyx":554
+ /* "MACS2/IO/CallPeakUnit.pyx":555
* ret_p_ptr = <int32_t *> ret_p.data
* ret_t_ptr = <float32_t *>ret_t.data
* ret_c_ptr = <float32_t *>ret_c.data # <<<<<<<<<<<<<<
@@ -8045,7 +8082,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ret_c_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_ret_c->data);
- /* "MACS2/IO/CallPeakUnit.pyx":556
+ /* "MACS2/IO/CallPeakUnit.pyx":557
* ret_c_ptr = <float32_t *>ret_c.data
*
* pre_p = 0 # <<<<<<<<<<<<<<
@@ -8054,7 +8091,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_pre_p = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":557
+ /* "MACS2/IO/CallPeakUnit.pyx":558
*
* pre_p = 0
* index_ret = 0 # <<<<<<<<<<<<<<
@@ -8063,7 +8100,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_index_ret = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":558
+ /* "MACS2/IO/CallPeakUnit.pyx":559
* pre_p = 0
* index_ret = 0
* it = 0 # <<<<<<<<<<<<<<
@@ -8072,7 +8109,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_it = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":559
+ /* "MACS2/IO/CallPeakUnit.pyx":560
* index_ret = 0
* it = 0
* ic = 0 # <<<<<<<<<<<<<<
@@ -8081,7 +8118,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ic = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":561
+ /* "MACS2/IO/CallPeakUnit.pyx":562
* ic = 0
*
* while it < lt and ic < lc: # <<<<<<<<<<<<<<
@@ -8100,7 +8137,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_L9_bool_binop_done:;
if (!__pyx_t_12) break;
- /* "MACS2/IO/CallPeakUnit.pyx":562
+ /* "MACS2/IO/CallPeakUnit.pyx":563
*
* while it < lt and ic < lc:
* if t_p_ptr[0] < c_p_ptr[0]: # <<<<<<<<<<<<<<
@@ -8110,7 +8147,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_t_12 = (((__pyx_v_t_p_ptr[0]) < (__pyx_v_c_p_ptr[0])) != 0);
if (__pyx_t_12) {
- /* "MACS2/IO/CallPeakUnit.pyx":564
+ /* "MACS2/IO/CallPeakUnit.pyx":565
* if t_p_ptr[0] < c_p_ptr[0]:
* # clip a region from pre_p to p1, then set pre_p as p1.
* ret_p_ptr[0] = t_p_ptr[0] # <<<<<<<<<<<<<<
@@ -8119,7 +8156,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
(__pyx_v_ret_p_ptr[0]) = (__pyx_v_t_p_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":565
+ /* "MACS2/IO/CallPeakUnit.pyx":566
* # clip a region from pre_p to p1, then set pre_p as p1.
* ret_p_ptr[0] = t_p_ptr[0]
* ret_t_ptr[0] = t_v_ptr[0] # <<<<<<<<<<<<<<
@@ -8128,7 +8165,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
(__pyx_v_ret_t_ptr[0]) = (__pyx_v_t_v_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":566
+ /* "MACS2/IO/CallPeakUnit.pyx":567
* ret_p_ptr[0] = t_p_ptr[0]
* ret_t_ptr[0] = t_v_ptr[0]
* ret_c_ptr[0] = c_v_ptr[0] # <<<<<<<<<<<<<<
@@ -8137,7 +8174,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
(__pyx_v_ret_c_ptr[0]) = (__pyx_v_c_v_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":567
+ /* "MACS2/IO/CallPeakUnit.pyx":568
* ret_t_ptr[0] = t_v_ptr[0]
* ret_c_ptr[0] = c_v_ptr[0]
* ret_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8146,7 +8183,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ret_p_ptr = (__pyx_v_ret_p_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":568
+ /* "MACS2/IO/CallPeakUnit.pyx":569
* ret_c_ptr[0] = c_v_ptr[0]
* ret_p_ptr += 1
* ret_t_ptr += 1 # <<<<<<<<<<<<<<
@@ -8155,7 +8192,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ret_t_ptr = (__pyx_v_ret_t_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":569
+ /* "MACS2/IO/CallPeakUnit.pyx":570
* ret_p_ptr += 1
* ret_t_ptr += 1
* ret_c_ptr += 1 # <<<<<<<<<<<<<<
@@ -8164,7 +8201,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ret_c_ptr = (__pyx_v_ret_c_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":570
+ /* "MACS2/IO/CallPeakUnit.pyx":571
* ret_t_ptr += 1
* ret_c_ptr += 1
* pre_p = t_p_ptr[0] # <<<<<<<<<<<<<<
@@ -8173,7 +8210,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_pre_p = (__pyx_v_t_p_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":571
+ /* "MACS2/IO/CallPeakUnit.pyx":572
* ret_c_ptr += 1
* pre_p = t_p_ptr[0]
* index_ret += 1 # <<<<<<<<<<<<<<
@@ -8182,7 +8219,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_index_ret = (__pyx_v_index_ret + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":573
+ /* "MACS2/IO/CallPeakUnit.pyx":574
* index_ret += 1
* # call for the next p1 and v1
* it += 1 # <<<<<<<<<<<<<<
@@ -8191,7 +8228,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_it = (__pyx_v_it + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":574
+ /* "MACS2/IO/CallPeakUnit.pyx":575
* # call for the next p1 and v1
* it += 1
* t_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8200,7 +8237,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_t_p_ptr = (__pyx_v_t_p_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":575
+ /* "MACS2/IO/CallPeakUnit.pyx":576
* it += 1
* t_p_ptr += 1
* t_v_ptr += 1 # <<<<<<<<<<<<<<
@@ -8211,7 +8248,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
goto __pyx_L11;
}
- /* "MACS2/IO/CallPeakUnit.pyx":576
+ /* "MACS2/IO/CallPeakUnit.pyx":577
* t_p_ptr += 1
* t_v_ptr += 1
* elif t_p_ptr[0] > c_p_ptr[0]: # <<<<<<<<<<<<<<
@@ -8221,7 +8258,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_t_12 = (((__pyx_v_t_p_ptr[0]) > (__pyx_v_c_p_ptr[0])) != 0);
if (__pyx_t_12) {
- /* "MACS2/IO/CallPeakUnit.pyx":578
+ /* "MACS2/IO/CallPeakUnit.pyx":579
* elif t_p_ptr[0] > c_p_ptr[0]:
* # clip a region from pre_p to p2, then set pre_p as p2.
* ret_p_ptr[0] = c_p_ptr[0] # <<<<<<<<<<<<<<
@@ -8230,7 +8267,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
(__pyx_v_ret_p_ptr[0]) = (__pyx_v_c_p_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":579
+ /* "MACS2/IO/CallPeakUnit.pyx":580
* # clip a region from pre_p to p2, then set pre_p as p2.
* ret_p_ptr[0] = c_p_ptr[0]
* ret_t_ptr[0] = t_v_ptr[0] # <<<<<<<<<<<<<<
@@ -8239,7 +8276,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
(__pyx_v_ret_t_ptr[0]) = (__pyx_v_t_v_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":580
+ /* "MACS2/IO/CallPeakUnit.pyx":581
* ret_p_ptr[0] = c_p_ptr[0]
* ret_t_ptr[0] = t_v_ptr[0]
* ret_c_ptr[0] = c_v_ptr[0] # <<<<<<<<<<<<<<
@@ -8248,7 +8285,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
(__pyx_v_ret_c_ptr[0]) = (__pyx_v_c_v_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":581
+ /* "MACS2/IO/CallPeakUnit.pyx":582
* ret_t_ptr[0] = t_v_ptr[0]
* ret_c_ptr[0] = c_v_ptr[0]
* ret_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8257,7 +8294,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ret_p_ptr = (__pyx_v_ret_p_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":582
+ /* "MACS2/IO/CallPeakUnit.pyx":583
* ret_c_ptr[0] = c_v_ptr[0]
* ret_p_ptr += 1
* ret_t_ptr += 1 # <<<<<<<<<<<<<<
@@ -8266,7 +8303,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ret_t_ptr = (__pyx_v_ret_t_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":583
+ /* "MACS2/IO/CallPeakUnit.pyx":584
* ret_p_ptr += 1
* ret_t_ptr += 1
* ret_c_ptr += 1 # <<<<<<<<<<<<<<
@@ -8275,7 +8312,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ret_c_ptr = (__pyx_v_ret_c_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":584
+ /* "MACS2/IO/CallPeakUnit.pyx":585
* ret_t_ptr += 1
* ret_c_ptr += 1
* pre_p = c_p_ptr[0] # <<<<<<<<<<<<<<
@@ -8284,7 +8321,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_pre_p = (__pyx_v_c_p_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":585
+ /* "MACS2/IO/CallPeakUnit.pyx":586
* ret_c_ptr += 1
* pre_p = c_p_ptr[0]
* index_ret += 1 # <<<<<<<<<<<<<<
@@ -8293,7 +8330,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_index_ret = (__pyx_v_index_ret + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":587
+ /* "MACS2/IO/CallPeakUnit.pyx":588
* index_ret += 1
* # call for the next p2 and v2
* ic += 1 # <<<<<<<<<<<<<<
@@ -8302,7 +8339,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ic = (__pyx_v_ic + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":588
+ /* "MACS2/IO/CallPeakUnit.pyx":589
* # call for the next p2 and v2
* ic += 1
* c_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8311,7 +8348,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_c_p_ptr = (__pyx_v_c_p_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":589
+ /* "MACS2/IO/CallPeakUnit.pyx":590
* ic += 1
* c_p_ptr += 1
* c_v_ptr += 1 # <<<<<<<<<<<<<<
@@ -8323,7 +8360,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":592
+ /* "MACS2/IO/CallPeakUnit.pyx":593
* else:
* # from pre_p to p1 or p2, then set pre_p as p1 or p2.
* ret_p_ptr[0] = t_p_ptr[0] # <<<<<<<<<<<<<<
@@ -8332,7 +8369,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
(__pyx_v_ret_p_ptr[0]) = (__pyx_v_t_p_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":593
+ /* "MACS2/IO/CallPeakUnit.pyx":594
* # from pre_p to p1 or p2, then set pre_p as p1 or p2.
* ret_p_ptr[0] = t_p_ptr[0]
* ret_t_ptr[0] = t_v_ptr[0] # <<<<<<<<<<<<<<
@@ -8341,7 +8378,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
(__pyx_v_ret_t_ptr[0]) = (__pyx_v_t_v_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":594
+ /* "MACS2/IO/CallPeakUnit.pyx":595
* ret_p_ptr[0] = t_p_ptr[0]
* ret_t_ptr[0] = t_v_ptr[0]
* ret_c_ptr[0] = c_v_ptr[0] # <<<<<<<<<<<<<<
@@ -8350,7 +8387,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
(__pyx_v_ret_c_ptr[0]) = (__pyx_v_c_v_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":595
+ /* "MACS2/IO/CallPeakUnit.pyx":596
* ret_t_ptr[0] = t_v_ptr[0]
* ret_c_ptr[0] = c_v_ptr[0]
* ret_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8359,7 +8396,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ret_p_ptr = (__pyx_v_ret_p_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":596
+ /* "MACS2/IO/CallPeakUnit.pyx":597
* ret_c_ptr[0] = c_v_ptr[0]
* ret_p_ptr += 1
* ret_t_ptr += 1 # <<<<<<<<<<<<<<
@@ -8368,7 +8405,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ret_t_ptr = (__pyx_v_ret_t_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":597
+ /* "MACS2/IO/CallPeakUnit.pyx":598
* ret_p_ptr += 1
* ret_t_ptr += 1
* ret_c_ptr += 1 # <<<<<<<<<<<<<<
@@ -8377,7 +8414,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ret_c_ptr = (__pyx_v_ret_c_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":598
+ /* "MACS2/IO/CallPeakUnit.pyx":599
* ret_t_ptr += 1
* ret_c_ptr += 1
* pre_p = t_p_ptr[0] # <<<<<<<<<<<<<<
@@ -8386,7 +8423,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_pre_p = (__pyx_v_t_p_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":599
+ /* "MACS2/IO/CallPeakUnit.pyx":600
* ret_c_ptr += 1
* pre_p = t_p_ptr[0]
* index_ret += 1 # <<<<<<<<<<<<<<
@@ -8395,7 +8432,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_index_ret = (__pyx_v_index_ret + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":601
+ /* "MACS2/IO/CallPeakUnit.pyx":602
* index_ret += 1
* # call for the next p1, v1, p2, v2.
* it += 1 # <<<<<<<<<<<<<<
@@ -8404,7 +8441,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_it = (__pyx_v_it + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":602
+ /* "MACS2/IO/CallPeakUnit.pyx":603
* # call for the next p1, v1, p2, v2.
* it += 1
* ic += 1 # <<<<<<<<<<<<<<
@@ -8413,7 +8450,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ic = (__pyx_v_ic + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":603
+ /* "MACS2/IO/CallPeakUnit.pyx":604
* it += 1
* ic += 1
* t_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8422,7 +8459,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_t_p_ptr = (__pyx_v_t_p_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":604
+ /* "MACS2/IO/CallPeakUnit.pyx":605
* ic += 1
* t_p_ptr += 1
* t_v_ptr += 1 # <<<<<<<<<<<<<<
@@ -8431,7 +8468,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_t_v_ptr = (__pyx_v_t_v_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":605
+ /* "MACS2/IO/CallPeakUnit.pyx":606
* t_p_ptr += 1
* t_v_ptr += 1
* c_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8440,7 +8477,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_c_p_ptr = (__pyx_v_c_p_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":606
+ /* "MACS2/IO/CallPeakUnit.pyx":607
* t_v_ptr += 1
* c_p_ptr += 1
* c_v_ptr += 1 # <<<<<<<<<<<<<<
@@ -8452,85 +8489,85 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_L11:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":608
+ /* "MACS2/IO/CallPeakUnit.pyx":609
* c_v_ptr += 1
*
* ret_p.resize( index_ret, refcheck=False) # <<<<<<<<<<<<<<
* ret_t.resize( index_ret, refcheck=False)
* ret_c.resize( index_ret, refcheck=False)
*/
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_ret_p), __pyx_n_s_resize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_ret_p), __pyx_n_s_resize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyInt_From_long(__pyx_v_index_ret); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_From_long(__pyx_v_index_ret); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":609
+ /* "MACS2/IO/CallPeakUnit.pyx":610
*
* ret_p.resize( index_ret, refcheck=False)
* ret_t.resize( index_ret, refcheck=False) # <<<<<<<<<<<<<<
* ret_c.resize( index_ret, refcheck=False)
* return [ret_p, ret_t, ret_c]
*/
- __pyx_t_11 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_ret_t), __pyx_n_s_resize); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_ret_t), __pyx_n_s_resize); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_2 = __Pyx_PyInt_From_long(__pyx_v_index_ret); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_From_long(__pyx_v_index_ret); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":610
+ /* "MACS2/IO/CallPeakUnit.pyx":611
* ret_p.resize( index_ret, refcheck=False)
* ret_t.resize( index_ret, refcheck=False)
* ret_c.resize( index_ret, refcheck=False) # <<<<<<<<<<<<<<
* return [ret_p, ret_t, ret_c]
*
*/
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_ret_c), __pyx_n_s_resize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_ret_c), __pyx_n_s_resize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyInt_From_long(__pyx_v_index_ret); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_From_long(__pyx_v_index_ret); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":611
+ /* "MACS2/IO/CallPeakUnit.pyx":612
* ret_t.resize( index_ret, refcheck=False)
* ret_c.resize( index_ret, refcheck=False)
* return [ret_p, ret_t, ret_c] # <<<<<<<<<<<<<<
@@ -8538,7 +8575,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
* cdef np.ndarray __cal_score ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2, cal_func ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_11 = PyList_New(3); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyList_New(3); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_INCREF(((PyObject *)__pyx_v_ret_p));
PyList_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_v_ret_p));
@@ -8553,7 +8590,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_t_11 = 0;
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":514
+ /* "MACS2/IO/CallPeakUnit.pyx":515
* return
*
* cdef list __chrom_pair_treat_ctrl ( self, treat_pv, ctrl_pv ): # <<<<<<<<<<<<<<
@@ -8601,7 +8638,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":613
+/* "MACS2/IO/CallPeakUnit.pyx":614
* return [ret_p, ret_t, ret_c]
*
* cdef np.ndarray __cal_score ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2, cal_func ): # <<<<<<<<<<<<<<
@@ -8656,16 +8693,16 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_pybuffernd_array2.rcbuffer = &__pyx_pybuffer_array2;
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array1.diminfo[0].strides = __pyx_pybuffernd_array1.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array1.diminfo[0].shape = __pyx_pybuffernd_array1.rcbuffer->pybuffer.shape[0];
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array2.diminfo[0].strides = __pyx_pybuffernd_array2.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array2.diminfo[0].shape = __pyx_pybuffernd_array2.rcbuffer->pybuffer.shape[0];
- /* "MACS2/IO/CallPeakUnit.pyx":617
+ /* "MACS2/IO/CallPeakUnit.pyx":618
* long i
* np.ndarray[np.float32_t, ndim=1] s
* assert array1.shape[0] == array2.shape[0] # <<<<<<<<<<<<<<
@@ -8676,39 +8713,39 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
if (unlikely(!Py_OptimizeFlag)) {
if (unlikely(!(((__pyx_v_array1->dimensions[0]) == (__pyx_v_array2->dimensions[0])) != 0))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
}
#endif
- /* "MACS2/IO/CallPeakUnit.pyx":618
+ /* "MACS2/IO/CallPeakUnit.pyx":619
* np.ndarray[np.float32_t, ndim=1] s
* assert array1.shape[0] == array2.shape[0]
* s = np.zeros(array1.shape[0], dtype="float32") # <<<<<<<<<<<<<<
* #ptr = <float *> s.data
* for i in range(array1.shape[0]):
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = ((PyArrayObject *)__pyx_t_4);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -8724,13 +8761,13 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
}
}
__pyx_pybuffernd_s.diminfo[0].strides = __pyx_pybuffernd_s.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_s.diminfo[0].shape = __pyx_pybuffernd_s.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = 0;
__pyx_v_s = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":620
+ /* "MACS2/IO/CallPeakUnit.pyx":621
* s = np.zeros(array1.shape[0], dtype="float32")
* #ptr = <float *> s.data
* for i in range(array1.shape[0]): # <<<<<<<<<<<<<<
@@ -8741,7 +8778,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) {
__pyx_v_i = __pyx_t_11;
- /* "MACS2/IO/CallPeakUnit.pyx":621
+ /* "MACS2/IO/CallPeakUnit.pyx":622
* #ptr = <float *> s.data
* for i in range(array1.shape[0]):
* s[i] = cal_func( array1[i], array2[i] ) # <<<<<<<<<<<<<<
@@ -8756,9 +8793,9 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
} else if (unlikely(__pyx_t_12 >= __pyx_pybuffernd_array1.diminfo[0].shape)) __pyx_t_6 = 0;
if (unlikely(__pyx_t_6 != -1)) {
__Pyx_RaiseBufferIndexError(__pyx_t_6);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = PyFloat_FromDouble((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_array1.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_array1.diminfo[0].strides))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_array1.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_array1.diminfo[0].strides))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_13 = __pyx_v_i;
__pyx_t_6 = -1;
@@ -8768,9 +8805,9 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
} else if (unlikely(__pyx_t_13 >= __pyx_pybuffernd_array2.diminfo[0].shape)) __pyx_t_6 = 0;
if (unlikely(__pyx_t_6 != -1)) {
__Pyx_RaiseBufferIndexError(__pyx_t_6);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = PyFloat_FromDouble((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_array2.rcbuffer->pybuffer.buf, __pyx_t_13, __pyx_pybuffernd_array2.diminfo[0].strides))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_array2.rcbuffer->pybuffer.buf, __pyx_t_13, __pyx_pybuffernd_array2.diminfo[0].strides))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_cal_func);
__pyx_t_2 = __pyx_v_cal_func; __pyx_t_14 = NULL;
@@ -8785,7 +8822,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_t_15 = 1;
}
}
- __pyx_t_16 = PyTuple_New(2+__pyx_t_15); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = PyTuple_New(2+__pyx_t_15); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_16);
if (__pyx_t_14) {
PyTuple_SET_ITEM(__pyx_t_16, 0, __pyx_t_14); __Pyx_GIVEREF(__pyx_t_14); __pyx_t_14 = NULL;
@@ -8796,11 +8833,11 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_1 = 0;
__pyx_t_3 = 0;
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_16, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_16, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_17 = __pyx_PyFloat_AsFloat(__pyx_t_4); if (unlikely((__pyx_t_17 == (npy_float32)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_17 = __pyx_PyFloat_AsFloat(__pyx_t_4); if (unlikely((__pyx_t_17 == (npy_float32)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_18 = __pyx_v_i;
__pyx_t_6 = -1;
@@ -8810,12 +8847,12 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
} else if (unlikely(__pyx_t_18 >= __pyx_pybuffernd_s.diminfo[0].shape)) __pyx_t_6 = 0;
if (unlikely(__pyx_t_6 != -1)) {
__Pyx_RaiseBufferIndexError(__pyx_t_6);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_s.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_s.diminfo[0].strides) = __pyx_t_17;
}
- /* "MACS2/IO/CallPeakUnit.pyx":623
+ /* "MACS2/IO/CallPeakUnit.pyx":624
* s[i] = cal_func( array1[i], array2[i] )
* #ptr += 1
* return s # <<<<<<<<<<<<<<
@@ -8827,7 +8864,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_r = ((PyArrayObject *)__pyx_v_s);
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":613
+ /* "MACS2/IO/CallPeakUnit.pyx":614
* return [ret_p, ret_t, ret_c]
*
* cdef np.ndarray __cal_score ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2, cal_func ): # <<<<<<<<<<<<<<
@@ -8863,7 +8900,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":625
+/* "MACS2/IO/CallPeakUnit.pyx":626
* return s
*
* cdef object __cal_pvalue_qvalue_table ( self ): # <<<<<<<<<<<<<<
@@ -8921,19 +8958,19 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__cal_pvalue_qvalue_table", 0);
- /* "MACS2/IO/CallPeakUnit.pyx":633
+ /* "MACS2/IO/CallPeakUnit.pyx":634
* str chrom
* np.ndarray pos_array, treat_array, ctrl_array, score_array
* dict pvalue_stat = {} # <<<<<<<<<<<<<<
* long n, pre_p, length, j, pre_l, l, i
* float this_v, pre_v, v, q, pre_q
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_pvalue_stat = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":638
+ /* "MACS2/IO/CallPeakUnit.pyx":639
* long N, k, this_l
* float f
* long nhcal = 0 # <<<<<<<<<<<<<<
@@ -8942,7 +8979,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_nhcal = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":639
+ /* "MACS2/IO/CallPeakUnit.pyx":640
* float f
* long nhcal = 0
* long npcal = 0 # <<<<<<<<<<<<<<
@@ -8951,24 +8988,24 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_npcal = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":646
+ /* "MACS2/IO/CallPeakUnit.pyx":647
* float32_t * ctrl_value_ptr
*
* logging.debug ( "Start to calculate pvalue stat..." ) # <<<<<<<<<<<<<<
*
* for i in range( len( self.chromosomes ) ):
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_debug); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_debug); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__14, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__14, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":648
+ /* "MACS2/IO/CallPeakUnit.pyx":649
* logging.debug ( "Start to calculate pvalue stat..." )
*
* for i in range( len( self.chromosomes ) ): # <<<<<<<<<<<<<<
@@ -8979,14 +9016,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
__Pyx_INCREF(__pyx_t_1);
if (unlikely(__pyx_t_1 == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = PyList_GET_SIZE(__pyx_t_1); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_GET_SIZE(__pyx_t_1); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
__pyx_v_i = __pyx_t_4;
- /* "MACS2/IO/CallPeakUnit.pyx":649
+ /* "MACS2/IO/CallPeakUnit.pyx":650
*
* for i in range( len( self.chromosomes ) ):
* chrom = self.chromosomes[ i ] # <<<<<<<<<<<<<<
@@ -8995,15 +9032,15 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
if (unlikely(__pyx_v_self->chromosomes == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_self->chromosomes, __pyx_v_i, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_self->chromosomes, __pyx_v_i, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_chrom, ((PyObject*)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":650
+ /* "MACS2/IO/CallPeakUnit.pyx":651
* for i in range( len( self.chromosomes ) ):
* chrom = self.chromosomes[ i ]
* pre_p = 0 # <<<<<<<<<<<<<<
@@ -9012,18 +9049,18 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_pre_p = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":652
+ /* "MACS2/IO/CallPeakUnit.pyx":653
* pre_p = 0
*
* self.__pileup_treat_ctrl_a_chromosome( chrom ) # <<<<<<<<<<<<<<
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl
*
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___pileup_treat_ctrl_a_chromosome(__pyx_v_self, __pyx_v_chrom); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___pileup_treat_ctrl_a_chromosome(__pyx_v_self, __pyx_v_chrom); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":653
+ /* "MACS2/IO/CallPeakUnit.pyx":654
*
* self.__pileup_treat_ctrl_a_chromosome( chrom )
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl # <<<<<<<<<<<<<<
@@ -9042,7 +9079,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
if (unlikely(size != 3)) {
if (size > 3) __Pyx_RaiseTooManyValuesError(3);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
__pyx_t_2 = PyList_GET_ITEM(sequence, 0);
@@ -9052,20 +9089,20 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
__Pyx_INCREF(__pyx_t_5);
__Pyx_INCREF(__pyx_t_6);
#else
- __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
#endif
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
} else {
- __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_pos_array, ((PyArrayObject *)__pyx_t_2));
__pyx_t_2 = 0;
__Pyx_XDECREF_SET(__pyx_v_treat_array, ((PyArrayObject *)__pyx_t_5));
@@ -9073,7 +9110,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
__Pyx_XDECREF_SET(__pyx_v_ctrl_array, ((PyArrayObject *)__pyx_t_6));
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":655
+ /* "MACS2/IO/CallPeakUnit.pyx":656
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl
*
* pos_ptr = <int32_t *> pos_array.data # <<<<<<<<<<<<<<
@@ -9082,7 +9119,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_pos_ptr = ((int32_t *)__pyx_v_pos_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":656
+ /* "MACS2/IO/CallPeakUnit.pyx":657
*
* pos_ptr = <int32_t *> pos_array.data
* treat_value_ptr = <float32_t *> treat_array.data # <<<<<<<<<<<<<<
@@ -9091,7 +9128,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_treat_value_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_treat_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":657
+ /* "MACS2/IO/CallPeakUnit.pyx":658
* pos_ptr = <int32_t *> pos_array.data
* treat_value_ptr = <float32_t *> treat_array.data
* ctrl_value_ptr = <float32_t *> ctrl_array.data # <<<<<<<<<<<<<<
@@ -9100,7 +9137,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_ctrl_value_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_ctrl_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":659
+ /* "MACS2/IO/CallPeakUnit.pyx":660
* ctrl_value_ptr = <float32_t *> ctrl_array.data
*
* for j in range(pos_array.shape[0]): # <<<<<<<<<<<<<<
@@ -9111,26 +9148,26 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_7; __pyx_t_8+=1) {
__pyx_v_j = __pyx_t_8;
- /* "MACS2/IO/CallPeakUnit.pyx":660
+ /* "MACS2/IO/CallPeakUnit.pyx":661
*
* for j in range(pos_array.shape[0]):
* this_v = get_pscore( int(treat_value_ptr[0]), ctrl_value_ptr[0] ) # <<<<<<<<<<<<<<
* this_l = pos_ptr[0] - pre_p
*
*/
- __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_get_pscore); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_get_pscore); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = PyFloat_FromDouble((__pyx_v_treat_value_ptr[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyFloat_FromDouble((__pyx_v_treat_value_ptr[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_2, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_2, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyFloat_FromDouble((__pyx_v_ctrl_value_ptr[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyFloat_FromDouble((__pyx_v_ctrl_value_ptr[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_9 = NULL;
__pyx_t_10 = 0;
@@ -9144,7 +9181,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
__pyx_t_10 = 1;
}
}
- __pyx_t_11 = PyTuple_New(2+__pyx_t_10); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyTuple_New(2+__pyx_t_10); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
if (__pyx_t_9) {
PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_9); __Pyx_GIVEREF(__pyx_t_9); __pyx_t_9 = NULL;
@@ -9155,15 +9192,15 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_5 = 0;
__pyx_t_2 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_11, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_11, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_12 = __pyx_PyFloat_AsFloat(__pyx_t_1); if (unlikely((__pyx_t_12 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __pyx_PyFloat_AsFloat(__pyx_t_1); if (unlikely((__pyx_t_12 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_this_v = __pyx_t_12;
- /* "MACS2/IO/CallPeakUnit.pyx":661
+ /* "MACS2/IO/CallPeakUnit.pyx":662
* for j in range(pos_array.shape[0]):
* this_v = get_pscore( int(treat_value_ptr[0]), ctrl_value_ptr[0] )
* this_l = pos_ptr[0] - pre_p # <<<<<<<<<<<<<<
@@ -9172,62 +9209,62 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_this_l = ((__pyx_v_pos_ptr[0]) - __pyx_v_pre_p);
- /* "MACS2/IO/CallPeakUnit.pyx":663
+ /* "MACS2/IO/CallPeakUnit.pyx":664
* this_l = pos_ptr[0] - pre_p
*
* if pvalue_stat.has_key( this_v ): # <<<<<<<<<<<<<<
* pvalue_stat[ this_v ] += this_l
* else:
*/
- __pyx_t_1 = PyFloat_FromDouble(__pyx_v_this_v); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_this_v); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_13 = PyDict_Contains(__pyx_v_pvalue_stat, __pyx_t_1); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyDict_Contains(__pyx_v_pvalue_stat, __pyx_t_1); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_14 = (__pyx_t_13 != 0);
if (__pyx_t_14) {
- /* "MACS2/IO/CallPeakUnit.pyx":664
+ /* "MACS2/IO/CallPeakUnit.pyx":665
*
* if pvalue_stat.has_key( this_v ):
* pvalue_stat[ this_v ] += this_l # <<<<<<<<<<<<<<
* else:
* pvalue_stat[ this_v ] = this_l
*/
- __pyx_t_1 = PyFloat_FromDouble(__pyx_v_this_v); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_this_v); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = __Pyx_PyDict_GetItem(__pyx_v_pvalue_stat, __pyx_t_1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_6 = __Pyx_PyDict_GetItem(__pyx_v_pvalue_stat, __pyx_t_1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 665; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_11 = __Pyx_PyInt_From_long(__pyx_v_this_l); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyInt_From_long(__pyx_v_this_l); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_t_6, __pyx_t_11); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_t_6, __pyx_t_11); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- if (unlikely(PyDict_SetItem(__pyx_v_pvalue_stat, __pyx_t_1, __pyx_t_2) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyDict_SetItem(__pyx_v_pvalue_stat, __pyx_t_1, __pyx_t_2) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L7;
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":666
+ /* "MACS2/IO/CallPeakUnit.pyx":667
* pvalue_stat[ this_v ] += this_l
* else:
* pvalue_stat[ this_v ] = this_l # <<<<<<<<<<<<<<
* pre_p = pos_ptr[0]
* pos_ptr += 1
*/
- __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v_this_l); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v_this_l); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyFloat_FromDouble(__pyx_v_this_v); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyFloat_FromDouble(__pyx_v_this_v); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (unlikely(PyDict_SetItem(__pyx_v_pvalue_stat, __pyx_t_2, __pyx_t_1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyDict_SetItem(__pyx_v_pvalue_stat, __pyx_t_2, __pyx_t_1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
__pyx_L7:;
- /* "MACS2/IO/CallPeakUnit.pyx":667
+ /* "MACS2/IO/CallPeakUnit.pyx":668
* else:
* pvalue_stat[ this_v ] = this_l
* pre_p = pos_ptr[0] # <<<<<<<<<<<<<<
@@ -9236,7 +9273,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_pre_p = (__pyx_v_pos_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":668
+ /* "MACS2/IO/CallPeakUnit.pyx":669
* pvalue_stat[ this_v ] = this_l
* pre_p = pos_ptr[0]
* pos_ptr += 1 # <<<<<<<<<<<<<<
@@ -9245,7 +9282,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_pos_ptr = (__pyx_v_pos_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":669
+ /* "MACS2/IO/CallPeakUnit.pyx":670
* pre_p = pos_ptr[0]
* pos_ptr += 1
* treat_value_ptr += 1 # <<<<<<<<<<<<<<
@@ -9254,7 +9291,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_treat_value_ptr = (__pyx_v_treat_value_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":670
+ /* "MACS2/IO/CallPeakUnit.pyx":671
* pos_ptr += 1
* treat_value_ptr += 1
* ctrl_value_ptr += 1 # <<<<<<<<<<<<<<
@@ -9264,7 +9301,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
__pyx_v_ctrl_value_ptr = (__pyx_v_ctrl_value_ptr + 1);
}
- /* "MACS2/IO/CallPeakUnit.pyx":672
+ /* "MACS2/IO/CallPeakUnit.pyx":673
* ctrl_value_ptr += 1
*
* nhcal += pos_array.shape[0] # <<<<<<<<<<<<<<
@@ -9274,7 +9311,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
__pyx_v_nhcal = (__pyx_v_nhcal + (__pyx_v_pos_array->dimensions[0]));
}
- /* "MACS2/IO/CallPeakUnit.pyx":677
+ /* "MACS2/IO/CallPeakUnit.pyx":678
* #logging.debug ( "calculate pvalue/access hash for %d times" % nhcal )
* #logging.debug ( "access hash for %d times" % nhcal )
* nhval = 0 # <<<<<<<<<<<<<<
@@ -9283,28 +9320,28 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_nhval = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":679
+ /* "MACS2/IO/CallPeakUnit.pyx":680
* nhval = 0
*
* N = sum(pvalue_stat.values()) # total length # <<<<<<<<<<<<<<
* k = 1 # rank
* f = -log10(N)
*/
- __pyx_t_1 = __Pyx_PyDict_Values(__pyx_v_pvalue_stat); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyDict_Values(__pyx_v_pvalue_stat); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_4 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_N = __pyx_t_4;
- /* "MACS2/IO/CallPeakUnit.pyx":680
+ /* "MACS2/IO/CallPeakUnit.pyx":681
*
* N = sum(pvalue_stat.values()) # total length
* k = 1 # rank # <<<<<<<<<<<<<<
@@ -9313,7 +9350,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_k = 1;
- /* "MACS2/IO/CallPeakUnit.pyx":681
+ /* "MACS2/IO/CallPeakUnit.pyx":682
* N = sum(pvalue_stat.values()) # total length
* k = 1 # rank
* f = -log10(N) # <<<<<<<<<<<<<<
@@ -9322,7 +9359,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_f = (-log10(__pyx_v_N));
- /* "MACS2/IO/CallPeakUnit.pyx":682
+ /* "MACS2/IO/CallPeakUnit.pyx":683
* k = 1 # rank
* f = -log10(N)
* pre_v = -2147483647 # <<<<<<<<<<<<<<
@@ -9331,7 +9368,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_pre_v = -2147483647.0;
- /* "MACS2/IO/CallPeakUnit.pyx":683
+ /* "MACS2/IO/CallPeakUnit.pyx":684
* f = -log10(N)
* pre_v = -2147483647
* pre_l = 0 # <<<<<<<<<<<<<<
@@ -9340,7 +9377,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_pre_l = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":684
+ /* "MACS2/IO/CallPeakUnit.pyx":685
* pre_v = -2147483647
* pre_l = 0
* pre_q = 2147483647 # save the previous q-value # <<<<<<<<<<<<<<
@@ -9349,14 +9386,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_pre_q = 2147483647.0;
- /* "MACS2/IO/CallPeakUnit.pyx":687
+ /* "MACS2/IO/CallPeakUnit.pyx":688
*
* #self.pqtable = {}
* self.pqtable = Float64HashTable() # <<<<<<<<<<<<<<
* unique_values = sorted(pvalue_stat.keys(), reverse=True) #sorted(unique_values,reverse=True)
* for i in range(len(unique_values)):
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_Float64HashTable); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_Float64HashTable); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_11 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) {
@@ -9369,10 +9406,10 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
}
}
if (__pyx_t_11) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_11); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_11); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -9382,32 +9419,32 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
__pyx_v_self->pqtable = __pyx_t_1;
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":688
+ /* "MACS2/IO/CallPeakUnit.pyx":689
* #self.pqtable = {}
* self.pqtable = Float64HashTable()
* unique_values = sorted(pvalue_stat.keys(), reverse=True) #sorted(unique_values,reverse=True) # <<<<<<<<<<<<<<
* for i in range(len(unique_values)):
* v = unique_values[i]
*/
- __pyx_t_1 = __Pyx_PyDict_Keys(__pyx_v_pvalue_stat); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyDict_Keys(__pyx_v_pvalue_stat); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_reverse, Py_True) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = __Pyx_PyObject_Call(__pyx_builtin_sorted, __pyx_t_2, __pyx_t_1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_reverse, Py_True) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_Call(__pyx_builtin_sorted, __pyx_t_2, __pyx_t_1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(PyList_CheckExact(__pyx_t_11))||((__pyx_t_11) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_11)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyList_CheckExact(__pyx_t_11))||((__pyx_t_11) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_11)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_unique_values = ((PyObject*)__pyx_t_11);
__pyx_t_11 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":689
+ /* "MACS2/IO/CallPeakUnit.pyx":690
* self.pqtable = Float64HashTable()
* unique_values = sorted(pvalue_stat.keys(), reverse=True) #sorted(unique_values,reverse=True)
* for i in range(len(unique_values)): # <<<<<<<<<<<<<<
@@ -9416,13 +9453,13 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
if (unlikely(__pyx_v_unique_values == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = PyList_GET_SIZE(__pyx_v_unique_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_GET_SIZE(__pyx_v_unique_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
__pyx_v_i = __pyx_t_4;
- /* "MACS2/IO/CallPeakUnit.pyx":690
+ /* "MACS2/IO/CallPeakUnit.pyx":691
* unique_values = sorted(pvalue_stat.keys(), reverse=True) #sorted(unique_values,reverse=True)
* for i in range(len(unique_values)):
* v = unique_values[i] # <<<<<<<<<<<<<<
@@ -9431,31 +9468,31 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
if (unlikely(__pyx_v_unique_values == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_11 = __Pyx_GetItemInt_List(__pyx_v_unique_values, __pyx_v_i, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_11 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_11 = __Pyx_GetItemInt_List(__pyx_v_unique_values, __pyx_v_i, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_11 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_12 = __pyx_PyFloat_AsFloat(__pyx_t_11); if (unlikely((__pyx_t_12 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __pyx_PyFloat_AsFloat(__pyx_t_11); if (unlikely((__pyx_t_12 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
__pyx_v_v = __pyx_t_12;
- /* "MACS2/IO/CallPeakUnit.pyx":691
+ /* "MACS2/IO/CallPeakUnit.pyx":692
* for i in range(len(unique_values)):
* v = unique_values[i]
* l = pvalue_stat[v] # <<<<<<<<<<<<<<
* q = v + (log10(k) + f)
* q = max(0,min(pre_q,q)) # make q-score monotonic
*/
- __pyx_t_11 = PyFloat_FromDouble(__pyx_v_v); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyFloat_FromDouble(__pyx_v_v); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_1 = __Pyx_PyDict_GetItem(__pyx_v_pvalue_stat, __pyx_t_11); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_PyDict_GetItem(__pyx_v_pvalue_stat, __pyx_t_11); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __pyx_t_8 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_8 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_8 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_l = __pyx_t_8;
- /* "MACS2/IO/CallPeakUnit.pyx":692
+ /* "MACS2/IO/CallPeakUnit.pyx":693
* v = unique_values[i]
* l = pvalue_stat[v]
* q = v + (log10(k) + f) # <<<<<<<<<<<<<<
@@ -9464,7 +9501,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_q = (__pyx_v_v + (log10(__pyx_v_k) + __pyx_v_f));
- /* "MACS2/IO/CallPeakUnit.pyx":693
+ /* "MACS2/IO/CallPeakUnit.pyx":694
* l = pvalue_stat[v]
* q = v + (log10(k) + f)
* q = max(0,min(pre_q,q)) # make q-score monotonic # <<<<<<<<<<<<<<
@@ -9487,22 +9524,22 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
}
__pyx_v_q = __pyx_t_16;
- /* "MACS2/IO/CallPeakUnit.pyx":694
+ /* "MACS2/IO/CallPeakUnit.pyx":695
* q = v + (log10(k) + f)
* q = max(0,min(pre_q,q)) # make q-score monotonic
* self.pqtable[ v ] = q # <<<<<<<<<<<<<<
* pre_v = v
* pre_q = q
*/
- __pyx_t_1 = PyFloat_FromDouble(__pyx_v_q); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_q); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_11 = PyFloat_FromDouble(__pyx_v_v); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyFloat_FromDouble(__pyx_v_v); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- if (unlikely(PyObject_SetItem(__pyx_v_self->pqtable, __pyx_t_11, __pyx_t_1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyObject_SetItem(__pyx_v_self->pqtable, __pyx_t_11, __pyx_t_1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":695
+ /* "MACS2/IO/CallPeakUnit.pyx":696
* q = max(0,min(pre_q,q)) # make q-score monotonic
* self.pqtable[ v ] = q
* pre_v = v # <<<<<<<<<<<<<<
@@ -9511,7 +9548,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_pre_v = __pyx_v_v;
- /* "MACS2/IO/CallPeakUnit.pyx":696
+ /* "MACS2/IO/CallPeakUnit.pyx":697
* self.pqtable[ v ] = q
* pre_v = v
* pre_q = q # <<<<<<<<<<<<<<
@@ -9520,7 +9557,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_pre_q = __pyx_v_q;
- /* "MACS2/IO/CallPeakUnit.pyx":697
+ /* "MACS2/IO/CallPeakUnit.pyx":698
* pre_v = v
* pre_q = q
* k+=l # <<<<<<<<<<<<<<
@@ -9529,7 +9566,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
*/
__pyx_v_k = (__pyx_v_k + __pyx_v_l);
- /* "MACS2/IO/CallPeakUnit.pyx":698
+ /* "MACS2/IO/CallPeakUnit.pyx":699
* pre_q = q
* k+=l
* nhcal += 1 # <<<<<<<<<<<<<<
@@ -9539,21 +9576,21 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
__pyx_v_nhcal = (__pyx_v_nhcal + 1);
}
- /* "MACS2/IO/CallPeakUnit.pyx":700
+ /* "MACS2/IO/CallPeakUnit.pyx":701
* nhcal += 1
*
* logging.debug( "access pq hash for %d times" % nhcal ) # <<<<<<<<<<<<<<
*
* return self.pqtable
*/
- __pyx_t_11 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_11, __pyx_n_s_debug); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_11, __pyx_n_s_debug); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __pyx_t_11 = __Pyx_PyInt_From_long(__pyx_v_nhcal); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyInt_From_long(__pyx_v_nhcal); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_6 = __Pyx_PyString_Format(__pyx_kp_s_access_pq_hash_for_d_times, __pyx_t_11); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyString_Format(__pyx_kp_s_access_pq_hash_for_d_times, __pyx_t_11); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
__pyx_t_11 = NULL;
@@ -9567,24 +9604,24 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
}
}
if (!__pyx_t_11) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_GOTREF(__pyx_t_1);
} else {
- __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_11); __Pyx_GIVEREF(__pyx_t_11); __pyx_t_11 = NULL;
PyTuple_SET_ITEM(__pyx_t_5, 0+1, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":702
+ /* "MACS2/IO/CallPeakUnit.pyx":703
* logging.debug( "access pq hash for %d times" % nhcal )
*
* return self.pqtable # <<<<<<<<<<<<<<
@@ -9596,7 +9633,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
__pyx_r = __pyx_v_self->pqtable;
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":625
+ /* "MACS2/IO/CallPeakUnit.pyx":626
* return s
*
* cdef object __cal_pvalue_qvalue_table ( self ): # <<<<<<<<<<<<<<
@@ -9626,7 +9663,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___cal_
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":705
+/* "MACS2/IO/CallPeakUnit.pyx":706
*
*
* cdef object __pre_computes ( self, int max_gap = 50, int min_length = 200 ): # <<<<<<<<<<<<<<
@@ -9721,19 +9758,19 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
}
- /* "MACS2/IO/CallPeakUnit.pyx":713
+ /* "MACS2/IO/CallPeakUnit.pyx":714
* str chrom
* np.ndarray pos_array, treat_array, ctrl_array, score_array
* dict pvalue_stat = {} # <<<<<<<<<<<<<<
* long n, pre_p, this_p, length, j, pre_l, l, i
* float this_v, pre_v, v, q, pre_q, this_t, this_c
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 714; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_pvalue_stat = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":718
+ /* "MACS2/IO/CallPeakUnit.pyx":719
* long N, k, this_l
* float f
* long nhcal = 0 # <<<<<<<<<<<<<<
@@ -9742,7 +9779,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_nhcal = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":719
+ /* "MACS2/IO/CallPeakUnit.pyx":720
* float f
* long nhcal = 0
* long npcal = 0 # <<<<<<<<<<<<<<
@@ -9751,58 +9788,58 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_npcal = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":735
+ /* "MACS2/IO/CallPeakUnit.pyx":736
* float32_t * score_array_ptr # score array pointer
*
* logging.debug ( "Start to calculate pvalue stat..." ) # <<<<<<<<<<<<<<
*
* tmplist = sorted( list(np.arange(0.3, 10.0, 0.3)), reverse = True )
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_debug); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_debug); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__15, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__15, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":737
+ /* "MACS2/IO/CallPeakUnit.pyx":738
* logging.debug ( "Start to calculate pvalue stat..." )
*
* tmplist = sorted( list(np.arange(0.3, 10.0, 0.3)), reverse = True ) # <<<<<<<<<<<<<<
*
* for i in range( len( self.chromosomes ) ):
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_arange); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_arange); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__16, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__16, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PySequence_List(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PySequence_List(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_reverse, Py_True) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_sorted, __pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_reverse, Py_True) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_sorted, __pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (!(likely(PyList_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyList_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_tmplist = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":739
+ /* "MACS2/IO/CallPeakUnit.pyx":740
* tmplist = sorted( list(np.arange(0.3, 10.0, 0.3)), reverse = True )
*
* for i in range( len( self.chromosomes ) ): # <<<<<<<<<<<<<<
@@ -9813,14 +9850,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__Pyx_INCREF(__pyx_t_3);
if (unlikely(__pyx_t_3 == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_4 = PyList_GET_SIZE(__pyx_t_3); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_GET_SIZE(__pyx_t_3); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
__pyx_v_i = __pyx_t_5;
- /* "MACS2/IO/CallPeakUnit.pyx":740
+ /* "MACS2/IO/CallPeakUnit.pyx":741
*
* for i in range( len( self.chromosomes ) ):
* chrom = self.chromosomes[ i ] # <<<<<<<<<<<<<<
@@ -9829,26 +9866,26 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
if (unlikely(__pyx_v_self->chromosomes == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_self->chromosomes, __pyx_v_i, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_self->chromosomes, __pyx_v_i, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- if (!(likely(PyString_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_chrom, ((PyObject*)__pyx_t_3));
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":741
+ /* "MACS2/IO/CallPeakUnit.pyx":742
* for i in range( len( self.chromosomes ) ):
* chrom = self.chromosomes[ i ]
* self.__pileup_treat_ctrl_a_chromosome( chrom ) # <<<<<<<<<<<<<<
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl
*
*/
- __pyx_t_3 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___pileup_treat_ctrl_a_chromosome(__pyx_v_self, __pyx_v_chrom); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___pileup_treat_ctrl_a_chromosome(__pyx_v_self, __pyx_v_chrom); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":742
+ /* "MACS2/IO/CallPeakUnit.pyx":743
* chrom = self.chromosomes[ i ]
* self.__pileup_treat_ctrl_a_chromosome( chrom )
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl # <<<<<<<<<<<<<<
@@ -9867,7 +9904,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
if (unlikely(size != 3)) {
if (size > 3) __Pyx_RaiseTooManyValuesError(3);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
__pyx_t_2 = PyList_GET_ITEM(sequence, 0);
@@ -9877,20 +9914,20 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_6);
#else
- __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
#endif
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
} else {
- __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_pos_array, ((PyArrayObject *)__pyx_t_2));
__pyx_t_2 = 0;
__Pyx_XDECREF_SET(__pyx_v_treat_array, ((PyArrayObject *)__pyx_t_1));
@@ -9898,19 +9935,19 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__Pyx_XDECREF_SET(__pyx_v_ctrl_array, ((PyArrayObject *)__pyx_t_6));
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":744
+ /* "MACS2/IO/CallPeakUnit.pyx":745
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl
*
* score_array = self.__cal_pscore( treat_array, ctrl_array ) # <<<<<<<<<<<<<<
*
* for n in range( len( tmplist ) ):
*/
- __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_pscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_pscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF_SET(__pyx_v_score_array, ((PyArrayObject *)__pyx_t_3));
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":746
+ /* "MACS2/IO/CallPeakUnit.pyx":747
* score_array = self.__cal_pscore( treat_array, ctrl_array )
*
* for n in range( len( tmplist ) ): # <<<<<<<<<<<<<<
@@ -9919,13 +9956,13 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
if (unlikely(__pyx_v_tmplist == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_7 = PyList_GET_SIZE(__pyx_v_tmplist); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyList_GET_SIZE(__pyx_v_tmplist); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_7; __pyx_t_8+=1) {
__pyx_v_n = __pyx_t_8;
- /* "MACS2/IO/CallPeakUnit.pyx":747
+ /* "MACS2/IO/CallPeakUnit.pyx":748
*
* for n in range( len( tmplist ) ):
* cutoff = tmplist[ n ] # <<<<<<<<<<<<<<
@@ -9934,15 +9971,15 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
if (unlikely(__pyx_v_tmplist == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_tmplist, __pyx_v_n, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_tmplist, __pyx_v_n, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_9 = __pyx_PyFloat_AsFloat(__pyx_t_3); if (unlikely((__pyx_t_9 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __pyx_PyFloat_AsFloat(__pyx_t_3); if (unlikely((__pyx_t_9 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_v_cutoff = __pyx_t_9;
- /* "MACS2/IO/CallPeakUnit.pyx":748
+ /* "MACS2/IO/CallPeakUnit.pyx":749
* for n in range( len( tmplist ) ):
* cutoff = tmplist[ n ]
* total_l = 0 # total length in potential peak # <<<<<<<<<<<<<<
@@ -9951,7 +9988,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_total_l = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":749
+ /* "MACS2/IO/CallPeakUnit.pyx":750
* cutoff = tmplist[ n ]
* total_l = 0 # total length in potential peak
* total_p = 0 # <<<<<<<<<<<<<<
@@ -9960,21 +9997,21 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_total_p = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":752
+ /* "MACS2/IO/CallPeakUnit.pyx":753
*
* # get the regions with scores above cutoffs
* above_cutoff = np.nonzero( score_array > cutoff )[0]# this is not an optimized method. It would be better to store score array in a 2-D ndarray? # <<<<<<<<<<<<<<
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
*/
- __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_nonzero); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_nonzero); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_v_score_array), __pyx_t_6, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_v_score_array), __pyx_t_6, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_t_6 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_1))) {
@@ -9987,73 +10024,73 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
}
if (!__pyx_t_6) {
- __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_GOTREF(__pyx_t_3);
} else {
- __pyx_t_10 = PyTuple_New(1+1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(1+1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_6 = NULL;
PyTuple_SET_ITEM(__pyx_t_10, 0+1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_10, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_10, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_above_cutoff, ((PyArrayObject *)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":753
+ /* "MACS2/IO/CallPeakUnit.pyx":754
* # get the regions with scores above cutoffs
* above_cutoff = np.nonzero( score_array > cutoff )[0]# this is not an optimized method. It would be better to store score array in a 2-D ndarray?
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff # <<<<<<<<<<<<<<
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
*
*/
- __pyx_t_1 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_above_cutoff_endpos, ((PyArrayObject *)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":754
+ /* "MACS2/IO/CallPeakUnit.pyx":755
* above_cutoff = np.nonzero( score_array > cutoff )[0]# this is not an optimized method. It would be better to store score array in a 2-D ndarray?
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff # <<<<<<<<<<<<<<
*
* if above_cutoff_endpos.size == 0:
*/
- __pyx_t_1 = PyNumber_Subtract(((PyObject *)__pyx_v_above_cutoff), __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Subtract(((PyObject *)__pyx_v_above_cutoff), __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), __pyx_t_1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), __pyx_t_1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_above_cutoff_startpos, ((PyArrayObject *)__pyx_t_3));
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":756
+ /* "MACS2/IO/CallPeakUnit.pyx":757
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
*
* if above_cutoff_endpos.size == 0: # <<<<<<<<<<<<<<
* continue
*
*/
- __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff_endpos), __pyx_n_s_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff_endpos), __pyx_n_s_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":757
+ /* "MACS2/IO/CallPeakUnit.pyx":758
*
* if above_cutoff_endpos.size == 0:
* continue # <<<<<<<<<<<<<<
@@ -10063,7 +10100,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
goto __pyx_L5_continue;
}
- /* "MACS2/IO/CallPeakUnit.pyx":760
+ /* "MACS2/IO/CallPeakUnit.pyx":761
*
* # first bit of region above cutoff
* acs_ptr = <int32_t *> above_cutoff_startpos.data # <<<<<<<<<<<<<<
@@ -10072,7 +10109,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_acs_ptr = ((int32_t *)__pyx_v_above_cutoff_startpos->data);
- /* "MACS2/IO/CallPeakUnit.pyx":761
+ /* "MACS2/IO/CallPeakUnit.pyx":762
* # first bit of region above cutoff
* acs_ptr = <int32_t *> above_cutoff_startpos.data
* ace_ptr = <int32_t *> above_cutoff_endpos.data # <<<<<<<<<<<<<<
@@ -10081,18 +10118,18 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_ace_ptr = ((int32_t *)__pyx_v_above_cutoff_endpos->data);
- /* "MACS2/IO/CallPeakUnit.pyx":763
+ /* "MACS2/IO/CallPeakUnit.pyx":764
* ace_ptr = <int32_t *> above_cutoff_endpos.data
*
* peak_content = [( acs_ptr[ 0 ], ace_ptr[ 0 ] ), ] # <<<<<<<<<<<<<<
* lastp = ace_ptr[ 0 ]
* acs_ptr += 1
*/
- __pyx_t_1 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_PyInt_From_int32_t((__pyx_v_ace_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int32_t((__pyx_v_ace_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
@@ -10100,7 +10137,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_1 = 0;
__pyx_t_3 = 0;
- __pyx_t_3 = PyList_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyList_SET_ITEM(__pyx_t_3, 0, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
@@ -10108,19 +10145,19 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__Pyx_XDECREF_SET(__pyx_v_peak_content, ((PyObject*)__pyx_t_3));
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":764
+ /* "MACS2/IO/CallPeakUnit.pyx":765
*
* peak_content = [( acs_ptr[ 0 ], ace_ptr[ 0 ] ), ]
* lastp = ace_ptr[ 0 ] # <<<<<<<<<<<<<<
* acs_ptr += 1
* ace_ptr += 1
*/
- __pyx_t_3 = __Pyx_PyInt_From_int32_t((__pyx_v_ace_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int32_t((__pyx_v_ace_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 765; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF_SET(__pyx_v_lastp, __pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":765
+ /* "MACS2/IO/CallPeakUnit.pyx":766
* peak_content = [( acs_ptr[ 0 ], ace_ptr[ 0 ] ), ]
* lastp = ace_ptr[ 0 ]
* acs_ptr += 1 # <<<<<<<<<<<<<<
@@ -10129,7 +10166,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_acs_ptr = (__pyx_v_acs_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":766
+ /* "MACS2/IO/CallPeakUnit.pyx":767
* lastp = ace_ptr[ 0 ]
* acs_ptr += 1
* ace_ptr += 1 # <<<<<<<<<<<<<<
@@ -10138,62 +10175,62 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_ace_ptr = (__pyx_v_ace_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":768
+ /* "MACS2/IO/CallPeakUnit.pyx":769
* ace_ptr += 1
*
* for i in range( 1, above_cutoff_startpos.size ): # <<<<<<<<<<<<<<
* tl = acs_ptr[ 0 ] - lastp
* if tl <= max_gap:
*/
- __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff_startpos), __pyx_n_s_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff_startpos), __pyx_n_s_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_12 = __Pyx_PyInt_As_long(__pyx_t_3); if (unlikely((__pyx_t_12 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyInt_As_long(__pyx_t_3); if (unlikely((__pyx_t_12 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
for (__pyx_t_13 = 1; __pyx_t_13 < __pyx_t_12; __pyx_t_13+=1) {
__pyx_v_i = __pyx_t_13;
- /* "MACS2/IO/CallPeakUnit.pyx":769
+ /* "MACS2/IO/CallPeakUnit.pyx":770
*
* for i in range( 1, above_cutoff_startpos.size ):
* tl = acs_ptr[ 0 ] - lastp # <<<<<<<<<<<<<<
* if tl <= max_gap:
* peak_content.append( ( acs_ptr[ 0 ], ace_ptr[ 0 ] ) )
*/
- __pyx_t_3 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_10 = PyNumber_Subtract(__pyx_t_3, __pyx_v_lastp); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyNumber_Subtract(__pyx_t_3, __pyx_v_lastp); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF_SET(__pyx_v_tl, __pyx_t_10);
__pyx_t_10 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":770
+ /* "MACS2/IO/CallPeakUnit.pyx":771
* for i in range( 1, above_cutoff_startpos.size ):
* tl = acs_ptr[ 0 ] - lastp
* if tl <= max_gap: # <<<<<<<<<<<<<<
* peak_content.append( ( acs_ptr[ 0 ], ace_ptr[ 0 ] ) )
* else:
*/
- __pyx_t_10 = __Pyx_PyInt_From_int(__pyx_v_max_gap); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyInt_From_int(__pyx_v_max_gap); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_tl, __pyx_t_10, Py_LE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_tl, __pyx_t_10, Py_LE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":771
+ /* "MACS2/IO/CallPeakUnit.pyx":772
* tl = acs_ptr[ 0 ] - lastp
* if tl <= max_gap:
* peak_content.append( ( acs_ptr[ 0 ], ace_ptr[ 0 ] ) ) # <<<<<<<<<<<<<<
* else:
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ]
*/
- __pyx_t_3 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_10 = __Pyx_PyInt_From_int32_t((__pyx_v_ace_ptr[0])); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyInt_From_int32_t((__pyx_v_ace_ptr[0])); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
@@ -10201,38 +10238,38 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__Pyx_GIVEREF(__pyx_t_10);
__pyx_t_3 = 0;
__pyx_t_10 = 0;
- __pyx_t_14 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_1); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_1); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L10;
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":773
+ /* "MACS2/IO/CallPeakUnit.pyx":774
* peak_content.append( ( acs_ptr[ 0 ], ace_ptr[ 0 ] ) )
* else:
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ] # <<<<<<<<<<<<<<
* if peak_length >= min_length: # if the peak is too small, reject it
* total_l += peak_length
*/
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_t_1, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_10 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_t_1, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_10 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_1, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_1, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Subtract(__pyx_t_10, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Subtract(__pyx_t_10, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_15 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_15 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_15 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_peak_length = __pyx_t_15;
- /* "MACS2/IO/CallPeakUnit.pyx":774
+ /* "MACS2/IO/CallPeakUnit.pyx":775
* else:
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ]
* if peak_length >= min_length: # if the peak is too small, reject it # <<<<<<<<<<<<<<
@@ -10242,7 +10279,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__pyx_t_11 = ((__pyx_v_peak_length >= __pyx_v_min_length) != 0);
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":775
+ /* "MACS2/IO/CallPeakUnit.pyx":776
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ]
* if peak_length >= min_length: # if the peak is too small, reject it
* total_l += peak_length # <<<<<<<<<<<<<<
@@ -10251,7 +10288,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_total_l = (__pyx_v_total_l + __pyx_v_peak_length);
- /* "MACS2/IO/CallPeakUnit.pyx":776
+ /* "MACS2/IO/CallPeakUnit.pyx":777
* if peak_length >= min_length: # if the peak is too small, reject it
* total_l += peak_length
* total_p += 1 # <<<<<<<<<<<<<<
@@ -10263,18 +10300,18 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
__pyx_L11:;
- /* "MACS2/IO/CallPeakUnit.pyx":777
+ /* "MACS2/IO/CallPeakUnit.pyx":778
* total_l += peak_length
* total_p += 1
* peak_content = [ ( acs_ptr[ 0 ], ace_ptr[ 0 ] ), ] # <<<<<<<<<<<<<<
* lastp = ace_ptr[ 0 ]
* acs_ptr += 1
*/
- __pyx_t_1 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_PyInt_From_int32_t((__pyx_v_ace_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int32_t((__pyx_v_ace_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
@@ -10282,7 +10319,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_1 = 0;
__pyx_t_3 = 0;
- __pyx_t_3 = PyList_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyList_SET_ITEM(__pyx_t_3, 0, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
@@ -10292,19 +10329,19 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
__pyx_L10:;
- /* "MACS2/IO/CallPeakUnit.pyx":778
+ /* "MACS2/IO/CallPeakUnit.pyx":779
* total_p += 1
* peak_content = [ ( acs_ptr[ 0 ], ace_ptr[ 0 ] ), ]
* lastp = ace_ptr[ 0 ] # <<<<<<<<<<<<<<
* acs_ptr += 1
* ace_ptr += 1
*/
- __pyx_t_3 = __Pyx_PyInt_From_int32_t((__pyx_v_ace_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int32_t((__pyx_v_ace_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF_SET(__pyx_v_lastp, __pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":779
+ /* "MACS2/IO/CallPeakUnit.pyx":780
* peak_content = [ ( acs_ptr[ 0 ], ace_ptr[ 0 ] ), ]
* lastp = ace_ptr[ 0 ]
* acs_ptr += 1 # <<<<<<<<<<<<<<
@@ -10313,7 +10350,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_acs_ptr = (__pyx_v_acs_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":780
+ /* "MACS2/IO/CallPeakUnit.pyx":781
* lastp = ace_ptr[ 0 ]
* acs_ptr += 1
* ace_ptr += 1 # <<<<<<<<<<<<<<
@@ -10323,7 +10360,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__pyx_v_ace_ptr = (__pyx_v_ace_ptr + 1);
}
- /* "MACS2/IO/CallPeakUnit.pyx":782
+ /* "MACS2/IO/CallPeakUnit.pyx":783
* ace_ptr += 1
*
* if peak_content: # <<<<<<<<<<<<<<
@@ -10333,32 +10370,32 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__pyx_t_11 = (__pyx_v_peak_content != Py_None) && (PyList_GET_SIZE(__pyx_v_peak_content) != 0);
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":783
+ /* "MACS2/IO/CallPeakUnit.pyx":784
*
* if peak_content:
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ] # <<<<<<<<<<<<<<
* if peak_length >= min_length: # if the peak is too small, reject it
* total_l += peak_length
*/
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_t_3, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_10 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_t_3, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_10 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyNumber_Subtract(__pyx_t_10, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_Subtract(__pyx_t_10, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_12 = __Pyx_PyInt_As_long(__pyx_t_3); if (unlikely((__pyx_t_12 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyInt_As_long(__pyx_t_3); if (unlikely((__pyx_t_12 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_v_peak_length = __pyx_t_12;
- /* "MACS2/IO/CallPeakUnit.pyx":784
+ /* "MACS2/IO/CallPeakUnit.pyx":785
* if peak_content:
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ]
* if peak_length >= min_length: # if the peak is too small, reject it # <<<<<<<<<<<<<<
@@ -10368,7 +10405,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__pyx_t_11 = ((__pyx_v_peak_length >= __pyx_v_min_length) != 0);
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":785
+ /* "MACS2/IO/CallPeakUnit.pyx":786
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ]
* if peak_length >= min_length: # if the peak is too small, reject it
* total_l += peak_length # <<<<<<<<<<<<<<
@@ -10377,7 +10414,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_total_l = (__pyx_v_total_l + __pyx_v_peak_length);
- /* "MACS2/IO/CallPeakUnit.pyx":786
+ /* "MACS2/IO/CallPeakUnit.pyx":787
* if peak_length >= min_length: # if the peak is too small, reject it
* total_l += peak_length
* total_p += 1 # <<<<<<<<<<<<<<
@@ -10392,7 +10429,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
__pyx_L12:;
- /* "MACS2/IO/CallPeakUnit.pyx":787
+ /* "MACS2/IO/CallPeakUnit.pyx":788
* total_l += peak_length
* total_p += 1
* self.pvalue_length[ cutoff ] = self.pvalue_length.get( cutoff, 0 ) + total_l # <<<<<<<<<<<<<<
@@ -10401,30 +10438,30 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
if (unlikely(__pyx_v_self->pvalue_length == Py_None)) {
PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_PyDict_GetItemDefault(__pyx_v_self->pvalue_length, __pyx_t_3, __pyx_int_0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyDict_GetItemDefault(__pyx_v_self->pvalue_length, __pyx_t_3, __pyx_int_0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v_total_l); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v_total_l); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_10 = PyNumber_Add(__pyx_t_1, __pyx_t_3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyNumber_Add(__pyx_t_1, __pyx_t_3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (unlikely(__pyx_v_self->pvalue_length == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- if (unlikely(PyDict_SetItem(__pyx_v_self->pvalue_length, __pyx_t_3, __pyx_t_10) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyDict_SetItem(__pyx_v_self->pvalue_length, __pyx_t_3, __pyx_t_10) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":788
+ /* "MACS2/IO/CallPeakUnit.pyx":789
* total_p += 1
* self.pvalue_length[ cutoff ] = self.pvalue_length.get( cutoff, 0 ) + total_l
* self.pvalue_npeaks[ cutoff ] = self.pvalue_npeaks.get( cutoff, 0 ) + total_p # <<<<<<<<<<<<<<
@@ -10433,32 +10470,32 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
if (unlikely(__pyx_v_self->pvalue_npeaks == Py_None)) {
PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_10 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_3 = __Pyx_PyDict_GetItemDefault(__pyx_v_self->pvalue_npeaks, __pyx_t_10, __pyx_int_0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyDict_GetItemDefault(__pyx_v_self->pvalue_npeaks, __pyx_t_10, __pyx_int_0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = __Pyx_PyInt_From_long(__pyx_v_total_p); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyInt_From_long(__pyx_v_total_p); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_1 = PyNumber_Add(__pyx_t_3, __pyx_t_10); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Add(__pyx_t_3, __pyx_t_10); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (unlikely(__pyx_v_self->pvalue_npeaks == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_10 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- if (unlikely(PyDict_SetItem(__pyx_v_self->pvalue_npeaks, __pyx_t_10, __pyx_t_1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyDict_SetItem(__pyx_v_self->pvalue_npeaks, __pyx_t_10, __pyx_t_1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_L5_continue:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":790
+ /* "MACS2/IO/CallPeakUnit.pyx":791
* self.pvalue_npeaks[ cutoff ] = self.pvalue_npeaks.get( cutoff, 0 ) + total_p
*
* pos_array_ptr = <int32_t *> pos_array.data # <<<<<<<<<<<<<<
@@ -10467,7 +10504,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_pos_array_ptr = ((int32_t *)__pyx_v_pos_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":791
+ /* "MACS2/IO/CallPeakUnit.pyx":792
*
* pos_array_ptr = <int32_t *> pos_array.data
* score_array_ptr = <float32_t *> score_array.data # <<<<<<<<<<<<<<
@@ -10476,7 +10513,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_score_array_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_score_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":793
+ /* "MACS2/IO/CallPeakUnit.pyx":794
* score_array_ptr = <float32_t *> score_array.data
*
* pre_p = 0 # <<<<<<<<<<<<<<
@@ -10485,7 +10522,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_pre_p = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":794
+ /* "MACS2/IO/CallPeakUnit.pyx":795
*
* pre_p = 0
* for i in range(pos_array.shape[0]): # <<<<<<<<<<<<<<
@@ -10496,7 +10533,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_16; __pyx_t_8+=1) {
__pyx_v_i = __pyx_t_8;
- /* "MACS2/IO/CallPeakUnit.pyx":795
+ /* "MACS2/IO/CallPeakUnit.pyx":796
* pre_p = 0
* for i in range(pos_array.shape[0]):
* this_p = pos_array_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -10505,7 +10542,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_this_p = (__pyx_v_pos_array_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":796
+ /* "MACS2/IO/CallPeakUnit.pyx":797
* for i in range(pos_array.shape[0]):
* this_p = pos_array_ptr[ 0 ]
* this_l = this_p - pre_p # <<<<<<<<<<<<<<
@@ -10514,7 +10551,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_this_l = (__pyx_v_this_p - __pyx_v_pre_p);
- /* "MACS2/IO/CallPeakUnit.pyx":797
+ /* "MACS2/IO/CallPeakUnit.pyx":798
* this_p = pos_array_ptr[ 0 ]
* this_l = this_p - pre_p
* this_v = score_array_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -10523,62 +10560,62 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_this_v = (__pyx_v_score_array_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":798
+ /* "MACS2/IO/CallPeakUnit.pyx":799
* this_l = this_p - pre_p
* this_v = score_array_ptr[ 0 ]
* if pvalue_stat.has_key( this_v ): # <<<<<<<<<<<<<<
* pvalue_stat[ this_v ] += this_l
* else:
*/
- __pyx_t_1 = PyFloat_FromDouble(__pyx_v_this_v); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_this_v); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_11 = PyDict_Contains(__pyx_v_pvalue_stat, __pyx_t_1); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyDict_Contains(__pyx_v_pvalue_stat, __pyx_t_1); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_17 = (__pyx_t_11 != 0);
if (__pyx_t_17) {
- /* "MACS2/IO/CallPeakUnit.pyx":799
+ /* "MACS2/IO/CallPeakUnit.pyx":800
* this_v = score_array_ptr[ 0 ]
* if pvalue_stat.has_key( this_v ):
* pvalue_stat[ this_v ] += this_l # <<<<<<<<<<<<<<
* else:
* pvalue_stat[ this_v ] = this_l
*/
- __pyx_t_1 = PyFloat_FromDouble(__pyx_v_this_v); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_this_v); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_10 = __Pyx_PyDict_GetItem(__pyx_v_pvalue_stat, __pyx_t_1); if (unlikely(__pyx_t_10 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_10 = __Pyx_PyDict_GetItem(__pyx_v_pvalue_stat, __pyx_t_1); if (unlikely(__pyx_t_10 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v_this_l); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v_this_l); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_t_10, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_t_10, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (unlikely(PyDict_SetItem(__pyx_v_pvalue_stat, __pyx_t_1, __pyx_t_2) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyDict_SetItem(__pyx_v_pvalue_stat, __pyx_t_1, __pyx_t_2) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L16;
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":801
+ /* "MACS2/IO/CallPeakUnit.pyx":802
* pvalue_stat[ this_v ] += this_l
* else:
* pvalue_stat[ this_v ] = this_l # <<<<<<<<<<<<<<
* pre_p = this_p #pos_array[ i ]
* pos_array_ptr += 1
*/
- __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v_this_l); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v_this_l); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyFloat_FromDouble(__pyx_v_this_v); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyFloat_FromDouble(__pyx_v_this_v); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (unlikely(PyDict_SetItem(__pyx_v_pvalue_stat, __pyx_t_2, __pyx_t_1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyDict_SetItem(__pyx_v_pvalue_stat, __pyx_t_2, __pyx_t_1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
__pyx_L16:;
- /* "MACS2/IO/CallPeakUnit.pyx":802
+ /* "MACS2/IO/CallPeakUnit.pyx":803
* else:
* pvalue_stat[ this_v ] = this_l
* pre_p = this_p #pos_array[ i ] # <<<<<<<<<<<<<<
@@ -10587,7 +10624,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_pre_p = __pyx_v_this_p;
- /* "MACS2/IO/CallPeakUnit.pyx":803
+ /* "MACS2/IO/CallPeakUnit.pyx":804
* pvalue_stat[ this_v ] = this_l
* pre_p = this_p #pos_array[ i ]
* pos_array_ptr += 1 # <<<<<<<<<<<<<<
@@ -10596,7 +10633,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_pos_array_ptr = (__pyx_v_pos_array_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":804
+ /* "MACS2/IO/CallPeakUnit.pyx":805
* pre_p = this_p #pos_array[ i ]
* pos_array_ptr += 1
* score_array_ptr += 1 # <<<<<<<<<<<<<<
@@ -10606,7 +10643,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__pyx_v_score_array_ptr = (__pyx_v_score_array_ptr + 1);
}
- /* "MACS2/IO/CallPeakUnit.pyx":806
+ /* "MACS2/IO/CallPeakUnit.pyx":807
* score_array_ptr += 1
*
* nhcal += pos_array.shape[0] # <<<<<<<<<<<<<<
@@ -10616,7 +10653,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__pyx_v_nhcal = (__pyx_v_nhcal + (__pyx_v_pos_array->dimensions[0]));
}
- /* "MACS2/IO/CallPeakUnit.pyx":813
+ /* "MACS2/IO/CallPeakUnit.pyx":814
* # add all pvalue cutoffs from cutoff-analysis part. So that we
* # can get the corresponding qvalues for them.
* for cutoff in tmplist: # <<<<<<<<<<<<<<
@@ -10625,33 +10662,33 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
if (unlikely(__pyx_v_tmplist == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_1 = __pyx_v_tmplist; __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = 0;
for (;;) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
#if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
- __pyx_t_9 = __pyx_PyFloat_AsFloat(__pyx_t_2); if (unlikely((__pyx_t_9 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __pyx_PyFloat_AsFloat(__pyx_t_2); if (unlikely((__pyx_t_9 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_cutoff = __pyx_t_9;
- /* "MACS2/IO/CallPeakUnit.pyx":814
+ /* "MACS2/IO/CallPeakUnit.pyx":815
* # can get the corresponding qvalues for them.
* for cutoff in tmplist:
* pvalue_stat[ cutoff ] = 0 # <<<<<<<<<<<<<<
*
* nhval = 0
*/
- __pyx_t_2 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (unlikely(PyDict_SetItem(__pyx_v_pvalue_stat, __pyx_t_2, __pyx_int_0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyDict_SetItem(__pyx_v_pvalue_stat, __pyx_t_2, __pyx_int_0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":813
+ /* "MACS2/IO/CallPeakUnit.pyx":814
* # add all pvalue cutoffs from cutoff-analysis part. So that we
* # can get the corresponding qvalues for them.
* for cutoff in tmplist: # <<<<<<<<<<<<<<
@@ -10661,7 +10698,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":816
+ /* "MACS2/IO/CallPeakUnit.pyx":817
* pvalue_stat[ cutoff ] = 0
*
* nhval = 0 # <<<<<<<<<<<<<<
@@ -10670,28 +10707,28 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_nhval = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":818
+ /* "MACS2/IO/CallPeakUnit.pyx":819
* nhval = 0
*
* N = sum(pvalue_stat.values()) # total length # <<<<<<<<<<<<<<
* k = 1 # rank
* f = -log10(N)
*/
- __pyx_t_1 = __Pyx_PyDict_Values(__pyx_v_pvalue_stat); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyDict_Values(__pyx_v_pvalue_stat); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_sum, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_5 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_5 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_5 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_N = __pyx_t_5;
- /* "MACS2/IO/CallPeakUnit.pyx":819
+ /* "MACS2/IO/CallPeakUnit.pyx":820
*
* N = sum(pvalue_stat.values()) # total length
* k = 1 # rank # <<<<<<<<<<<<<<
@@ -10700,7 +10737,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_k = 1;
- /* "MACS2/IO/CallPeakUnit.pyx":820
+ /* "MACS2/IO/CallPeakUnit.pyx":821
* N = sum(pvalue_stat.values()) # total length
* k = 1 # rank
* f = -log10(N) # <<<<<<<<<<<<<<
@@ -10709,7 +10746,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_f = (-log10(__pyx_v_N));
- /* "MACS2/IO/CallPeakUnit.pyx":821
+ /* "MACS2/IO/CallPeakUnit.pyx":822
* k = 1 # rank
* f = -log10(N)
* pre_v = -2147483647 # <<<<<<<<<<<<<<
@@ -10718,7 +10755,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_pre_v = -2147483647.0;
- /* "MACS2/IO/CallPeakUnit.pyx":822
+ /* "MACS2/IO/CallPeakUnit.pyx":823
* f = -log10(N)
* pre_v = -2147483647
* pre_l = 0 # <<<<<<<<<<<<<<
@@ -10727,7 +10764,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_pre_l = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":823
+ /* "MACS2/IO/CallPeakUnit.pyx":824
* pre_v = -2147483647
* pre_l = 0
* pre_q = 2147483647 # save the previous q-value # <<<<<<<<<<<<<<
@@ -10736,14 +10773,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_pre_q = 2147483647.0;
- /* "MACS2/IO/CallPeakUnit.pyx":825
+ /* "MACS2/IO/CallPeakUnit.pyx":826
* pre_q = 2147483647 # save the previous q-value
*
* self.pqtable = Float64HashTable() # <<<<<<<<<<<<<<
* unique_values = sorted(pvalue_stat.keys(), reverse=True) #sorted(unique_values,reverse=True)
* for i in range(len(unique_values)):
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_Float64HashTable); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_Float64HashTable); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) {
@@ -10756,10 +10793,10 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
}
if (__pyx_t_3) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -10769,32 +10806,32 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__pyx_v_self->pqtable = __pyx_t_1;
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":826
+ /* "MACS2/IO/CallPeakUnit.pyx":827
*
* self.pqtable = Float64HashTable()
* unique_values = sorted(pvalue_stat.keys(), reverse=True) #sorted(unique_values,reverse=True) # <<<<<<<<<<<<<<
* for i in range(len(unique_values)):
* v = unique_values[i]
*/
- __pyx_t_1 = __Pyx_PyDict_Keys(__pyx_v_pvalue_stat); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyDict_Keys(__pyx_v_pvalue_stat); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_reverse, Py_True) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_sorted, __pyx_t_2, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_reverse, Py_True) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_sorted, __pyx_t_2, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(PyList_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyList_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_unique_values = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":827
+ /* "MACS2/IO/CallPeakUnit.pyx":828
* self.pqtable = Float64HashTable()
* unique_values = sorted(pvalue_stat.keys(), reverse=True) #sorted(unique_values,reverse=True)
* for i in range(len(unique_values)): # <<<<<<<<<<<<<<
@@ -10803,13 +10840,13 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
if (unlikely(__pyx_v_unique_values == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_4 = PyList_GET_SIZE(__pyx_v_unique_values); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_GET_SIZE(__pyx_v_unique_values); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
__pyx_v_i = __pyx_t_5;
- /* "MACS2/IO/CallPeakUnit.pyx":828
+ /* "MACS2/IO/CallPeakUnit.pyx":829
* unique_values = sorted(pvalue_stat.keys(), reverse=True) #sorted(unique_values,reverse=True)
* for i in range(len(unique_values)):
* v = unique_values[i] # <<<<<<<<<<<<<<
@@ -10818,31 +10855,31 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
if (unlikely(__pyx_v_unique_values == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_unique_values, __pyx_v_i, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_unique_values, __pyx_v_i, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_9 = __pyx_PyFloat_AsFloat(__pyx_t_3); if (unlikely((__pyx_t_9 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __pyx_PyFloat_AsFloat(__pyx_t_3); if (unlikely((__pyx_t_9 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_v_v = __pyx_t_9;
- /* "MACS2/IO/CallPeakUnit.pyx":829
+ /* "MACS2/IO/CallPeakUnit.pyx":830
* for i in range(len(unique_values)):
* v = unique_values[i]
* l = pvalue_stat[v] # <<<<<<<<<<<<<<
* q = v + (log10(k) + f)
* q = max(0,min(pre_q,q)) # make q-score monotonic
*/
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_v); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_v); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_PyDict_GetItem(__pyx_v_pvalue_stat, __pyx_t_3); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_PyDict_GetItem(__pyx_v_pvalue_stat, __pyx_t_3); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_8 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_8 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyInt_As_long(__pyx_t_1); if (unlikely((__pyx_t_8 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_l = __pyx_t_8;
- /* "MACS2/IO/CallPeakUnit.pyx":830
+ /* "MACS2/IO/CallPeakUnit.pyx":831
* v = unique_values[i]
* l = pvalue_stat[v]
* q = v + (log10(k) + f) # <<<<<<<<<<<<<<
@@ -10851,7 +10888,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_q = (__pyx_v_v + (log10(__pyx_v_k) + __pyx_v_f));
- /* "MACS2/IO/CallPeakUnit.pyx":831
+ /* "MACS2/IO/CallPeakUnit.pyx":832
* l = pvalue_stat[v]
* q = v + (log10(k) + f)
* q = max(0,min(pre_q,q)) # make q-score monotonic # <<<<<<<<<<<<<<
@@ -10874,22 +10911,22 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
__pyx_v_q = __pyx_t_19;
- /* "MACS2/IO/CallPeakUnit.pyx":832
+ /* "MACS2/IO/CallPeakUnit.pyx":833
* q = v + (log10(k) + f)
* q = max(0,min(pre_q,q)) # make q-score monotonic
* self.pqtable[ v ] = q # <<<<<<<<<<<<<<
* pre_v = v
* pre_q = q
*/
- __pyx_t_1 = PyFloat_FromDouble(__pyx_v_q); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_q); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_v); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_v); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- if (unlikely(PyObject_SetItem(__pyx_v_self->pqtable, __pyx_t_3, __pyx_t_1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyObject_SetItem(__pyx_v_self->pqtable, __pyx_t_3, __pyx_t_1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":833
+ /* "MACS2/IO/CallPeakUnit.pyx":834
* q = max(0,min(pre_q,q)) # make q-score monotonic
* self.pqtable[ v ] = q
* pre_v = v # <<<<<<<<<<<<<<
@@ -10898,7 +10935,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_pre_v = __pyx_v_v;
- /* "MACS2/IO/CallPeakUnit.pyx":834
+ /* "MACS2/IO/CallPeakUnit.pyx":835
* self.pqtable[ v ] = q
* pre_v = v
* pre_q = q # <<<<<<<<<<<<<<
@@ -10907,7 +10944,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_pre_q = __pyx_v_q;
- /* "MACS2/IO/CallPeakUnit.pyx":835
+ /* "MACS2/IO/CallPeakUnit.pyx":836
* pre_v = v
* pre_q = q
* k+=l # <<<<<<<<<<<<<<
@@ -10916,7 +10953,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
__pyx_v_k = (__pyx_v_k + __pyx_v_l);
- /* "MACS2/IO/CallPeakUnit.pyx":836
+ /* "MACS2/IO/CallPeakUnit.pyx":837
* pre_q = q
* k+=l
* nhcal += 1 # <<<<<<<<<<<<<<
@@ -10926,21 +10963,21 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__pyx_v_nhcal = (__pyx_v_nhcal + 1);
}
- /* "MACS2/IO/CallPeakUnit.pyx":838
+ /* "MACS2/IO/CallPeakUnit.pyx":839
* nhcal += 1
*
* logging.debug( "access pq hash for %d times" % nhcal ) # <<<<<<<<<<<<<<
*
* # write pvalue and total length of predicted peaks
*/
- __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_debug); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_debug); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v_nhcal); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v_nhcal); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_10 = __Pyx_PyString_Format(__pyx_kp_s_access_pq_hash_for_d_times, __pyx_t_3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyString_Format(__pyx_kp_s_access_pq_hash_for_d_times, __pyx_t_3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_3 = NULL;
@@ -10954,31 +10991,31 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
}
if (!__pyx_t_3) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_10); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_10); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_GOTREF(__pyx_t_1);
} else {
- __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = NULL;
PyTuple_SET_ITEM(__pyx_t_6, 0+1, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
__pyx_t_10 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_6, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_6, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":841
+ /* "MACS2/IO/CallPeakUnit.pyx":842
*
* # write pvalue and total length of predicted peaks
* fhd = file( self.cutoff_analysis_filename, "w" ) # <<<<<<<<<<<<<<
* fhd.write( "pscore\tqscore\tnpeaks\tlpeaks\tavelpeak\n" )
* x = []
*/
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_self->cutoff_analysis_filename);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->cutoff_analysis_filename);
@@ -10986,51 +11023,51 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__Pyx_INCREF(__pyx_n_s_w);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_n_s_w);
__Pyx_GIVEREF(__pyx_n_s_w);
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_file, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_file, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_fhd = __pyx_t_2;
__pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":842
+ /* "MACS2/IO/CallPeakUnit.pyx":843
* # write pvalue and total length of predicted peaks
* fhd = file( self.cutoff_analysis_filename, "w" )
* fhd.write( "pscore\tqscore\tnpeaks\tlpeaks\tavelpeak\n" ) # <<<<<<<<<<<<<<
* x = []
* y = []
*/
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_fhd, __pyx_n_s_write); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_fhd, __pyx_n_s_write); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__17, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__17, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":843
+ /* "MACS2/IO/CallPeakUnit.pyx":844
* fhd = file( self.cutoff_analysis_filename, "w" )
* fhd.write( "pscore\tqscore\tnpeaks\tlpeaks\tavelpeak\n" )
* x = [] # <<<<<<<<<<<<<<
* y = []
* for cutoff in tmplist:
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_x = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":844
+ /* "MACS2/IO/CallPeakUnit.pyx":845
* fhd.write( "pscore\tqscore\tnpeaks\tlpeaks\tavelpeak\n" )
* x = []
* y = [] # <<<<<<<<<<<<<<
* for cutoff in tmplist:
* fhd.write( "%.2f\t%.2f\t%d\t%d\t%.2f\n" % ( cutoff, self.pqtable[ cutoff ], self.pvalue_npeaks[ cutoff ], self.pvalue_length[ cutoff ], self.pvalue_length[ cutoff ]/self.pvalue_npeaks[ cutoff ] ) )
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_y = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":845
+ /* "MACS2/IO/CallPeakUnit.pyx":846
* x = []
* y = []
* for cutoff in tmplist: # <<<<<<<<<<<<<<
@@ -11039,77 +11076,77 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
if (unlikely(__pyx_v_tmplist == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_1 = __pyx_v_tmplist; __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = 0;
for (;;) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
#if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
- __pyx_t_19 = __pyx_PyFloat_AsFloat(__pyx_t_2); if (unlikely((__pyx_t_19 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_19 = __pyx_PyFloat_AsFloat(__pyx_t_2); if (unlikely((__pyx_t_19 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_cutoff = __pyx_t_19;
- /* "MACS2/IO/CallPeakUnit.pyx":846
+ /* "MACS2/IO/CallPeakUnit.pyx":847
* y = []
* for cutoff in tmplist:
* fhd.write( "%.2f\t%.2f\t%d\t%d\t%.2f\n" % ( cutoff, self.pqtable[ cutoff ], self.pvalue_npeaks[ cutoff ], self.pvalue_length[ cutoff ], self.pvalue_length[ cutoff ]/self.pvalue_npeaks[ cutoff ] ) ) # <<<<<<<<<<<<<<
* x.append( cutoff )
* y.append( self.pvalue_length[ cutoff ] )
*/
- __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_fhd, __pyx_n_s_write); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_fhd, __pyx_n_s_write); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_10 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_20 = PyObject_GetItem(__pyx_v_self->pqtable, __pyx_t_3); if (unlikely(__pyx_t_20 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_20 = PyObject_GetItem(__pyx_v_self->pqtable, __pyx_t_3); if (unlikely(__pyx_t_20 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_20);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (unlikely(__pyx_v_self->pvalue_npeaks == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_21 = __Pyx_PyDict_GetItem(__pyx_v_self->pvalue_npeaks, __pyx_t_3); if (unlikely(__pyx_t_21 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_21 = __Pyx_PyDict_GetItem(__pyx_v_self->pvalue_npeaks, __pyx_t_3); if (unlikely(__pyx_t_21 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_21);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (unlikely(__pyx_v_self->pvalue_length == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_22 = __Pyx_PyDict_GetItem(__pyx_v_self->pvalue_length, __pyx_t_3); if (unlikely(__pyx_t_22 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_22 = __Pyx_PyDict_GetItem(__pyx_v_self->pvalue_length, __pyx_t_3); if (unlikely(__pyx_t_22 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (unlikely(__pyx_v_self->pvalue_length == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_23 = __Pyx_PyDict_GetItem(__pyx_v_self->pvalue_length, __pyx_t_3); if (unlikely(__pyx_t_23 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_23 = __Pyx_PyDict_GetItem(__pyx_v_self->pvalue_length, __pyx_t_3); if (unlikely(__pyx_t_23 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_23);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (unlikely(__pyx_v_self->pvalue_npeaks == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_24 = __Pyx_PyDict_GetItem(__pyx_v_self->pvalue_npeaks, __pyx_t_3); if (unlikely(__pyx_t_24 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_24 = __Pyx_PyDict_GetItem(__pyx_v_self->pvalue_npeaks, __pyx_t_3); if (unlikely(__pyx_t_24 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_24);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyNumber_Divide(__pyx_t_23, __pyx_t_24); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyNumber_Divide(__pyx_t_23, __pyx_t_24); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
__Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0;
- __pyx_t_24 = PyTuple_New(5); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_24 = PyTuple_New(5); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_24);
PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
@@ -11126,7 +11163,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__pyx_t_21 = 0;
__pyx_t_22 = 0;
__pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyString_Format(__pyx_kp_s_2f_2f_d_d_2f, __pyx_t_24); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyString_Format(__pyx_kp_s_2f_2f_d_d_2f, __pyx_t_24); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0;
__pyx_t_24 = NULL;
@@ -11140,36 +11177,36 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
}
if (!__pyx_t_24) {
- __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_GOTREF(__pyx_t_2);
} else {
- __pyx_t_22 = PyTuple_New(1+1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyTuple_New(1+1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_24); __Pyx_GIVEREF(__pyx_t_24); __pyx_t_24 = NULL;
PyTuple_SET_ITEM(__pyx_t_22, 0+1, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_22, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_22, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":847
+ /* "MACS2/IO/CallPeakUnit.pyx":848
* for cutoff in tmplist:
* fhd.write( "%.2f\t%.2f\t%d\t%d\t%.2f\n" % ( cutoff, self.pqtable[ cutoff ], self.pvalue_npeaks[ cutoff ], self.pvalue_length[ cutoff ], self.pvalue_length[ cutoff ]/self.pvalue_npeaks[ cutoff ] ) )
* x.append( cutoff ) # <<<<<<<<<<<<<<
* y.append( self.pvalue_length[ cutoff ] )
* fhd.close()
*/
- __pyx_t_2 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_14 = __Pyx_PyList_Append(__pyx_v_x, __pyx_t_2); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyList_Append(__pyx_v_x, __pyx_t_2); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":848
+ /* "MACS2/IO/CallPeakUnit.pyx":849
* fhd.write( "%.2f\t%.2f\t%d\t%d\t%.2f\n" % ( cutoff, self.pqtable[ cutoff ], self.pvalue_npeaks[ cutoff ], self.pvalue_length[ cutoff ], self.pvalue_length[ cutoff ]/self.pvalue_npeaks[ cutoff ] ) )
* x.append( cutoff )
* y.append( self.pvalue_length[ cutoff ] ) # <<<<<<<<<<<<<<
@@ -11178,17 +11215,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
*/
if (unlikely(__pyx_v_self->pvalue_length == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_2 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = __Pyx_PyDict_GetItem(__pyx_v_self->pvalue_length, __pyx_t_2); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 848; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_6 = __Pyx_PyDict_GetItem(__pyx_v_self->pvalue_length, __pyx_t_2); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_14 = __Pyx_PyList_Append(__pyx_v_y, __pyx_t_6); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyList_Append(__pyx_v_y, __pyx_t_6); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":845
+ /* "MACS2/IO/CallPeakUnit.pyx":846
* x = []
* y = []
* for cutoff in tmplist: # <<<<<<<<<<<<<<
@@ -11198,14 +11235,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":849
+ /* "MACS2/IO/CallPeakUnit.pyx":850
* x.append( cutoff )
* y.append( self.pvalue_length[ cutoff ] )
* fhd.close() # <<<<<<<<<<<<<<
* logging.info( "#3 Analysis of cutoff vs num of peaks or total length has been saved in %s" % self.cutoff_analysis_filename )
* logging.info( "#3 Suggest a cutoff..." )
*/
- __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_fhd, __pyx_n_s_close); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_v_fhd, __pyx_n_s_close); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_2 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_6))) {
@@ -11218,28 +11255,28 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
}
if (__pyx_t_2) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":850
+ /* "MACS2/IO/CallPeakUnit.pyx":851
* y.append( self.pvalue_length[ cutoff ] )
* fhd.close()
* logging.info( "#3 Analysis of cutoff vs num of peaks or total length has been saved in %s" % self.cutoff_analysis_filename ) # <<<<<<<<<<<<<<
* logging.info( "#3 Suggest a cutoff..." )
* optimal_cutoff, optimal_length = find_optimal_cutoff( x, y )
*/
- __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyString_Format(__pyx_kp_s_3_Analysis_of_cutoff_vs_num_of, __pyx_v_self->cutoff_analysis_filename); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyString_Format(__pyx_kp_s_3_Analysis_of_cutoff_vs_num_of, __pyx_v_self->cutoff_analysis_filename); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_22 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) {
@@ -11252,48 +11289,48 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
}
if (!__pyx_t_22) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_GOTREF(__pyx_t_1);
} else {
- __pyx_t_3 = PyTuple_New(1+1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1+1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_22); __Pyx_GIVEREF(__pyx_t_22); __pyx_t_22 = NULL;
PyTuple_SET_ITEM(__pyx_t_3, 0+1, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":851
+ /* "MACS2/IO/CallPeakUnit.pyx":852
* fhd.close()
* logging.info( "#3 Analysis of cutoff vs num of peaks or total length has been saved in %s" % self.cutoff_analysis_filename )
* logging.info( "#3 Suggest a cutoff..." ) # <<<<<<<<<<<<<<
* optimal_cutoff, optimal_length = find_optimal_cutoff( x, y )
* logging.info( "#3 -10log10pvalue cutoff %.2f will call approximately %d bps regions as significant regions" % ( optimal_cutoff, optimal_length ) )
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__18, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__18, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":852
+ /* "MACS2/IO/CallPeakUnit.pyx":853
* logging.info( "#3 Analysis of cutoff vs num of peaks or total length has been saved in %s" % self.cutoff_analysis_filename )
* logging.info( "#3 Suggest a cutoff..." )
* optimal_cutoff, optimal_length = find_optimal_cutoff( x, y ) # <<<<<<<<<<<<<<
* logging.info( "#3 -10log10pvalue cutoff %.2f will call approximately %d bps regions as significant regions" % ( optimal_cutoff, optimal_length ) )
* return self.pqtable
*/
- __pyx_t_1 = __pyx_f_5MACS2_2IO_12CallPeakUnit_find_optimal_cutoff(__pyx_v_x, __pyx_v_y); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_5MACS2_2IO_12CallPeakUnit_find_optimal_cutoff(__pyx_v_x, __pyx_v_y); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (likely(__pyx_t_1 != Py_None)) {
PyObject* sequence = __pyx_t_1;
@@ -11305,7 +11342,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
if (unlikely(size != 2)) {
if (size > 2) __Pyx_RaiseTooManyValuesError(2);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 0);
@@ -11313,33 +11350,33 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__Pyx_INCREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_3);
#else
- __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
#endif
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
} else {
- __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_v_optimal_cutoff = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_v_optimal_length = __pyx_t_3;
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":853
+ /* "MACS2/IO/CallPeakUnit.pyx":854
* logging.info( "#3 Suggest a cutoff..." )
* optimal_cutoff, optimal_length = find_optimal_cutoff( x, y )
* logging.info( "#3 -10log10pvalue cutoff %.2f will call approximately %d bps regions as significant regions" % ( optimal_cutoff, optimal_length ) ) # <<<<<<<<<<<<<<
* return self.pqtable
*
*/
- __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_optimal_cutoff);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_optimal_cutoff);
@@ -11347,7 +11384,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__Pyx_INCREF(__pyx_v_optimal_length);
PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_optimal_length);
__Pyx_GIVEREF(__pyx_v_optimal_length);
- __pyx_t_6 = __Pyx_PyString_Format(__pyx_kp_s_3_10log10pvalue_cutoff_2f_will, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyString_Format(__pyx_kp_s_3_10log10pvalue_cutoff_2f_will, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_3 = NULL;
@@ -11361,24 +11398,24 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
}
}
if (!__pyx_t_3) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_GOTREF(__pyx_t_1);
} else {
- __pyx_t_22 = PyTuple_New(1+1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyTuple_New(1+1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = NULL;
PyTuple_SET_ITEM(__pyx_t_22, 0+1, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_22, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_22, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":854
+ /* "MACS2/IO/CallPeakUnit.pyx":855
* optimal_cutoff, optimal_length = find_optimal_cutoff( x, y )
* logging.info( "#3 -10log10pvalue cutoff %.2f will call approximately %d bps regions as significant regions" % ( optimal_cutoff, optimal_length ) )
* return self.pqtable # <<<<<<<<<<<<<<
@@ -11390,7 +11427,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
__pyx_r = __pyx_v_self->pqtable;
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":705
+ /* "MACS2/IO/CallPeakUnit.pyx":706
*
*
* cdef object __pre_computes ( self, int max_gap = 50, int min_length = 200 ): # <<<<<<<<<<<<<<
@@ -11437,7 +11474,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___pre_
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":857
+/* "MACS2/IO/CallPeakUnit.pyx":858
*
*
* cpdef call_peaks ( self, list scoring_function_symbols, list score_cutoff_s, int min_length = 200, # <<<<<<<<<<<<<<
@@ -11450,7 +11487,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
int __pyx_v_min_length = ((int)200);
int __pyx_v_max_gap = ((int)50);
- /* "MACS2/IO/CallPeakUnit.pyx":858
+ /* "MACS2/IO/CallPeakUnit.pyx":859
*
* cpdef call_peaks ( self, list scoring_function_symbols, list score_cutoff_s, int min_length = 200,
* int max_gap = 50, bool call_summits = False, bool auto_cutoff = False ): # <<<<<<<<<<<<<<
@@ -11495,7 +11532,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
}
}
- /* "MACS2/IO/CallPeakUnit.pyx":857
+ /* "MACS2/IO/CallPeakUnit.pyx":858
*
*
* cpdef call_peaks ( self, list scoring_function_symbols, list score_cutoff_s, int min_length = 200, # <<<<<<<<<<<<<<
@@ -11506,13 +11543,13 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
if (unlikely(__pyx_skip_dispatch)) ;
/* Check if overridden in Python */
else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) {
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_call_peaks); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_call_peaks); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_9call_peaks)) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_min_length); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_min_length); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_max_gap); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_max_gap); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(__pyx_t_1);
__pyx_t_5 = __pyx_t_1; __pyx_t_6 = NULL;
@@ -11527,7 +11564,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
__pyx_t_7 = 1;
}
}
- __pyx_t_8 = PyTuple_New(6+__pyx_t_7); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(6+__pyx_t_7); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
if (__pyx_t_6) {
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_6 = NULL;
@@ -11550,7 +11587,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
__Pyx_GIVEREF(((PyObject *)__pyx_v_auto_cutoff));
__pyx_t_3 = 0;
__pyx_t_4 = 0;
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_8, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_8, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -11562,14 +11599,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":873
+ /* "MACS2/IO/CallPeakUnit.pyx":874
* bytes tmp_bytes
*
* peaks = PeakIO() # <<<<<<<<<<<<<<
*
* # prepare p-q table
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_PeakIO); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_PeakIO); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_5 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) {
@@ -11582,72 +11619,72 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
}
}
if (__pyx_t_5) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_peaks = __pyx_t_1;
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":876
+ /* "MACS2/IO/CallPeakUnit.pyx":877
*
* # prepare p-q table
* if not self.pqtable: # <<<<<<<<<<<<<<
* logging.info("#3 Pre-compute pvalue-qvalue table...")
* if auto_cutoff:
*/
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_v_self->pqtable); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_v_self->pqtable); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_10 = ((!__pyx_t_9) != 0);
if (__pyx_t_10) {
- /* "MACS2/IO/CallPeakUnit.pyx":877
+ /* "MACS2/IO/CallPeakUnit.pyx":878
* # prepare p-q table
* if not self.pqtable:
* logging.info("#3 Pre-compute pvalue-qvalue table...") # <<<<<<<<<<<<<<
* if auto_cutoff:
* logging.info("#3 Cutoff will be automatically decided!")
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__19, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__19, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":878
+ /* "MACS2/IO/CallPeakUnit.pyx":879
* if not self.pqtable:
* logging.info("#3 Pre-compute pvalue-qvalue table...")
* if auto_cutoff: # <<<<<<<<<<<<<<
* logging.info("#3 Cutoff will be automatically decided!")
* self.__pre_computes( max_gap = max_gap, min_length = min_length )
*/
- __pyx_t_10 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_auto_cutoff)); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_auto_cutoff)); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_10) {
- /* "MACS2/IO/CallPeakUnit.pyx":879
+ /* "MACS2/IO/CallPeakUnit.pyx":880
* logging.info("#3 Pre-compute pvalue-qvalue table...")
* if auto_cutoff:
* logging.info("#3 Cutoff will be automatically decided!") # <<<<<<<<<<<<<<
* self.__pre_computes( max_gap = max_gap, min_length = min_length )
* else:
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__20, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__20, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":880
+ /* "MACS2/IO/CallPeakUnit.pyx":881
* if auto_cutoff:
* logging.info("#3 Cutoff will be automatically decided!")
* self.__pre_computes( max_gap = max_gap, min_length = min_length ) # <<<<<<<<<<<<<<
@@ -11657,21 +11694,21 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
__pyx_t_11.__pyx_n = 2;
__pyx_t_11.max_gap = __pyx_v_max_gap;
__pyx_t_11.min_length = __pyx_v_min_length;
- __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___pre_computes(__pyx_v_self, &__pyx_t_11); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___pre_computes(__pyx_v_self, &__pyx_t_11); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L4;
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":882
+ /* "MACS2/IO/CallPeakUnit.pyx":883
* self.__pre_computes( max_gap = max_gap, min_length = min_length )
* else:
* self.__cal_pvalue_qvalue_table() # <<<<<<<<<<<<<<
*
*
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_pvalue_qvalue_table(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_pvalue_qvalue_table(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
@@ -11680,17 +11717,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
}
__pyx_L3:;
- /* "MACS2/IO/CallPeakUnit.pyx":886
+ /* "MACS2/IO/CallPeakUnit.pyx":887
*
* # prepare bedGraph file
* if self.save_bedGraph: # <<<<<<<<<<<<<<
* self.bedGraph_treat_f = fopen( self.bedGraph_treat_filename, "w" )
* self.bedGraph_ctrl_f = fopen( self.bedGraph_control_filename, "w" )
*/
- __pyx_t_10 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->save_bedGraph)); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->save_bedGraph)); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_10) {
- /* "MACS2/IO/CallPeakUnit.pyx":887
+ /* "MACS2/IO/CallPeakUnit.pyx":888
* # prepare bedGraph file
* if self.save_bedGraph:
* self.bedGraph_treat_f = fopen( self.bedGraph_treat_filename, "w" ) # <<<<<<<<<<<<<<
@@ -11699,7 +11736,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
*/
__pyx_v_self->bedGraph_treat_f = fopen(__pyx_v_self->bedGraph_treat_filename, __pyx_k_w);
- /* "MACS2/IO/CallPeakUnit.pyx":888
+ /* "MACS2/IO/CallPeakUnit.pyx":889
* if self.save_bedGraph:
* self.bedGraph_treat_f = fopen( self.bedGraph_treat_filename, "w" )
* self.bedGraph_ctrl_f = fopen( self.bedGraph_control_filename, "w" ) # <<<<<<<<<<<<<<
@@ -11708,38 +11745,38 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
*/
__pyx_v_self->bedGraph_ctrl_f = fopen(__pyx_v_self->bedGraph_control_filename, __pyx_k_w);
- /* "MACS2/IO/CallPeakUnit.pyx":890
+ /* "MACS2/IO/CallPeakUnit.pyx":891
* self.bedGraph_ctrl_f = fopen( self.bedGraph_control_filename, "w" )
*
* logging.info ("#3 In the peak calling step, the following will be performed simultaneously:") # <<<<<<<<<<<<<<
* logging.info ("#3 Write bedGraph files for treatment pileup (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_treat_pileup.bdg")
* logging.info ("#3 Write bedGraph files for control lambda (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_control_lambda.bdg")
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__21, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__21, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":891
+ /* "MACS2/IO/CallPeakUnit.pyx":892
*
* logging.info ("#3 In the peak calling step, the following will be performed simultaneously:")
* logging.info ("#3 Write bedGraph files for treatment pileup (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_treat_pileup.bdg") # <<<<<<<<<<<<<<
* logging.info ("#3 Write bedGraph files for control lambda (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_control_lambda.bdg")
*
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_info); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_info); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_3_Write_bedGraph_files_for_trea, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_3_Write_bedGraph_files_for_trea, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_8 = PyNumber_Add(__pyx_t_2, __pyx_kp_s_treat_pileup_bdg); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Add(__pyx_t_2, __pyx_kp_s_treat_pileup_bdg); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = NULL;
@@ -11753,38 +11790,38 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
}
}
if (!__pyx_t_2) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_8); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_8); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_GOTREF(__pyx_t_1);
} else {
- __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = NULL;
PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
__pyx_t_8 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":892
+ /* "MACS2/IO/CallPeakUnit.pyx":893
* logging.info ("#3 In the peak calling step, the following will be performed simultaneously:")
* logging.info ("#3 Write bedGraph files for treatment pileup (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_treat_pileup.bdg")
* logging.info ("#3 Write bedGraph files for control lambda (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_control_lambda.bdg") # <<<<<<<<<<<<<<
*
* if self.save_SPMR:
*/
- __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_PyString_Format(__pyx_kp_s_3_Write_bedGraph_files_for_cont, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyString_Format(__pyx_kp_s_3_Write_bedGraph_files_for_cont, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_8 = PyNumber_Add(__pyx_t_5, __pyx_kp_s_control_lambda_bdg); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Add(__pyx_t_5, __pyx_kp_s_control_lambda_bdg); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_5 = NULL;
@@ -11798,53 +11835,53 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
}
}
if (!__pyx_t_5) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_8); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_8); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_GOTREF(__pyx_t_1);
} else {
- __pyx_t_2 = PyTuple_New(1+1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1+1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL;
PyTuple_SET_ITEM(__pyx_t_2, 0+1, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
__pyx_t_8 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":894
+ /* "MACS2/IO/CallPeakUnit.pyx":895
* logging.info ("#3 Write bedGraph files for control lambda (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_control_lambda.bdg")
*
* if self.save_SPMR: # <<<<<<<<<<<<<<
* logging.info ( "#3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads." )
* elif self.treat_scaling_factor == 1:
*/
- __pyx_t_10 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->save_SPMR)); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->save_SPMR)); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_10) {
- /* "MACS2/IO/CallPeakUnit.pyx":895
+ /* "MACS2/IO/CallPeakUnit.pyx":896
*
* if self.save_SPMR:
* logging.info ( "#3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads." ) # <<<<<<<<<<<<<<
* elif self.treat_scaling_factor == 1:
* logging.info ( "#3 Pileup will be based on sequencing depth in treatment." )
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_tuple__22, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_tuple__22, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L6;
}
- /* "MACS2/IO/CallPeakUnit.pyx":896
+ /* "MACS2/IO/CallPeakUnit.pyx":897
* if self.save_SPMR:
* logging.info ( "#3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads." )
* elif self.treat_scaling_factor == 1: # <<<<<<<<<<<<<<
@@ -11854,19 +11891,19 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
__pyx_t_10 = ((__pyx_v_self->treat_scaling_factor == 1.0) != 0);
if (__pyx_t_10) {
- /* "MACS2/IO/CallPeakUnit.pyx":897
+ /* "MACS2/IO/CallPeakUnit.pyx":898
* logging.info ( "#3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads." )
* elif self.treat_scaling_factor == 1:
* logging.info ( "#3 Pileup will be based on sequencing depth in treatment." ) # <<<<<<<<<<<<<<
* else:
* logging.info ( "#3 Pileup will be based on sequencing depth in control." )
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_tuple__23, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_tuple__23, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -11874,45 +11911,45 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":899
+ /* "MACS2/IO/CallPeakUnit.pyx":900
* logging.info ( "#3 Pileup will be based on sequencing depth in treatment." )
* else:
* logging.info ( "#3 Pileup will be based on sequencing depth in control." ) # <<<<<<<<<<<<<<
*
* if self.trackline:
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 900; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 900; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_tuple__24, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_tuple__24, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 900; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
__pyx_L6:;
- /* "MACS2/IO/CallPeakUnit.pyx":901
+ /* "MACS2/IO/CallPeakUnit.pyx":902
* logging.info ( "#3 Pileup will be based on sequencing depth in control." )
*
* if self.trackline: # <<<<<<<<<<<<<<
* # this line is REQUIRED by the wiggle format for UCSC browser
* tmp_bytes = ("track type=bedGraph name=\"treatment pileup\" description=\"treatment pileup after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode()
*/
- __pyx_t_10 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->trackline)); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->trackline)); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_10) {
- /* "MACS2/IO/CallPeakUnit.pyx":903
+ /* "MACS2/IO/CallPeakUnit.pyx":904
* if self.trackline:
* # this line is REQUIRED by the wiggle format for UCSC browser
* tmp_bytes = ("track type=bedGraph name=\"treatment pileup\" description=\"treatment pileup after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode() # <<<<<<<<<<<<<<
* fprintf( self.bedGraph_treat_f, tmp_bytes )
* tmp_bytes = ("track type=bedGraph name=\"control lambda\" description=\"control lambda after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode()
*/
- __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_track_type_bedGraph_name_treatme, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_track_type_bedGraph_name_treatme, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_4 = NULL;
@@ -11926,37 +11963,37 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
}
}
if (__pyx_t_4) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_tmp_bytes = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":904
+ /* "MACS2/IO/CallPeakUnit.pyx":905
* # this line is REQUIRED by the wiggle format for UCSC browser
* tmp_bytes = ("track type=bedGraph name=\"treatment pileup\" description=\"treatment pileup after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode()
* fprintf( self.bedGraph_treat_f, tmp_bytes ) # <<<<<<<<<<<<<<
* tmp_bytes = ("track type=bedGraph name=\"control lambda\" description=\"control lambda after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode()
* fprintf( self.bedGraph_ctrl_f, tmp_bytes )
*/
- __pyx_t_12 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
fprintf(__pyx_v_self->bedGraph_treat_f, __pyx_t_12);
- /* "MACS2/IO/CallPeakUnit.pyx":905
+ /* "MACS2/IO/CallPeakUnit.pyx":906
* tmp_bytes = ("track type=bedGraph name=\"treatment pileup\" description=\"treatment pileup after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode()
* fprintf( self.bedGraph_treat_f, tmp_bytes )
* tmp_bytes = ("track type=bedGraph name=\"control lambda\" description=\"control lambda after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode() # <<<<<<<<<<<<<<
* fprintf( self.bedGraph_ctrl_f, tmp_bytes )
*
*/
- __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_track_type_bedGraph_name_control, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_track_type_bedGraph_name_control, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_encode); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_encode); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = NULL;
@@ -11970,25 +12007,25 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
}
}
if (__pyx_t_2) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF_SET(__pyx_v_tmp_bytes, ((PyObject*)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":906
+ /* "MACS2/IO/CallPeakUnit.pyx":907
* fprintf( self.bedGraph_treat_f, tmp_bytes )
* tmp_bytes = ("track type=bedGraph name=\"control lambda\" description=\"control lambda after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode()
* fprintf( self.bedGraph_ctrl_f, tmp_bytes ) # <<<<<<<<<<<<<<
*
* logging.info("#3 Call peaks for each chromosome...")
*/
- __pyx_t_12 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
fprintf(__pyx_v_self->bedGraph_ctrl_f, __pyx_t_12);
goto __pyx_L7;
}
@@ -11997,24 +12034,24 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
}
__pyx_L5:;
- /* "MACS2/IO/CallPeakUnit.pyx":908
+ /* "MACS2/IO/CallPeakUnit.pyx":909
* fprintf( self.bedGraph_ctrl_f, tmp_bytes )
*
* logging.info("#3 Call peaks for each chromosome...") # <<<<<<<<<<<<<<
* for chrom in self.chromosomes:
* # treat/control bedGraph will be saved if requested by user.
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_tuple__25, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_tuple__25, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":909
+ /* "MACS2/IO/CallPeakUnit.pyx":910
*
* logging.info("#3 Call peaks for each chromosome...")
* for chrom in self.chromosomes: # <<<<<<<<<<<<<<
@@ -12023,21 +12060,21 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
*/
if (unlikely(__pyx_v_self->chromosomes == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_1 = __pyx_v_self->chromosomes; __Pyx_INCREF(__pyx_t_1); __pyx_t_7 = 0;
for (;;) {
if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_1)) break;
#if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_7); __Pyx_INCREF(__pyx_t_4); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_7); __Pyx_INCREF(__pyx_t_4); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
- if (!(likely(PyString_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_4))||((__pyx_t_4) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_4)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_chrom, ((PyObject*)__pyx_t_4));
__pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":911
+ /* "MACS2/IO/CallPeakUnit.pyx":912
* for chrom in self.chromosomes:
* # treat/control bedGraph will be saved if requested by user.
* self.__chrom_call_peak_using_certain_criteria ( peaks, chrom, scoring_function_symbols, score_cutoff_s, min_length, max_gap, call_summits, self.save_bedGraph ) # <<<<<<<<<<<<<<
@@ -12046,12 +12083,12 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
*/
__pyx_t_4 = ((PyObject *)__pyx_v_self->save_bedGraph);
__Pyx_INCREF(__pyx_t_4);
- __pyx_t_2 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___chrom_call_peak_using_certain_criteria(__pyx_v_self, __pyx_v_peaks, __pyx_v_chrom, __pyx_v_scoring_function_symbols, __pyx_v_score_cutoff_s, __pyx_v_min_length, __pyx_v_max_gap, __pyx_v_call_summits, ((PyBoolObject *)__pyx_t_4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___chrom_call_peak_using_certain_criteria(__pyx_v_self, __pyx_v_peaks, __pyx_v_chrom, __pyx_v_scoring_function_symbols, __pyx_v_score_cutoff_s, __pyx_v_min_length, __pyx_v_max_gap, __pyx_v_call_summits, ((PyBoolObject *)__pyx_t_4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 912; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":909
+ /* "MACS2/IO/CallPeakUnit.pyx":910
*
* logging.info("#3 Call peaks for each chromosome...")
* for chrom in self.chromosomes: # <<<<<<<<<<<<<<
@@ -12061,17 +12098,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":915
+ /* "MACS2/IO/CallPeakUnit.pyx":916
*
* # close bedGraph file
* if self.save_bedGraph: # <<<<<<<<<<<<<<
* fclose(self.bedGraph_treat_f)
* fclose(self.bedGraph_ctrl_f)
*/
- __pyx_t_10 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->save_bedGraph)); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->save_bedGraph)); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 916; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_10) {
- /* "MACS2/IO/CallPeakUnit.pyx":916
+ /* "MACS2/IO/CallPeakUnit.pyx":917
* # close bedGraph file
* if self.save_bedGraph:
* fclose(self.bedGraph_treat_f) # <<<<<<<<<<<<<<
@@ -12080,7 +12117,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
*/
fclose(__pyx_v_self->bedGraph_treat_f);
- /* "MACS2/IO/CallPeakUnit.pyx":917
+ /* "MACS2/IO/CallPeakUnit.pyx":918
* if self.save_bedGraph:
* fclose(self.bedGraph_treat_f)
* fclose(self.bedGraph_ctrl_f) # <<<<<<<<<<<<<<
@@ -12089,7 +12126,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
*/
fclose(__pyx_v_self->bedGraph_ctrl_f);
- /* "MACS2/IO/CallPeakUnit.pyx":918
+ /* "MACS2/IO/CallPeakUnit.pyx":919
* fclose(self.bedGraph_treat_f)
* fclose(self.bedGraph_ctrl_f)
* self.save_bedGraph = False # <<<<<<<<<<<<<<
@@ -12105,7 +12142,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
}
__pyx_L10:;
- /* "MACS2/IO/CallPeakUnit.pyx":922
+ /* "MACS2/IO/CallPeakUnit.pyx":923
* #print "time to build peak regions: %f" % self.test_time
*
* return peaks # <<<<<<<<<<<<<<
@@ -12117,7 +12154,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
__pyx_r = __pyx_v_peaks;
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":857
+ /* "MACS2/IO/CallPeakUnit.pyx":858
*
*
* cpdef call_peaks ( self, list scoring_function_symbols, list score_cutoff_s, int min_length = 200, # <<<<<<<<<<<<<<
@@ -12165,7 +12202,7 @@ static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_9call
static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_scoring_function_symbols,&__pyx_n_s_score_cutoff_s,&__pyx_n_s_min_length,&__pyx_n_s_max_gap,&__pyx_n_s_call_summits,&__pyx_n_s_auto_cutoff,0};
PyObject* values[6] = {0,0,0,0,0,0};
- /* "MACS2/IO/CallPeakUnit.pyx":858
+ /* "MACS2/IO/CallPeakUnit.pyx":859
*
* cpdef call_peaks ( self, list scoring_function_symbols, list score_cutoff_s, int min_length = 200,
* int max_gap = 50, bool call_summits = False, bool auto_cutoff = False ): # <<<<<<<<<<<<<<
@@ -12195,7 +12232,7 @@ static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_9call
case 1:
if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_score_cutoff_s)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("call_peaks", 0, 2, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("call_peaks", 0, 2, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (kw_args > 0) {
@@ -12219,7 +12256,7 @@ static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_9call
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "call_peaks") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "call_peaks") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -12236,12 +12273,12 @@ static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_9call
__pyx_v_scoring_function_symbols = ((PyObject*)values[0]);
__pyx_v_score_cutoff_s = ((PyObject*)values[1]);
if (values[2]) {
- __pyx_v_min_length = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_min_length == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_min_length = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_min_length == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_min_length = ((int)200);
}
if (values[3]) {
- __pyx_v_max_gap = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_max_gap == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_max_gap = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_max_gap == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_max_gap = ((int)50);
}
@@ -12250,19 +12287,19 @@ static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_9call
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("call_peaks", 0, 2, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("call_peaks", 0, 2, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("MACS2.IO.CallPeakUnit.CallerFromAlignments.call_peaks", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_scoring_function_symbols), (&PyList_Type), 1, "scoring_function_symbols", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_score_cutoff_s), (&PyList_Type), 1, "score_cutoff_s", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_call_summits), __pyx_ptype_7cpython_4bool_bool, 1, "call_summits", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_auto_cutoff), __pyx_ptype_7cpython_4bool_bool, 1, "auto_cutoff", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_scoring_function_symbols), (&PyList_Type), 1, "scoring_function_symbols", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_score_cutoff_s), (&PyList_Type), 1, "score_cutoff_s", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_call_summits), __pyx_ptype_7cpython_4bool_bool, 1, "call_summits", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_auto_cutoff), __pyx_ptype_7cpython_4bool_bool, 1, "auto_cutoff", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = __pyx_pf_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_8call_peaks(((struct __pyx_obj_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self), __pyx_v_scoring_function_symbols, __pyx_v_score_cutoff_s, __pyx_v_min_length, __pyx_v_max_gap, __pyx_v_call_summits, __pyx_v_auto_cutoff);
- /* "MACS2/IO/CallPeakUnit.pyx":857
+ /* "MACS2/IO/CallPeakUnit.pyx":858
*
*
* cpdef call_peaks ( self, list scoring_function_symbols, list score_cutoff_s, int min_length = 200, # <<<<<<<<<<<<<<
@@ -12294,7 +12331,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_8call
__pyx_t_2.max_gap = __pyx_v_max_gap;
__pyx_t_2.call_summits = __pyx_v_call_summits;
__pyx_t_2.auto_cutoff = __pyx_v_auto_cutoff;
- __pyx_t_1 = __pyx_vtabptr_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments->call_peaks(__pyx_v_self, __pyx_v_scoring_function_symbols, __pyx_v_score_cutoff_s, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_vtabptr_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments->call_peaks(__pyx_v_self, __pyx_v_scoring_function_symbols, __pyx_v_score_cutoff_s, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -12311,7 +12348,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_8call
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":924
+/* "MACS2/IO/CallPeakUnit.pyx":925
* return peaks
*
* cdef __chrom_call_peak_using_certain_criteria ( self, peaks, str chrom, list scoring_function_s, list score_cutoff_s, int min_length, # <<<<<<<<<<<<<<
@@ -12407,7 +12444,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_pybuffernd_ctrl_array.data = NULL;
__pyx_pybuffernd_ctrl_array.rcbuffer = &__pyx_pybuffer_ctrl_array;
- /* "MACS2/IO/CallPeakUnit.pyx":960
+ /* "MACS2/IO/CallPeakUnit.pyx":961
*
*
* assert len(scoring_function_s) == len(score_cutoff_s), "number of functions and cutoffs should be the same!" # <<<<<<<<<<<<<<
@@ -12418,45 +12455,45 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
if (unlikely(!Py_OptimizeFlag)) {
if (unlikely(__pyx_v_scoring_function_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = PyList_GET_SIZE(__pyx_v_scoring_function_s); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_GET_SIZE(__pyx_v_scoring_function_s); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(__pyx_v_score_cutoff_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_2 = PyList_GET_SIZE(__pyx_v_score_cutoff_s); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_GET_SIZE(__pyx_v_score_cutoff_s); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(!((__pyx_t_1 == __pyx_t_2) != 0))) {
PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_number_of_functions_and_cutoffs);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
}
#endif
- /* "MACS2/IO/CallPeakUnit.pyx":962
+ /* "MACS2/IO/CallPeakUnit.pyx":963
* assert len(scoring_function_s) == len(score_cutoff_s), "number of functions and cutoffs should be the same!"
*
* peak_content = [] # to store points above cutoff # <<<<<<<<<<<<<<
*
* # first, build pileup, self.chr_pos_treat_ctrl
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 962; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_v_peak_content = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":966
+ /* "MACS2/IO/CallPeakUnit.pyx":967
* # first, build pileup, self.chr_pos_treat_ctrl
* # this step will be speeped up if pqtable is pre-computed.
* self.__pileup_treat_ctrl_a_chromosome( chrom ) # <<<<<<<<<<<<<<
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl
*
*/
- __pyx_t_3 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___pileup_treat_ctrl_a_chromosome(__pyx_v_self, __pyx_v_chrom); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 966; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___pileup_treat_ctrl_a_chromosome(__pyx_v_self, __pyx_v_chrom); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":967
+ /* "MACS2/IO/CallPeakUnit.pyx":968
* # this step will be speeped up if pqtable is pre-computed.
* self.__pileup_treat_ctrl_a_chromosome( chrom )
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl # <<<<<<<<<<<<<<
@@ -12475,7 +12512,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
if (unlikely(size != 3)) {
if (size > 3) __Pyx_RaiseTooManyValuesError(3);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
__pyx_t_4 = PyList_GET_ITEM(sequence, 0);
@@ -12485,20 +12522,20 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__Pyx_INCREF(__pyx_t_5);
__Pyx_INCREF(__pyx_t_6);
#else
- __pyx_t_4 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
#endif
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
} else {
- __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = ((PyArrayObject *)__pyx_t_4);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -12514,7 +12551,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
__pyx_pybuffernd_pos_array.diminfo[0].strides = __pyx_pybuffernd_pos_array.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_pos_array.diminfo[0].shape = __pyx_pybuffernd_pos_array.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_7 = 0;
__pyx_v_pos_array = ((PyArrayObject *)__pyx_t_4);
@@ -12534,7 +12571,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
__pyx_pybuffernd_treat_array.diminfo[0].strides = __pyx_pybuffernd_treat_array.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_treat_array.diminfo[0].shape = __pyx_pybuffernd_treat_array.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_12 = 0;
__pyx_v_treat_array = ((PyArrayObject *)__pyx_t_5);
@@ -12554,49 +12591,49 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
__pyx_pybuffernd_ctrl_array.diminfo[0].strides = __pyx_pybuffernd_ctrl_array.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_ctrl_array.diminfo[0].shape = __pyx_pybuffernd_ctrl_array.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_12 = 0;
__pyx_v_ctrl_array = ((PyArrayObject *)__pyx_t_6);
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":970
+ /* "MACS2/IO/CallPeakUnit.pyx":971
*
* # while save_bedGraph is true, invoke __write_bedGraph_for_a_chromosome
* if save_bedGraph: # <<<<<<<<<<<<<<
* self.__write_bedGraph_for_a_chromosome ( chrom )
*
*/
- __pyx_t_13 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_save_bedGraph)); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_save_bedGraph)); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_13) {
- /* "MACS2/IO/CallPeakUnit.pyx":971
+ /* "MACS2/IO/CallPeakUnit.pyx":972
* # while save_bedGraph is true, invoke __write_bedGraph_for_a_chromosome
* if save_bedGraph:
* self.__write_bedGraph_for_a_chromosome ( chrom ) # <<<<<<<<<<<<<<
*
* # keep all types of scores needed
*/
- __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___write_bedGraph_for_a_chromosome(__pyx_v_self, __pyx_v_chrom)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___write_bedGraph_for_a_chromosome(__pyx_v_self, __pyx_v_chrom)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L3;
}
__pyx_L3:;
- /* "MACS2/IO/CallPeakUnit.pyx":975
+ /* "MACS2/IO/CallPeakUnit.pyx":976
* # keep all types of scores needed
* #t0 = ttime()
* score_array_s = [] # <<<<<<<<<<<<<<
* for i in range(len(scoring_function_s)):
* s = scoring_function_s[i]
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_v_score_array_s = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":976
+ /* "MACS2/IO/CallPeakUnit.pyx":977
* #t0 = ttime()
* score_array_s = []
* for i in range(len(scoring_function_s)): # <<<<<<<<<<<<<<
@@ -12605,13 +12642,13 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
if (unlikely(__pyx_v_scoring_function_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_2 = PyList_GET_SIZE(__pyx_v_scoring_function_s); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_GET_SIZE(__pyx_v_scoring_function_s); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_2; __pyx_t_8+=1) {
__pyx_v_i = __pyx_t_8;
- /* "MACS2/IO/CallPeakUnit.pyx":977
+ /* "MACS2/IO/CallPeakUnit.pyx":978
* score_array_s = []
* for i in range(len(scoring_function_s)):
* s = scoring_function_s[i] # <<<<<<<<<<<<<<
@@ -12620,129 +12657,129 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
if (unlikely(__pyx_v_scoring_function_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 978; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_scoring_function_s, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_scoring_function_s, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 978; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- if (!(likely(PyString_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 978; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_s, ((PyObject*)__pyx_t_3));
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":978
+ /* "MACS2/IO/CallPeakUnit.pyx":979
* for i in range(len(scoring_function_s)):
* s = scoring_function_s[i]
* if s == 'p': # <<<<<<<<<<<<<<
* score_array_s.append( self.__cal_pscore( treat_array, ctrl_array ) )
* elif s == 'q':
*/
- __pyx_t_13 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_p, Py_EQ)); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 978; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_p, Py_EQ)); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 979; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_14 = (__pyx_t_13 != 0);
if (__pyx_t_14) {
- /* "MACS2/IO/CallPeakUnit.pyx":979
+ /* "MACS2/IO/CallPeakUnit.pyx":980
* s = scoring_function_s[i]
* if s == 'p':
* score_array_s.append( self.__cal_pscore( treat_array, ctrl_array ) ) # <<<<<<<<<<<<<<
* elif s == 'q':
* score_array_s.append( self.__cal_qscore( treat_array, ctrl_array ) )
*/
- __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_pscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 979; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_pscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 980; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_15 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 979; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 980; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L6;
}
- /* "MACS2/IO/CallPeakUnit.pyx":980
+ /* "MACS2/IO/CallPeakUnit.pyx":981
* if s == 'p':
* score_array_s.append( self.__cal_pscore( treat_array, ctrl_array ) )
* elif s == 'q': # <<<<<<<<<<<<<<
* score_array_s.append( self.__cal_qscore( treat_array, ctrl_array ) )
* elif s == 'f':
*/
- __pyx_t_14 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_q, Py_EQ)); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 980; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_q, Py_EQ)); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_13 = (__pyx_t_14 != 0);
if (__pyx_t_13) {
- /* "MACS2/IO/CallPeakUnit.pyx":981
+ /* "MACS2/IO/CallPeakUnit.pyx":982
* score_array_s.append( self.__cal_pscore( treat_array, ctrl_array ) )
* elif s == 'q':
* score_array_s.append( self.__cal_qscore( treat_array, ctrl_array ) ) # <<<<<<<<<<<<<<
* elif s == 'f':
* score_array_s.append( self.__cal_FE( treat_array, ctrl_array ) )
*/
- __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_qscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_qscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 982; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_15 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 982; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L6;
}
- /* "MACS2/IO/CallPeakUnit.pyx":982
+ /* "MACS2/IO/CallPeakUnit.pyx":983
* elif s == 'q':
* score_array_s.append( self.__cal_qscore( treat_array, ctrl_array ) )
* elif s == 'f': # <<<<<<<<<<<<<<
* score_array_s.append( self.__cal_FE( treat_array, ctrl_array ) )
* elif s == 's':
*/
- __pyx_t_13 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_f, Py_EQ)); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 982; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_f, Py_EQ)); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_14 = (__pyx_t_13 != 0);
if (__pyx_t_14) {
- /* "MACS2/IO/CallPeakUnit.pyx":983
+ /* "MACS2/IO/CallPeakUnit.pyx":984
* score_array_s.append( self.__cal_qscore( treat_array, ctrl_array ) )
* elif s == 'f':
* score_array_s.append( self.__cal_FE( treat_array, ctrl_array ) ) # <<<<<<<<<<<<<<
* elif s == 's':
* score_array_s.append( self.__cal_subtraction( treat_array, ctrl_array ) )
*/
- __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_FE(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_FE(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 984; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_15 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 984; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L6;
}
- /* "MACS2/IO/CallPeakUnit.pyx":984
+ /* "MACS2/IO/CallPeakUnit.pyx":985
* elif s == 'f':
* score_array_s.append( self.__cal_FE( treat_array, ctrl_array ) )
* elif s == 's': # <<<<<<<<<<<<<<
* score_array_s.append( self.__cal_subtraction( treat_array, ctrl_array ) )
*
*/
- __pyx_t_14 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_s, Py_EQ)); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 984; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_s, Py_EQ)); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_13 = (__pyx_t_14 != 0);
if (__pyx_t_13) {
- /* "MACS2/IO/CallPeakUnit.pyx":985
+ /* "MACS2/IO/CallPeakUnit.pyx":986
* score_array_s.append( self.__cal_FE( treat_array, ctrl_array ) )
* elif s == 's':
* score_array_s.append( self.__cal_subtraction( treat_array, ctrl_array ) ) # <<<<<<<<<<<<<<
*
* #self.test_time += ttime() - t0
*/
- __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_subtraction(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_subtraction(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_15 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L6;
}
__pyx_L6:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":992
+ /* "MACS2/IO/CallPeakUnit.pyx":993
* #t0 = ttime()
* # get the regions with scores above cutoffs
* above_cutoff = np.nonzero( apply_multiple_cutoffs(score_array_s,score_cutoff_s) )[0] # this is not an optimized method. It would be better to store score array in a 2-D ndarray? # <<<<<<<<<<<<<<
* above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff
*/
- __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_nonzero); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_nonzero); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = ((PyObject *)__pyx_f_5MACS2_2IO_12CallPeakUnit_apply_multiple_cutoffs(__pyx_v_score_array_s, __pyx_v_score_cutoff_s)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = ((PyObject *)__pyx_f_5MACS2_2IO_12CallPeakUnit_apply_multiple_cutoffs(__pyx_v_score_array_s, __pyx_v_score_cutoff_s)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_4 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_5))) {
@@ -12755,59 +12792,59 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
if (!__pyx_t_4) {
- __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_GOTREF(__pyx_t_3);
} else {
- __pyx_t_16 = PyTuple_New(1+1); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = PyTuple_New(1+1); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_16);
PyTuple_SET_ITEM(__pyx_t_16, 0, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); __pyx_t_4 = NULL;
PyTuple_SET_ITEM(__pyx_t_16, 0+1, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_16, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_16, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_above_cutoff = ((PyArrayObject *)__pyx_t_5);
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":993
+ /* "MACS2/IO/CallPeakUnit.pyx":994
* # get the regions with scores above cutoffs
* above_cutoff = np.nonzero( apply_multiple_cutoffs(score_array_s,score_cutoff_s) )[0] # this is not an optimized method. It would be better to store score array in a 2-D ndarray?
* above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices # <<<<<<<<<<<<<<
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
*/
- __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_arange); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_arange); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_pos_array->dimensions[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_pos_array->dimensions[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_16 = PyTuple_New(1); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = PyTuple_New(1); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_16);
PyTuple_SET_ITEM(__pyx_t_16, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_16, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_16, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_GetItem(__pyx_t_6, ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_5 = PyObject_GetItem(__pyx_t_6, ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = ((PyArrayObject *)__pyx_t_5);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -12823,22 +12860,22 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
__pyx_pybuffernd_above_cutoff_index_array.diminfo[0].strides = __pyx_pybuffernd_above_cutoff_index_array.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_above_cutoff_index_array.diminfo[0].shape = __pyx_pybuffernd_above_cutoff_index_array.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_7 = 0;
__pyx_v_above_cutoff_index_array = ((PyArrayObject *)__pyx_t_5);
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":994
+ /* "MACS2/IO/CallPeakUnit.pyx":995
* above_cutoff = np.nonzero( apply_multiple_cutoffs(score_array_s,score_cutoff_s) )[0] # this is not an optimized method. It would be better to store score array in a 2-D ndarray?
* above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff # <<<<<<<<<<<<<<
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
*
*/
- __pyx_t_5 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_5 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_5);
- if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = ((PyArrayObject *)__pyx_t_5);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -12854,25 +12891,25 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
__pyx_pybuffernd_above_cutoff_endpos.diminfo[0].strides = __pyx_pybuffernd_above_cutoff_endpos.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_above_cutoff_endpos.diminfo[0].shape = __pyx_pybuffernd_above_cutoff_endpos.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_7 = 0;
__pyx_v_above_cutoff_endpos = ((PyArrayObject *)__pyx_t_5);
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":995
+ /* "MACS2/IO/CallPeakUnit.pyx":996
* above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff # <<<<<<<<<<<<<<
*
* if above_cutoff.size == 0:
*/
- __pyx_t_5 = PyNumber_Subtract(((PyObject *)__pyx_v_above_cutoff), __pyx_int_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Subtract(((PyObject *)__pyx_v_above_cutoff), __pyx_int_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 996; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), __pyx_t_5); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_6 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), __pyx_t_5); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 996; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 996; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = ((PyArrayObject *)__pyx_t_6);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -12888,28 +12925,28 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
__pyx_pybuffernd_above_cutoff_startpos.diminfo[0].strides = __pyx_pybuffernd_above_cutoff_startpos.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_above_cutoff_startpos.diminfo[0].shape = __pyx_pybuffernd_above_cutoff_startpos.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 996; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_7 = 0;
__pyx_v_above_cutoff_startpos = ((PyArrayObject *)__pyx_t_6);
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":997
+ /* "MACS2/IO/CallPeakUnit.pyx":998
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
*
* if above_cutoff.size == 0: # <<<<<<<<<<<<<<
* # nothing above cutoff
* return peaks
*/
- __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff), __pyx_n_s_size); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff), __pyx_n_s_size); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 998; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_6, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_6, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 998; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_13 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 998; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_13) {
- /* "MACS2/IO/CallPeakUnit.pyx":999
+ /* "MACS2/IO/CallPeakUnit.pyx":1000
* if above_cutoff.size == 0:
* # nothing above cutoff
* return peaks # <<<<<<<<<<<<<<
@@ -12922,22 +12959,22 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
goto __pyx_L0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1001
+ /* "MACS2/IO/CallPeakUnit.pyx":1002
* return peaks
*
* if above_cutoff[0] == 0: # <<<<<<<<<<<<<<
* # first element > cutoff, fix the first point as 0. otherwise it would be the last item in data[chrom]['pos']
* above_cutoff_startpos[0] = 0
*/
- __pyx_t_5 = __Pyx_GetItemInt(((PyObject *)__pyx_v_above_cutoff), 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1001; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_5 = __Pyx_GetItemInt(((PyObject *)__pyx_v_above_cutoff), 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyObject_RichCompare(__pyx_t_5, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_5, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_13 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (__pyx_t_13) {
- /* "MACS2/IO/CallPeakUnit.pyx":1003
+ /* "MACS2/IO/CallPeakUnit.pyx":1004
* if above_cutoff[0] == 0:
* # first element > cutoff, fix the first point as 0. otherwise it would be the last item in data[chrom]['pos']
* above_cutoff_startpos[0] = 0 # <<<<<<<<<<<<<<
@@ -12952,14 +12989,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
} else if (unlikely(__pyx_t_17 >= __pyx_pybuffernd_above_cutoff_startpos.diminfo[0].shape)) __pyx_t_8 = 0;
if (unlikely(__pyx_t_8 != -1)) {
__Pyx_RaiseBufferIndexError(__pyx_t_8);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1003; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1004; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_above_cutoff_startpos.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_above_cutoff_startpos.diminfo[0].strides) = 0;
goto __pyx_L8;
}
__pyx_L8:;
- /* "MACS2/IO/CallPeakUnit.pyx":1010
+ /* "MACS2/IO/CallPeakUnit.pyx":1011
*
* # first bit of region above cutoff
* acs_ptr = <int32_t *>above_cutoff_startpos.data # <<<<<<<<<<<<<<
@@ -12968,7 +13005,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_acs_ptr = ((int32_t *)__pyx_v_above_cutoff_startpos->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1011
+ /* "MACS2/IO/CallPeakUnit.pyx":1012
* # first bit of region above cutoff
* acs_ptr = <int32_t *>above_cutoff_startpos.data
* ace_ptr = <int32_t *>above_cutoff_endpos.data # <<<<<<<<<<<<<<
@@ -12977,7 +13014,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ace_ptr = ((int32_t *)__pyx_v_above_cutoff_endpos->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1012
+ /* "MACS2/IO/CallPeakUnit.pyx":1013
* acs_ptr = <int32_t *>above_cutoff_startpos.data
* ace_ptr = <int32_t *>above_cutoff_endpos.data
* acia_ptr= <int32_t *>above_cutoff_index_array.data # <<<<<<<<<<<<<<
@@ -12986,7 +13023,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_acia_ptr = ((int32_t *)__pyx_v_above_cutoff_index_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1013
+ /* "MACS2/IO/CallPeakUnit.pyx":1014
* ace_ptr = <int32_t *>above_cutoff_endpos.data
* acia_ptr= <int32_t *>above_cutoff_index_array.data
* treat_array_ptr = <float32_t *> treat_array.data # <<<<<<<<<<<<<<
@@ -12995,7 +13032,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_treat_array_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_treat_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1014
+ /* "MACS2/IO/CallPeakUnit.pyx":1015
* acia_ptr= <int32_t *>above_cutoff_index_array.data
* treat_array_ptr = <float32_t *> treat_array.data
* ctrl_array_ptr = <float32_t *> ctrl_array.data # <<<<<<<<<<<<<<
@@ -13004,7 +13041,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ctrl_array_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_ctrl_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1016
+ /* "MACS2/IO/CallPeakUnit.pyx":1017
* ctrl_array_ptr = <float32_t *> ctrl_array.data
*
* ts = acs_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -13013,7 +13050,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ts = (__pyx_v_acs_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1017
+ /* "MACS2/IO/CallPeakUnit.pyx":1018
*
* ts = acs_ptr[ 0 ]
* te = ace_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -13022,7 +13059,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_te = (__pyx_v_ace_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1018
+ /* "MACS2/IO/CallPeakUnit.pyx":1019
* ts = acs_ptr[ 0 ]
* te = ace_ptr[ 0 ]
* ti = acia_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -13031,7 +13068,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ti = (__pyx_v_acia_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1019
+ /* "MACS2/IO/CallPeakUnit.pyx":1020
* te = ace_ptr[ 0 ]
* ti = acia_ptr[ 0 ]
* tp = treat_array_ptr[ ti ] # <<<<<<<<<<<<<<
@@ -13040,7 +13077,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_tp = (__pyx_v_treat_array_ptr[__pyx_v_ti]);
- /* "MACS2/IO/CallPeakUnit.pyx":1020
+ /* "MACS2/IO/CallPeakUnit.pyx":1021
* ti = acia_ptr[ 0 ]
* tp = treat_array_ptr[ ti ]
* cp = ctrl_array_ptr[ ti ] # <<<<<<<<<<<<<<
@@ -13049,24 +13086,24 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_cp = (__pyx_v_ctrl_array_ptr[__pyx_v_ti]);
- /* "MACS2/IO/CallPeakUnit.pyx":1022
+ /* "MACS2/IO/CallPeakUnit.pyx":1023
* cp = ctrl_array_ptr[ ti ]
*
* peak_content.append( ( ts, te, tp, cp, ti ) ) # <<<<<<<<<<<<<<
* lastp = te
* acs_ptr += 1
*/
- __pyx_t_6 = __Pyx_PyInt_From_long(__pyx_v_ts); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_From_long(__pyx_v_ts); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = __Pyx_PyInt_From_long(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_long(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_16 = PyFloat_FromDouble(__pyx_v_tp); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = PyFloat_FromDouble(__pyx_v_tp); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_16);
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = __Pyx_PyInt_From_long(__pyx_v_ti); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_From_long(__pyx_v_ti); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_18 = PyTuple_New(5); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_18 = PyTuple_New(5); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_18);
PyTuple_SET_ITEM(__pyx_t_18, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
@@ -13083,10 +13120,10 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_t_16 = 0;
__pyx_t_3 = 0;
__pyx_t_4 = 0;
- __pyx_t_15 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_18); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_18); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1023
+ /* "MACS2/IO/CallPeakUnit.pyx":1024
*
* peak_content.append( ( ts, te, tp, cp, ti ) )
* lastp = te # <<<<<<<<<<<<<<
@@ -13095,7 +13132,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_lastp = __pyx_v_te;
- /* "MACS2/IO/CallPeakUnit.pyx":1024
+ /* "MACS2/IO/CallPeakUnit.pyx":1025
* peak_content.append( ( ts, te, tp, cp, ti ) )
* lastp = te
* acs_ptr += 1 # <<<<<<<<<<<<<<
@@ -13104,7 +13141,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_acs_ptr = (__pyx_v_acs_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1025
+ /* "MACS2/IO/CallPeakUnit.pyx":1026
* lastp = te
* acs_ptr += 1
* ace_ptr += 1 # <<<<<<<<<<<<<<
@@ -13113,7 +13150,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ace_ptr = (__pyx_v_ace_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1026
+ /* "MACS2/IO/CallPeakUnit.pyx":1027
* acs_ptr += 1
* ace_ptr += 1
* acia_ptr+= 1 # <<<<<<<<<<<<<<
@@ -13122,7 +13159,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_acia_ptr = (__pyx_v_acia_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1028
+ /* "MACS2/IO/CallPeakUnit.pyx":1029
* acia_ptr+= 1
*
* for i in range( 1, above_cutoff_startpos.shape[0] ): # <<<<<<<<<<<<<<
@@ -13133,7 +13170,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
for (__pyx_t_8 = 1; __pyx_t_8 < __pyx_t_19; __pyx_t_8+=1) {
__pyx_v_i = __pyx_t_8;
- /* "MACS2/IO/CallPeakUnit.pyx":1029
+ /* "MACS2/IO/CallPeakUnit.pyx":1030
*
* for i in range( 1, above_cutoff_startpos.shape[0] ):
* ts = acs_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -13142,7 +13179,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ts = (__pyx_v_acs_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1030
+ /* "MACS2/IO/CallPeakUnit.pyx":1031
* for i in range( 1, above_cutoff_startpos.shape[0] ):
* ts = acs_ptr[ 0 ]
* te = ace_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -13151,7 +13188,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_te = (__pyx_v_ace_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1031
+ /* "MACS2/IO/CallPeakUnit.pyx":1032
* ts = acs_ptr[ 0 ]
* te = ace_ptr[ 0 ]
* ti = acia_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -13160,7 +13197,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ti = (__pyx_v_acia_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1032
+ /* "MACS2/IO/CallPeakUnit.pyx":1033
* te = ace_ptr[ 0 ]
* ti = acia_ptr[ 0 ]
* acs_ptr += 1 # <<<<<<<<<<<<<<
@@ -13169,7 +13206,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_acs_ptr = (__pyx_v_acs_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1033
+ /* "MACS2/IO/CallPeakUnit.pyx":1034
* ti = acia_ptr[ 0 ]
* acs_ptr += 1
* ace_ptr += 1 # <<<<<<<<<<<<<<
@@ -13178,7 +13215,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ace_ptr = (__pyx_v_ace_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1034
+ /* "MACS2/IO/CallPeakUnit.pyx":1035
* acs_ptr += 1
* ace_ptr += 1
* acia_ptr+= 1 # <<<<<<<<<<<<<<
@@ -13187,7 +13224,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_acia_ptr = (__pyx_v_acia_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1035
+ /* "MACS2/IO/CallPeakUnit.pyx":1036
* ace_ptr += 1
* acia_ptr+= 1
* tp = treat_array_ptr[ ti ] # <<<<<<<<<<<<<<
@@ -13196,7 +13233,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_tp = (__pyx_v_treat_array_ptr[__pyx_v_ti]);
- /* "MACS2/IO/CallPeakUnit.pyx":1036
+ /* "MACS2/IO/CallPeakUnit.pyx":1037
* acia_ptr+= 1
* tp = treat_array_ptr[ ti ]
* cp = ctrl_array_ptr[ ti ] # <<<<<<<<<<<<<<
@@ -13205,7 +13242,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_cp = (__pyx_v_ctrl_array_ptr[__pyx_v_ti]);
- /* "MACS2/IO/CallPeakUnit.pyx":1037
+ /* "MACS2/IO/CallPeakUnit.pyx":1038
* tp = treat_array_ptr[ ti ]
* cp = ctrl_array_ptr[ ti ]
* tl = ts - lastp # <<<<<<<<<<<<<<
@@ -13214,7 +13251,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_tl = (__pyx_v_ts - __pyx_v_lastp);
- /* "MACS2/IO/CallPeakUnit.pyx":1038
+ /* "MACS2/IO/CallPeakUnit.pyx":1039
* cp = ctrl_array_ptr[ ti ]
* tl = ts - lastp
* if tl <= max_gap: # <<<<<<<<<<<<<<
@@ -13224,24 +13261,24 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_t_13 = ((__pyx_v_tl <= __pyx_v_max_gap) != 0);
if (__pyx_t_13) {
- /* "MACS2/IO/CallPeakUnit.pyx":1040
+ /* "MACS2/IO/CallPeakUnit.pyx":1041
* if tl <= max_gap:
* # append.
* peak_content.append( ( ts, te, tp, cp, ti ) ) # <<<<<<<<<<<<<<
* lastp = te #above_cutoff_endpos[i]
* else:
*/
- __pyx_t_18 = __Pyx_PyInt_From_long(__pyx_v_ts); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1040; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_18 = __Pyx_PyInt_From_long(__pyx_v_ts); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_18);
- __pyx_t_4 = __Pyx_PyInt_From_long(__pyx_v_te); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1040; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_From_long(__pyx_v_te); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_tp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1040; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_tp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_16 = PyFloat_FromDouble(__pyx_v_cp); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1040; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = PyFloat_FromDouble(__pyx_v_cp); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_16);
- __pyx_t_5 = __Pyx_PyInt_From_long(__pyx_v_ti); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1040; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_long(__pyx_v_ti); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyTuple_New(5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1040; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyTuple_New(5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_18);
__Pyx_GIVEREF(__pyx_t_18);
@@ -13258,10 +13295,10 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_t_3 = 0;
__pyx_t_16 = 0;
__pyx_t_5 = 0;
- __pyx_t_15 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_6); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1040; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_6); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1041; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1041
+ /* "MACS2/IO/CallPeakUnit.pyx":1042
* # append.
* peak_content.append( ( ts, te, tp, cp, ti ) )
* lastp = te #above_cutoff_endpos[i] # <<<<<<<<<<<<<<
@@ -13273,17 +13310,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1044
+ /* "MACS2/IO/CallPeakUnit.pyx":1045
* else:
* # close
* if call_summits: # <<<<<<<<<<<<<<
* self.__close_peak_with_subpeaks (peak_content, peaks, min_length, chrom, min_length, score_array_s, score_cutoff_s = score_cutoff_s ) # smooth length is min_length, i.e. fragment size 'd'
* else:
*/
- __pyx_t_13 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_call_summits)); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1044; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_call_summits)); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1045; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_13) {
- /* "MACS2/IO/CallPeakUnit.pyx":1045
+ /* "MACS2/IO/CallPeakUnit.pyx":1046
* # close
* if call_summits:
* self.__close_peak_with_subpeaks (peak_content, peaks, min_length, chrom, min_length, score_array_s, score_cutoff_s = score_cutoff_s ) # smooth length is min_length, i.e. fragment size 'd' # <<<<<<<<<<<<<<
@@ -13292,14 +13329,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_t_20.__pyx_n = 1;
__pyx_t_20.score_cutoff_s = __pyx_v_score_cutoff_s;
- __pyx_t_6 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_with_subpeaks(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, __pyx_v_min_length, __pyx_v_score_array_s, &__pyx_t_20)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1045; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_with_subpeaks(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, __pyx_v_min_length, __pyx_v_score_array_s, &__pyx_t_20)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
goto __pyx_L12;
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1047
+ /* "MACS2/IO/CallPeakUnit.pyx":1048
* self.__close_peak_with_subpeaks (peak_content, peaks, min_length, chrom, min_length, score_array_s, score_cutoff_s = score_cutoff_s ) # smooth length is min_length, i.e. fragment size 'd'
* else:
* self.__close_peak_wo_subpeaks (peak_content, peaks, min_length, chrom, min_length, score_array_s, score_cutoff_s = score_cutoff_s ) # smooth length is min_length, i.e. fragment size 'd' # <<<<<<<<<<<<<<
@@ -13308,30 +13345,30 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_t_21.__pyx_n = 1;
__pyx_t_21.score_cutoff_s = __pyx_v_score_cutoff_s;
- __pyx_t_6 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_wo_subpeaks(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, __pyx_v_min_length, __pyx_v_score_array_s, &__pyx_t_21)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_wo_subpeaks(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, __pyx_v_min_length, __pyx_v_score_array_s, &__pyx_t_21)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
}
__pyx_L12:;
- /* "MACS2/IO/CallPeakUnit.pyx":1048
+ /* "MACS2/IO/CallPeakUnit.pyx":1049
* else:
* self.__close_peak_wo_subpeaks (peak_content, peaks, min_length, chrom, min_length, score_array_s, score_cutoff_s = score_cutoff_s ) # smooth length is min_length, i.e. fragment size 'd'
* peak_content = [ ( ts, te, tp, cp, ti ), ] # <<<<<<<<<<<<<<
* lastp = te #above_cutoff_endpos[i]
* # save the last peak
*/
- __pyx_t_6 = __Pyx_PyInt_From_long(__pyx_v_ts); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_From_long(__pyx_v_ts); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = __Pyx_PyInt_From_long(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_long(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_16 = PyFloat_FromDouble(__pyx_v_tp); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = PyFloat_FromDouble(__pyx_v_tp); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_16);
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_cp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = __Pyx_PyInt_From_long(__pyx_v_ti); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_From_long(__pyx_v_ti); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_18 = PyTuple_New(5); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_18 = PyTuple_New(5); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_18);
PyTuple_SET_ITEM(__pyx_t_18, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
@@ -13348,7 +13385,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_t_16 = 0;
__pyx_t_3 = 0;
__pyx_t_4 = 0;
- __pyx_t_4 = PyList_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
PyList_SET_ITEM(__pyx_t_4, 0, __pyx_t_18);
__Pyx_GIVEREF(__pyx_t_18);
@@ -13356,7 +13393,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__Pyx_DECREF_SET(__pyx_v_peak_content, ((PyObject*)__pyx_t_4));
__pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1049
+ /* "MACS2/IO/CallPeakUnit.pyx":1050
* self.__close_peak_wo_subpeaks (peak_content, peaks, min_length, chrom, min_length, score_array_s, score_cutoff_s = score_cutoff_s ) # smooth length is min_length, i.e. fragment size 'd'
* peak_content = [ ( ts, te, tp, cp, ti ), ]
* lastp = te #above_cutoff_endpos[i] # <<<<<<<<<<<<<<
@@ -13368,7 +13405,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_L11:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1051
+ /* "MACS2/IO/CallPeakUnit.pyx":1052
* lastp = te #above_cutoff_endpos[i]
* # save the last peak
* if not peak_content: # <<<<<<<<<<<<<<
@@ -13379,7 +13416,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_t_14 = ((!__pyx_t_13) != 0);
if (__pyx_t_14) {
- /* "MACS2/IO/CallPeakUnit.pyx":1052
+ /* "MACS2/IO/CallPeakUnit.pyx":1053
* # save the last peak
* if not peak_content:
* return peaks # <<<<<<<<<<<<<<
@@ -13393,17 +13430,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1054
+ /* "MACS2/IO/CallPeakUnit.pyx":1055
* return peaks
* else:
* if call_summits: # <<<<<<<<<<<<<<
* self.__close_peak_with_subpeaks (peak_content, peaks, min_length, chrom, min_length, score_array_s, score_cutoff_s = score_cutoff_s ) # smooth length is min_length, i.e. fragment size 'd'
* else:
*/
- __pyx_t_14 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_call_summits)); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_call_summits)); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1055; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_14) {
- /* "MACS2/IO/CallPeakUnit.pyx":1055
+ /* "MACS2/IO/CallPeakUnit.pyx":1056
* else:
* if call_summits:
* self.__close_peak_with_subpeaks (peak_content, peaks, min_length, chrom, min_length, score_array_s, score_cutoff_s = score_cutoff_s ) # smooth length is min_length, i.e. fragment size 'd' # <<<<<<<<<<<<<<
@@ -13412,14 +13449,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_t_20.__pyx_n = 1;
__pyx_t_20.score_cutoff_s = __pyx_v_score_cutoff_s;
- __pyx_t_4 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_with_subpeaks(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, __pyx_v_min_length, __pyx_v_score_array_s, &__pyx_t_20)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1055; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_with_subpeaks(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, __pyx_v_min_length, __pyx_v_score_array_s, &__pyx_t_20)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1056; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
goto __pyx_L14;
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1057
+ /* "MACS2/IO/CallPeakUnit.pyx":1058
* self.__close_peak_with_subpeaks (peak_content, peaks, min_length, chrom, min_length, score_array_s, score_cutoff_s = score_cutoff_s ) # smooth length is min_length, i.e. fragment size 'd'
* else:
* self.__close_peak_wo_subpeaks (peak_content, peaks, min_length, chrom, min_length, score_array_s, score_cutoff_s = score_cutoff_s ) # smooth length is min_length, i.e. fragment size 'd' # <<<<<<<<<<<<<<
@@ -13428,14 +13465,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_t_21.__pyx_n = 1;
__pyx_t_21.score_cutoff_s = __pyx_v_score_cutoff_s;
- __pyx_t_4 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_wo_subpeaks(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, __pyx_v_min_length, __pyx_v_score_array_s, &__pyx_t_21)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_wo_subpeaks(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, __pyx_v_min_length, __pyx_v_score_array_s, &__pyx_t_21)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1058; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
}
__pyx_L14:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1060
+ /* "MACS2/IO/CallPeakUnit.pyx":1061
*
* #print "close peaks -- chrom:",chrom," time:", ttime() - t0
* return peaks # <<<<<<<<<<<<<<
@@ -13447,7 +13484,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_r = __pyx_v_peaks;
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":924
+ /* "MACS2/IO/CallPeakUnit.pyx":925
* return peaks
*
* cdef __chrom_call_peak_using_certain_criteria ( self, peaks, str chrom, list scoring_function_s, list score_cutoff_s, int min_length, # <<<<<<<<<<<<<<
@@ -13498,7 +13535,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1062
+/* "MACS2/IO/CallPeakUnit.pyx":1063
* return peaks
*
* cdef bool __close_peak_wo_subpeaks (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<<
@@ -13556,7 +13593,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
- /* "MACS2/IO/CallPeakUnit.pyx":1077
+ /* "MACS2/IO/CallPeakUnit.pyx":1078
* int tlist_scores_p
*
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ] # <<<<<<<<<<<<<<
@@ -13565,57 +13602,57 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1077; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1077; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_1, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1077; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_1, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1077; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1077; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_1, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1077; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_1, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Subtract(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1077; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Subtract(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_v_peak_length = __pyx_t_1;
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1078
+ /* "MACS2/IO/CallPeakUnit.pyx":1079
*
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ]
* if peak_length >= min_length: # if the peak is too small, reject it # <<<<<<<<<<<<<<
* tsummit = []
* summit_pos = 0
*/
- __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_min_length); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_min_length); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1079; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_peak_length, __pyx_t_1, Py_GE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_peak_length, __pyx_t_1, Py_GE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1079; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1079; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_4) {
- /* "MACS2/IO/CallPeakUnit.pyx":1079
+ /* "MACS2/IO/CallPeakUnit.pyx":1080
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ]
* if peak_length >= min_length: # if the peak is too small, reject it
* tsummit = [] # <<<<<<<<<<<<<<
* summit_pos = 0
* summit_value = 0
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1079; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1080; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_v_tsummit = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1080
+ /* "MACS2/IO/CallPeakUnit.pyx":1081
* if peak_length >= min_length: # if the peak is too small, reject it
* tsummit = []
* summit_pos = 0 # <<<<<<<<<<<<<<
@@ -13624,7 +13661,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_summit_pos = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1081
+ /* "MACS2/IO/CallPeakUnit.pyx":1082
* tsummit = []
* summit_pos = 0
* summit_value = 0 # <<<<<<<<<<<<<<
@@ -13633,7 +13670,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_summit_value = 0.0;
- /* "MACS2/IO/CallPeakUnit.pyx":1082
+ /* "MACS2/IO/CallPeakUnit.pyx":1083
* summit_pos = 0
* summit_value = 0
* for i in range(len(peak_content)): # <<<<<<<<<<<<<<
@@ -13642,13 +13679,13 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1082; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_5 = PyList_GET_SIZE(__pyx_v_peak_content); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1082; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyList_GET_SIZE(__pyx_v_peak_content); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
__pyx_v_i = __pyx_t_6;
- /* "MACS2/IO/CallPeakUnit.pyx":1083
+ /* "MACS2/IO/CallPeakUnit.pyx":1084
* summit_value = 0
* for i in range(len(peak_content)):
* (tstart, tend, ttreat_p, tctrl_p, tlist_scores_p) = peak_content[i] # <<<<<<<<<<<<<<
@@ -13657,9 +13694,9 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) {
PyObject* sequence = __pyx_t_3;
@@ -13671,7 +13708,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
if (unlikely(size != 5)) {
if (size > 5) __Pyx_RaiseTooManyValuesError(5);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
@@ -13697,7 +13734,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
Py_ssize_t i;
PyObject** temps[5] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_7,&__pyx_t_8,&__pyx_t_9};
for (i=0; i < 5; i++) {
- PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(item);
*(temps[i]) = item;
}
@@ -13707,7 +13744,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
} else {
Py_ssize_t index = -1;
PyObject** temps[5] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_7,&__pyx_t_8,&__pyx_t_9};
- __pyx_t_10 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
@@ -13716,7 +13753,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_GOTREF(item);
*(temps[index]) = item;
}
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_11 = NULL;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
goto __pyx_L7_unpacking_done;
@@ -13724,18 +13761,18 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_11 = NULL;
if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L7_unpacking_done:;
}
- __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_13 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_14 = __pyx_PyFloat_AsFloat(__pyx_t_7); if (unlikely((__pyx_t_14 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __pyx_PyFloat_AsFloat(__pyx_t_7); if (unlikely((__pyx_t_14 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_8); if (unlikely((__pyx_t_15 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_8); if (unlikely((__pyx_t_15 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_16 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_16 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_16 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_v_tstart = __pyx_t_12;
__pyx_v_tend = __pyx_t_13;
@@ -13743,7 +13780,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_v_tctrl_p = __pyx_t_15;
__pyx_v_tlist_scores_p = __pyx_t_16;
- /* "MACS2/IO/CallPeakUnit.pyx":1084
+ /* "MACS2/IO/CallPeakUnit.pyx":1085
* for i in range(len(peak_content)):
* (tstart, tend, ttreat_p, tctrl_p, tlist_scores_p) = peak_content[i]
* tscore = ttreat_p #self.pqtable[ get_pscore(int(ttreat_p), tctrl_p) ] # use qscore as general score to find summit # <<<<<<<<<<<<<<
@@ -13752,7 +13789,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_tscore = __pyx_v_ttreat_p;
- /* "MACS2/IO/CallPeakUnit.pyx":1085
+ /* "MACS2/IO/CallPeakUnit.pyx":1086
* (tstart, tend, ttreat_p, tctrl_p, tlist_scores_p) = peak_content[i]
* tscore = ttreat_p #self.pqtable[ get_pscore(int(ttreat_p), tctrl_p) ] # use qscore as general score to find summit
* if not summit_value or summit_value < tscore: # <<<<<<<<<<<<<<
@@ -13770,16 +13807,16 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_L9_bool_binop_done:;
if (__pyx_t_4) {
- /* "MACS2/IO/CallPeakUnit.pyx":1086
+ /* "MACS2/IO/CallPeakUnit.pyx":1087
* tscore = ttreat_p #self.pqtable[ get_pscore(int(ttreat_p), tctrl_p) ] # use qscore as general score to find summit
* if not summit_value or summit_value < tscore:
* tsummit = [(tend + tstart) / 2, ] # <<<<<<<<<<<<<<
* tsummit_index = [ i, ]
* summit_value = tscore
*/
- __pyx_t_3 = __Pyx_PyInt_From_long(__Pyx_div_long((__pyx_v_tend + __pyx_v_tstart), 2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_long(__Pyx_div_long((__pyx_v_tend + __pyx_v_tstart), 2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1087; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_9 = PyList_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyList_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1087; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
PyList_SET_ITEM(__pyx_t_9, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
@@ -13787,16 +13824,16 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_DECREF_SET(__pyx_v_tsummit, ((PyObject*)__pyx_t_9));
__pyx_t_9 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1087
+ /* "MACS2/IO/CallPeakUnit.pyx":1088
* if not summit_value or summit_value < tscore:
* tsummit = [(tend + tstart) / 2, ]
* tsummit_index = [ i, ] # <<<<<<<<<<<<<<
* summit_value = tscore
* elif summit_value == tscore:
*/
- __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1087; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1088; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_3 = PyList_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1087; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1088; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyList_SET_ITEM(__pyx_t_3, 0, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
@@ -13804,7 +13841,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_XDECREF_SET(__pyx_v_tsummit_index, ((PyObject*)__pyx_t_3));
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1088
+ /* "MACS2/IO/CallPeakUnit.pyx":1089
* tsummit = [(tend + tstart) / 2, ]
* tsummit_index = [ i, ]
* summit_value = tscore # <<<<<<<<<<<<<<
@@ -13815,7 +13852,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
goto __pyx_L8;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1089
+ /* "MACS2/IO/CallPeakUnit.pyx":1090
* tsummit_index = [ i, ]
* summit_value = tscore
* elif summit_value == tscore: # <<<<<<<<<<<<<<
@@ -13825,96 +13862,96 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_4 = ((__pyx_v_summit_value == __pyx_v_tscore) != 0);
if (__pyx_t_4) {
- /* "MACS2/IO/CallPeakUnit.pyx":1091
+ /* "MACS2/IO/CallPeakUnit.pyx":1092
* elif summit_value == tscore:
* # remember continuous summit values
* tsummit.append(int((tend + tstart) / 2)) # <<<<<<<<<<<<<<
* tsummit_index.append( i )
* # the middle of all highest points in peak region is defined as summit
*/
- __pyx_t_3 = __Pyx_PyInt_From_long(__Pyx_div_long((__pyx_v_tend + __pyx_v_tstart), 2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1091; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_long(__Pyx_div_long((__pyx_v_tend + __pyx_v_tstart), 2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1091; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_9, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1091; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_9, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_18 = __Pyx_PyList_Append(__pyx_v_tsummit, __pyx_t_3); if (unlikely(__pyx_t_18 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1091; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_18 = __Pyx_PyList_Append(__pyx_v_tsummit, __pyx_t_3); if (unlikely(__pyx_t_18 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1092
+ /* "MACS2/IO/CallPeakUnit.pyx":1093
* # remember continuous summit values
* tsummit.append(int((tend + tstart) / 2))
* tsummit_index.append( i ) # <<<<<<<<<<<<<<
* # the middle of all highest points in peak region is defined as summit
* midindex = int((len(tsummit) + 1) / 2) - 1
*/
- if (unlikely(!__pyx_v_tsummit_index)) { __Pyx_RaiseUnboundLocalError("tsummit_index"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1092; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__pyx_v_tsummit_index)) { __Pyx_RaiseUnboundLocalError("tsummit_index"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_18 = __Pyx_PyList_Append(__pyx_v_tsummit_index, __pyx_t_3); if (unlikely(__pyx_t_18 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_18 = __Pyx_PyList_Append(__pyx_v_tsummit_index, __pyx_t_3); if (unlikely(__pyx_t_18 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L8;
}
__pyx_L8:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1094
+ /* "MACS2/IO/CallPeakUnit.pyx":1095
* tsummit_index.append( i )
* # the middle of all highest points in peak region is defined as summit
* midindex = int((len(tsummit) + 1) / 2) - 1 # <<<<<<<<<<<<<<
* summit_pos = tsummit[ midindex ]
* summit_index = tsummit_index[ midindex ]
*/
- __pyx_t_5 = PyList_GET_SIZE(__pyx_v_tsummit); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PyInt_FromSsize_t(__Pyx_div_Py_ssize_t((__pyx_t_5 + 1), 2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyList_GET_SIZE(__pyx_v_tsummit); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1095; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromSsize_t(__Pyx_div_Py_ssize_t((__pyx_t_5 + 1), 2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1095; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1095; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_9, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_9, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1095; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyNumber_Subtract(__pyx_t_3, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyNumber_Subtract(__pyx_t_3, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1095; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1095; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_v_midindex = __pyx_t_6;
- /* "MACS2/IO/CallPeakUnit.pyx":1095
+ /* "MACS2/IO/CallPeakUnit.pyx":1096
* # the middle of all highest points in peak region is defined as summit
* midindex = int((len(tsummit) + 1) / 2) - 1
* summit_pos = tsummit[ midindex ] # <<<<<<<<<<<<<<
* summit_index = tsummit_index[ midindex ]
*
*/
- __pyx_t_9 = __Pyx_GetItemInt_List(__pyx_v_tsummit, __pyx_v_midindex, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1095; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_9 = __Pyx_GetItemInt_List(__pyx_v_tsummit, __pyx_v_midindex, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1096; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_6 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1095; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_v_summit_pos = __pyx_t_6;
- /* "MACS2/IO/CallPeakUnit.pyx":1096
+ /* "MACS2/IO/CallPeakUnit.pyx":1097
* midindex = int((len(tsummit) + 1) / 2) - 1
* summit_pos = tsummit[ midindex ]
* summit_index = tsummit_index[ midindex ] # <<<<<<<<<<<<<<
*
* summit_treat = peak_content[ summit_index ][ 2 ]
*/
- if (unlikely(!__pyx_v_tsummit_index)) { __Pyx_RaiseUnboundLocalError("tsummit_index"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1096; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_9 = __Pyx_GetItemInt_List(__pyx_v_tsummit_index, __pyx_v_midindex, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1096; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ if (unlikely(!__pyx_v_tsummit_index)) { __Pyx_RaiseUnboundLocalError("tsummit_index"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1097; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_9 = __Pyx_GetItemInt_List(__pyx_v_tsummit_index, __pyx_v_midindex, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1097; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_6 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_6 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1097; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_v_summit_index = __pyx_t_6;
- /* "MACS2/IO/CallPeakUnit.pyx":1098
+ /* "MACS2/IO/CallPeakUnit.pyx":1099
* summit_index = tsummit_index[ midindex ]
*
* summit_treat = peak_content[ summit_index ][ 2 ] # <<<<<<<<<<<<<<
@@ -13923,18 +13960,18 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_9 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_summit_index, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1098; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_9 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_summit_index, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1099; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_9, 2, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1098; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_9, 2, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1099; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_3); if (unlikely((__pyx_t_15 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_3); if (unlikely((__pyx_t_15 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_v_summit_treat = __pyx_t_15;
- /* "MACS2/IO/CallPeakUnit.pyx":1099
+ /* "MACS2/IO/CallPeakUnit.pyx":1100
*
* summit_treat = peak_content[ summit_index ][ 2 ]
* summit_ctrl = peak_content[ summit_index ][ 3 ] # <<<<<<<<<<<<<<
@@ -13943,18 +13980,18 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_summit_index, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1099; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_summit_index, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1100; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_t_3, 3, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1099; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_t_3, 3, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1100; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_9); if (unlikely((__pyx_t_15 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_9); if (unlikely((__pyx_t_15 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_v_summit_ctrl = __pyx_t_15;
- /* "MACS2/IO/CallPeakUnit.pyx":1102
+ /* "MACS2/IO/CallPeakUnit.pyx":1103
*
* # this is a double-check to see if the summit can pass cutoff values.
* for i in range(len(score_cutoff_s)): # <<<<<<<<<<<<<<
@@ -13963,13 +14000,13 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_score_cutoff_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1102; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_5 = PyList_GET_SIZE(__pyx_v_score_cutoff_s); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1102; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyList_GET_SIZE(__pyx_v_score_cutoff_s); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
__pyx_v_i = __pyx_t_6;
- /* "MACS2/IO/CallPeakUnit.pyx":1103
+ /* "MACS2/IO/CallPeakUnit.pyx":1104
* # this is a double-check to see if the summit can pass cutoff values.
* for i in range(len(score_cutoff_s)):
* if score_cutoff_s[i] > score_array_s[ i ][ peak_content[ summit_index ][ 4 ] ]: # <<<<<<<<<<<<<<
@@ -13978,37 +14015,37 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_score_cutoff_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_9 = __Pyx_GetItemInt_List(__pyx_v_score_cutoff_s, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_9 = __Pyx_GetItemInt_List(__pyx_v_score_cutoff_s, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1104; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_9);
if (unlikely(__pyx_v_score_array_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_score_array_s, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_score_array_s, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1104; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_8 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_summit_index, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_summit_index, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1104; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_8, 4, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_8, 4, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1104; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_GetItem(__pyx_t_3, __pyx_t_7); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = PyObject_GetItem(__pyx_t_3, __pyx_t_7); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1104; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_9, __pyx_t_8, Py_GT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_9, __pyx_t_8, Py_GT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_4) {
- /* "MACS2/IO/CallPeakUnit.pyx":1104
+ /* "MACS2/IO/CallPeakUnit.pyx":1105
* for i in range(len(score_cutoff_s)):
* if score_cutoff_s[i] > score_array_s[ i ][ peak_content[ summit_index ][ 4 ] ]:
* return False # not passed, then disgard this peak. # <<<<<<<<<<<<<<
@@ -14022,26 +14059,26 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
- /* "MACS2/IO/CallPeakUnit.pyx":1106
+ /* "MACS2/IO/CallPeakUnit.pyx":1107
* return False # not passed, then disgard this peak.
*
* summit_p_score = get_pscore( int(summit_treat), summit_ctrl ) # <<<<<<<<<<<<<<
* summit_q_score = self.pqtable[ summit_p_score ]
*
*/
- __pyx_t_8 = __Pyx_GetModuleGlobalName(__pyx_n_s_get_pscore); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetModuleGlobalName(__pyx_n_s_get_pscore); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyFloat_FromDouble(__pyx_v_summit_treat); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyFloat_FromDouble(__pyx_v_summit_treat); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_9 = 0;
- __pyx_t_9 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_3, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_3, NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_summit_ctrl); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_summit_ctrl); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_2 = NULL;
__pyx_t_5 = 0;
@@ -14055,7 +14092,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_5 = 1;
}
}
- __pyx_t_1 = PyTuple_New(2+__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2+__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (__pyx_t_2) {
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = NULL;
@@ -14066,41 +14103,41 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_9 = 0;
__pyx_t_3 = 0;
- __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_t_1, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_t_1, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_7); if (unlikely((__pyx_t_15 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_7); if (unlikely((__pyx_t_15 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_v_summit_p_score = __pyx_t_15;
- /* "MACS2/IO/CallPeakUnit.pyx":1107
+ /* "MACS2/IO/CallPeakUnit.pyx":1108
*
* summit_p_score = get_pscore( int(summit_treat), summit_ctrl )
* summit_q_score = self.pqtable[ summit_p_score ] # <<<<<<<<<<<<<<
*
* peaks.add( chrom, # chromosome
*/
- __pyx_t_7 = PyFloat_FromDouble(__pyx_v_summit_p_score); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyFloat_FromDouble(__pyx_v_summit_p_score); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyObject_GetItem(__pyx_v_self->pqtable, __pyx_t_7); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1107; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_self->pqtable, __pyx_t_7); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1108; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_8); if (unlikely((__pyx_t_15 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_8); if (unlikely((__pyx_t_15 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_v_summit_q_score = __pyx_t_15;
- /* "MACS2/IO/CallPeakUnit.pyx":1109
+ /* "MACS2/IO/CallPeakUnit.pyx":1110
* summit_q_score = self.pqtable[ summit_p_score ]
*
* peaks.add( chrom, # chromosome # <<<<<<<<<<<<<<
* peak_content[0][0], # start
* peak_content[-1][1], # end
*/
- __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_add); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_add); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- /* "MACS2/IO/CallPeakUnit.pyx":1110
+ /* "MACS2/IO/CallPeakUnit.pyx":1111
*
* peaks.add( chrom, # chromosome
* peak_content[0][0], # start # <<<<<<<<<<<<<<
@@ -14109,15 +14146,15 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1110; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1111; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_7, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1110; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_7, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1111; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1111
+ /* "MACS2/IO/CallPeakUnit.pyx":1112
* peaks.add( chrom, # chromosome
* peak_content[0][0], # start
* peak_content[-1][1], # end # <<<<<<<<<<<<<<
@@ -14126,22 +14163,22 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1111; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_7 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1112; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_7, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1111; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_7, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1112; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1109
+ /* "MACS2/IO/CallPeakUnit.pyx":1110
* summit_q_score = self.pqtable[ summit_p_score ]
*
* peaks.add( chrom, # chromosome # <<<<<<<<<<<<<<
* peak_content[0][0], # start
* peak_content[-1][1], # end
*/
- __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_chrom);
@@ -14152,58 +14189,58 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_1 = 0;
__pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- /* "MACS2/IO/CallPeakUnit.pyx":1112
+ /* "MACS2/IO/CallPeakUnit.pyx":1113
* peak_content[0][0], # start
* peak_content[-1][1], # end
* summit = summit_pos, # summit position # <<<<<<<<<<<<<<
* peak_score = summit_q_score, # score at summit
* pileup = summit_treat, # pileup
*/
- __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_summit_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_summit_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1113; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_summit, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_summit, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1113
+ /* "MACS2/IO/CallPeakUnit.pyx":1114
* peak_content[-1][1], # end
* summit = summit_pos, # summit position
* peak_score = summit_q_score, # score at summit # <<<<<<<<<<<<<<
* pileup = summit_treat, # pileup
* pscore = summit_p_score, # pvalue
*/
- __pyx_t_1 = PyFloat_FromDouble(__pyx_v_summit_q_score); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1113; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_summit_q_score); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_peak_score, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_peak_score, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1114
+ /* "MACS2/IO/CallPeakUnit.pyx":1115
* summit = summit_pos, # summit position
* peak_score = summit_q_score, # score at summit
* pileup = summit_treat, # pileup # <<<<<<<<<<<<<<
* pscore = summit_p_score, # pvalue
* fold_change = float ( summit_treat + self.pseudocount ) / ( summit_ctrl + self.pseudocount ), # fold change
*/
- __pyx_t_1 = PyFloat_FromDouble(__pyx_v_summit_treat); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_summit_treat); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_pileup, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_pileup, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1115
+ /* "MACS2/IO/CallPeakUnit.pyx":1116
* peak_score = summit_q_score, # score at summit
* pileup = summit_treat, # pileup
* pscore = summit_p_score, # pvalue # <<<<<<<<<<<<<<
* fold_change = float ( summit_treat + self.pseudocount ) / ( summit_ctrl + self.pseudocount ), # fold change
* qscore = summit_q_score # qvalue
*/
- __pyx_t_1 = PyFloat_FromDouble(__pyx_v_summit_p_score); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_summit_p_score); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_pscore, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_pscore, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1116
+ /* "MACS2/IO/CallPeakUnit.pyx":1117
* pileup = summit_treat, # pileup
* pscore = summit_p_score, # pvalue
* fold_change = float ( summit_treat + self.pseudocount ) / ( summit_ctrl + self.pseudocount ), # fold change # <<<<<<<<<<<<<<
@@ -14219,40 +14256,40 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
#ifdef WITH_THREAD
PyGILState_Release(__pyx_gilstate_save);
#endif
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = PyFloat_FromDouble((((double)(__pyx_v_summit_treat + __pyx_v_self->pseudocount)) / __pyx_t_15)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble((((double)(__pyx_v_summit_treat + __pyx_v_self->pseudocount)) / __pyx_t_15)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_fold_change, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_fold_change, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1118
+ /* "MACS2/IO/CallPeakUnit.pyx":1119
* fold_change = float ( summit_treat + self.pseudocount ) / ( summit_ctrl + self.pseudocount ), # fold change
* qscore = summit_q_score # qvalue
* ) # <<<<<<<<<<<<<<
* # start a new peak
* return True
*/
- __pyx_t_1 = PyFloat_FromDouble(__pyx_v_summit_q_score); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_summit_q_score); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_qscore, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_qscore, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1109
+ /* "MACS2/IO/CallPeakUnit.pyx":1110
* summit_q_score = self.pqtable[ summit_p_score ]
*
* peaks.add( chrom, # chromosome # <<<<<<<<<<<<<<
* peak_content[0][0], # start
* peak_content[-1][1], # end
*/
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_t_7, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_t_7, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1120
+ /* "MACS2/IO/CallPeakUnit.pyx":1121
* )
* # start a new peak
* return True # <<<<<<<<<<<<<<
@@ -14265,7 +14302,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
goto __pyx_L0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1062
+ /* "MACS2/IO/CallPeakUnit.pyx":1063
* return peaks
*
* cdef bool __close_peak_wo_subpeaks (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<<
@@ -14295,7 +14332,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1122
+/* "MACS2/IO/CallPeakUnit.pyx":1123
* return True
*
* cdef bool __close_peak_with_subpeaks (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<<
@@ -14382,7 +14419,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_pybuffernd_summit_offsets.data = NULL;
__pyx_pybuffernd_summit_offsets.rcbuffer = &__pyx_pybuffer_summit_offsets;
- /* "MACS2/IO/CallPeakUnit.pyx":1139
+ /* "MACS2/IO/CallPeakUnit.pyx":1140
* int tlist_scores_p
*
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ] # <<<<<<<<<<<<<<
@@ -14391,41 +14428,41 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1140; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_1, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_1, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1140; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1140; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_1, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_1, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1140; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Subtract(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Subtract(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_v_peak_length = __pyx_t_1;
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1141
+ /* "MACS2/IO/CallPeakUnit.pyx":1142
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ]
*
* if peak_length < min_length: return # if the region is too small, reject it # <<<<<<<<<<<<<<
*
* # Add 10 bp padding to peak region so that we can get true minima
*/
- __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_min_length); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_min_length); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_peak_length, __pyx_t_1, Py_LT); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_peak_length, __pyx_t_1, Py_LT); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_4) {
__Pyx_XDECREF(((PyObject *)__pyx_r));
@@ -14433,7 +14470,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
goto __pyx_L0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1144
+ /* "MACS2/IO/CallPeakUnit.pyx":1145
*
* # Add 10 bp padding to peak region so that we can get true minima
* end = peak_content[ -1 ][ 1 ] + 10 # <<<<<<<<<<<<<<
@@ -14442,21 +14479,21 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_3, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_3, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyNumber_Add(__pyx_t_1, __pyx_int_10); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_Add(__pyx_t_1, __pyx_int_10); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_v_end = __pyx_t_5;
- /* "MACS2/IO/CallPeakUnit.pyx":1145
+ /* "MACS2/IO/CallPeakUnit.pyx":1146
* # Add 10 bp padding to peak region so that we can get true minima
* end = peak_content[ -1 ][ 1 ] + 10
* start = peak_content[ 0 ][ 0 ] - 10 # <<<<<<<<<<<<<<
@@ -14465,21 +14502,21 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1146; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1146; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1146; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyNumber_Subtract(__pyx_t_1, __pyx_int_10); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_Subtract(__pyx_t_1, __pyx_int_10); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1146; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1146; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_v_start = __pyx_t_5;
- /* "MACS2/IO/CallPeakUnit.pyx":1146
+ /* "MACS2/IO/CallPeakUnit.pyx":1147
* end = peak_content[ -1 ][ 1 ] + 10
* start = peak_content[ 0 ][ 0 ] - 10
* if start < 0: # <<<<<<<<<<<<<<
@@ -14489,7 +14526,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_4 = ((__pyx_v_start < 0) != 0);
if (__pyx_t_4) {
- /* "MACS2/IO/CallPeakUnit.pyx":1147
+ /* "MACS2/IO/CallPeakUnit.pyx":1148
* start = peak_content[ 0 ][ 0 ] - 10
* if start < 0:
* start_boundary = 10 + start # this is the offset of original peak boundary in peakdata list. # <<<<<<<<<<<<<<
@@ -14498,7 +14535,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_start_boundary = (10 + __pyx_v_start);
- /* "MACS2/IO/CallPeakUnit.pyx":1148
+ /* "MACS2/IO/CallPeakUnit.pyx":1149
* if start < 0:
* start_boundary = 10 + start # this is the offset of original peak boundary in peakdata list.
* start = 0 # <<<<<<<<<<<<<<
@@ -14510,7 +14547,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1150
+ /* "MACS2/IO/CallPeakUnit.pyx":1151
* start = 0
* else:
* start_boundary = 10 # this is the offset of original peak boundary in peakdata list. # <<<<<<<<<<<<<<
@@ -14521,34 +14558,34 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
__pyx_L4:;
- /* "MACS2/IO/CallPeakUnit.pyx":1152
+ /* "MACS2/IO/CallPeakUnit.pyx":1153
* start_boundary = 10 # this is the offset of original peak boundary in peakdata list.
*
* peakdata = np.zeros(end - start, dtype='float32') # save the scores (qscore) for each position in this region # <<<<<<<<<<<<<<
* peakindices = np.zeros(end - start, dtype='int32') # save the indices for each position in this region
* for i in range(len(peak_content)):
*/
- __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyInt_From_int((__pyx_v_end - __pyx_v_start)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int((__pyx_v_end - __pyx_v_start)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = ((PyArrayObject *)__pyx_t_6);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -14564,40 +14601,40 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
__pyx_pybuffernd_peakdata.diminfo[0].strides = __pyx_pybuffernd_peakdata.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_peakdata.diminfo[0].shape = __pyx_pybuffernd_peakdata.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_7 = 0;
__pyx_v_peakdata = ((PyArrayObject *)__pyx_t_6);
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1153
+ /* "MACS2/IO/CallPeakUnit.pyx":1154
*
* peakdata = np.zeros(end - start, dtype='float32') # save the scores (qscore) for each position in this region
* peakindices = np.zeros(end - start, dtype='int32') # save the indices for each position in this region # <<<<<<<<<<<<<<
* for i in range(len(peak_content)):
* (tstart, tend, ttreat_p, tctrl_p, tlist_scores_p) = peak_content[i]
*/
- __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_zeros); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_zeros); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyInt_From_int((__pyx_v_end - __pyx_v_start)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_From_int((__pyx_v_end - __pyx_v_start)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_11 = ((PyArrayObject *)__pyx_t_1);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -14613,13 +14650,13 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
__pyx_pybuffernd_peakindices.diminfo[0].strides = __pyx_pybuffernd_peakindices.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_peakindices.diminfo[0].shape = __pyx_pybuffernd_peakindices.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_11 = 0;
__pyx_v_peakindices = ((PyArrayObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1154
+ /* "MACS2/IO/CallPeakUnit.pyx":1155
* peakdata = np.zeros(end - start, dtype='float32') # save the scores (qscore) for each position in this region
* peakindices = np.zeros(end - start, dtype='int32') # save the indices for each position in this region
* for i in range(len(peak_content)): # <<<<<<<<<<<<<<
@@ -14628,13 +14665,13 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_12 = PyList_GET_SIZE(__pyx_v_peak_content); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyList_GET_SIZE(__pyx_v_peak_content); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_12; __pyx_t_5+=1) {
__pyx_v_i = __pyx_t_5;
- /* "MACS2/IO/CallPeakUnit.pyx":1155
+ /* "MACS2/IO/CallPeakUnit.pyx":1156
* peakindices = np.zeros(end - start, dtype='int32') # save the indices for each position in this region
* for i in range(len(peak_content)):
* (tstart, tend, ttreat_p, tctrl_p, tlist_scores_p) = peak_content[i] # <<<<<<<<<<<<<<
@@ -14643,9 +14680,9 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1156; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
PyObject* sequence = __pyx_t_1;
@@ -14657,7 +14694,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
if (unlikely(size != 5)) {
if (size > 5) __Pyx_RaiseTooManyValuesError(5);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
@@ -14683,7 +14720,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
Py_ssize_t i;
PyObject** temps[5] = {&__pyx_t_6,&__pyx_t_2,&__pyx_t_3,&__pyx_t_13,&__pyx_t_14};
for (i=0; i < 5; i++) {
- PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(item);
*(temps[i]) = item;
}
@@ -14693,7 +14730,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
} else {
Py_ssize_t index = -1;
PyObject** temps[5] = {&__pyx_t_6,&__pyx_t_2,&__pyx_t_3,&__pyx_t_13,&__pyx_t_14};
- __pyx_t_15 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_16 = Py_TYPE(__pyx_t_15)->tp_iternext;
@@ -14702,7 +14739,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_GOTREF(item);
*(temps[index]) = item;
}
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_16(__pyx_t_15), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_16(__pyx_t_15), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_16 = NULL;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
goto __pyx_L8_unpacking_done;
@@ -14710,18 +14747,18 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
__pyx_t_16 = NULL;
if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L8_unpacking_done:;
}
- __pyx_t_17 = __Pyx_PyInt_As_int(__pyx_t_6); if (unlikely((__pyx_t_17 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_17 = __Pyx_PyInt_As_int(__pyx_t_6); if (unlikely((__pyx_t_17 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_18 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_18 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_18 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_18 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_19 = __pyx_PyFloat_AsFloat(__pyx_t_3); if (unlikely((__pyx_t_19 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_19 = __pyx_PyFloat_AsFloat(__pyx_t_3); if (unlikely((__pyx_t_19 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_20 = __pyx_PyFloat_AsFloat(__pyx_t_13); if (unlikely((__pyx_t_20 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_20 = __pyx_PyFloat_AsFloat(__pyx_t_13); if (unlikely((__pyx_t_20 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_t_21 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_21 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_21 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_21 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
__pyx_v_tstart = __pyx_t_17;
__pyx_v_tend = __pyx_t_18;
@@ -14729,7 +14766,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_v_tctrl_p = __pyx_t_20;
__pyx_v_tlist_scores_p = __pyx_t_21;
- /* "MACS2/IO/CallPeakUnit.pyx":1157
+ /* "MACS2/IO/CallPeakUnit.pyx":1158
* (tstart, tend, ttreat_p, tctrl_p, tlist_scores_p) = peak_content[i]
* #tscore = self.pqtable[ get_pscore(int(ttreat_p), tctrl_p) ] # use qscore as general score to find summit
* tscore = ttreat_p # use pileup as general score to find summit # <<<<<<<<<<<<<<
@@ -14738,7 +14775,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_tscore = __pyx_v_ttreat_p;
- /* "MACS2/IO/CallPeakUnit.pyx":1158
+ /* "MACS2/IO/CallPeakUnit.pyx":1159
* #tscore = self.pqtable[ get_pscore(int(ttreat_p), tctrl_p) ] # use qscore as general score to find summit
* tscore = ttreat_p # use pileup as general score to find summit
* m = tstart - start + start_boundary # <<<<<<<<<<<<<<
@@ -14747,7 +14784,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_m = ((__pyx_v_tstart - __pyx_v_start) + __pyx_v_start_boundary);
- /* "MACS2/IO/CallPeakUnit.pyx":1159
+ /* "MACS2/IO/CallPeakUnit.pyx":1160
* tscore = ttreat_p # use pileup as general score to find summit
* m = tstart - start + start_boundary
* n = tend - start + start_boundary # <<<<<<<<<<<<<<
@@ -14756,41 +14793,41 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_n = ((__pyx_v_tend - __pyx_v_start) + __pyx_v_start_boundary);
- /* "MACS2/IO/CallPeakUnit.pyx":1160
+ /* "MACS2/IO/CallPeakUnit.pyx":1161
* m = tstart - start + start_boundary
* n = tend - start + start_boundary
* peakdata[m:n] = tscore # <<<<<<<<<<<<<<
* peakindices[m:n] = i
*
*/
- __pyx_t_1 = PyFloat_FromDouble(__pyx_v_tscore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_tscore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (__Pyx_PyObject_SetSlice(((PyObject *)__pyx_v_peakdata), __pyx_t_1, __pyx_v_m, __pyx_v_n, NULL, NULL, NULL, 1, 1, 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_PyObject_SetSlice(((PyObject *)__pyx_v_peakdata), __pyx_t_1, __pyx_v_m, __pyx_v_n, NULL, NULL, NULL, 1, 1, 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1161
+ /* "MACS2/IO/CallPeakUnit.pyx":1162
* n = tend - start + start_boundary
* peakdata[m:n] = tscore
* peakindices[m:n] = i # <<<<<<<<<<<<<<
*
* summit_offsets = maxima(peakdata, smoothlen) # offsets are the indices for summits in peakdata/peakindices array.
*/
- __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_i); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (__Pyx_PyObject_SetSlice(((PyObject *)__pyx_v_peakindices), __pyx_t_1, __pyx_v_m, __pyx_v_n, NULL, NULL, NULL, 1, 1, 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_PyObject_SetSlice(((PyObject *)__pyx_v_peakindices), __pyx_t_1, __pyx_v_m, __pyx_v_n, NULL, NULL, NULL, 1, 1, 1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1163
+ /* "MACS2/IO/CallPeakUnit.pyx":1164
* peakindices[m:n] = i
*
* summit_offsets = maxima(peakdata, smoothlen) # offsets are the indices for summits in peakdata/peakindices array. # <<<<<<<<<<<<<<
* #print "maxima:",summit_offsets
* if summit_offsets.shape[0] == 0:
*/
- __pyx_t_14 = __Pyx_GetModuleGlobalName(__pyx_n_s_maxima); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_GetModuleGlobalName(__pyx_n_s_maxima); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
- __pyx_t_13 = __Pyx_PyInt_From_int(__pyx_v_smoothlen); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyInt_From_int(__pyx_v_smoothlen); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
__pyx_t_3 = NULL;
__pyx_t_12 = 0;
@@ -14804,7 +14841,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_12 = 1;
}
}
- __pyx_t_2 = PyTuple_New(2+__pyx_t_12); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(2+__pyx_t_12); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
if (__pyx_t_3) {
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = NULL;
@@ -14815,11 +14852,11 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
PyTuple_SET_ITEM(__pyx_t_2, 1+__pyx_t_12, __pyx_t_13);
__Pyx_GIVEREF(__pyx_t_13);
__pyx_t_13 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_14, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_14, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_11 = ((PyArrayObject *)__pyx_t_1);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -14835,13 +14872,13 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
__pyx_pybuffernd_summit_offsets.diminfo[0].strides = __pyx_pybuffernd_summit_offsets.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_summit_offsets.diminfo[0].shape = __pyx_pybuffernd_summit_offsets.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_11 = 0;
__pyx_v_summit_offsets = ((PyArrayObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1165
+ /* "MACS2/IO/CallPeakUnit.pyx":1166
* summit_offsets = maxima(peakdata, smoothlen) # offsets are the indices for summits in peakdata/peakindices array.
* #print "maxima:",summit_offsets
* if summit_offsets.shape[0] == 0: # <<<<<<<<<<<<<<
@@ -14851,7 +14888,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_4 = (((__pyx_v_summit_offsets->dimensions[0]) == 0) != 0);
if (__pyx_t_4) {
- /* "MACS2/IO/CallPeakUnit.pyx":1167
+ /* "MACS2/IO/CallPeakUnit.pyx":1168
* if summit_offsets.shape[0] == 0:
* # **failsafe** if no summits, fall back on old approach #
* return self.__close_peak_wo_subpeaks(peak_content, peaks, min_length, chrom, smoothlen, score_array_s, score_cutoff_s) # <<<<<<<<<<<<<<
@@ -14861,7 +14898,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_XDECREF(((PyObject *)__pyx_r));
__pyx_t_22.__pyx_n = 1;
__pyx_t_22.score_cutoff_s = __pyx_v_score_cutoff_s;
- __pyx_t_1 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_wo_subpeaks(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, __pyx_v_smoothlen, __pyx_v_score_array_s, &__pyx_t_22)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1167; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_wo_subpeaks(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, __pyx_v_smoothlen, __pyx_v_score_array_s, &__pyx_t_22)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = ((PyBoolObject *)__pyx_t_1);
__pyx_t_1 = 0;
@@ -14869,19 +14906,19 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1170
+ /* "MACS2/IO/CallPeakUnit.pyx":1171
* else:
* # remove maxima that occurred in padding
* m = np.searchsorted(summit_offsets, start_boundary) # <<<<<<<<<<<<<<
* n = np.searchsorted(summit_offsets, peak_length + start_boundary, 'right')
* summit_offsets = summit_offsets[m:n]
*/
- __pyx_t_14 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_14, __pyx_n_s_searchsorted); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_14, __pyx_n_s_searchsorted); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- __pyx_t_14 = __Pyx_PyInt_From_int(__pyx_v_start_boundary); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyInt_From_int(__pyx_v_start_boundary); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
__pyx_t_13 = NULL;
__pyx_t_12 = 0;
@@ -14895,7 +14932,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_12 = 1;
}
}
- __pyx_t_3 = PyTuple_New(2+__pyx_t_12); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(2+__pyx_t_12); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
if (__pyx_t_13) {
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_13); __Pyx_GIVEREF(__pyx_t_13); __pyx_t_13 = NULL;
@@ -14906,29 +14943,29 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
PyTuple_SET_ITEM(__pyx_t_3, 1+__pyx_t_12, __pyx_t_14);
__Pyx_GIVEREF(__pyx_t_14);
__pyx_t_14 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_m = __pyx_t_5;
- /* "MACS2/IO/CallPeakUnit.pyx":1171
+ /* "MACS2/IO/CallPeakUnit.pyx":1172
* # remove maxima that occurred in padding
* m = np.searchsorted(summit_offsets, start_boundary)
* n = np.searchsorted(summit_offsets, peak_length + start_boundary, 'right') # <<<<<<<<<<<<<<
* summit_offsets = summit_offsets[m:n]
*
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_searchsorted); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_searchsorted); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_start_boundary); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_start_boundary); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_14 = PyNumber_Add(__pyx_v_peak_length, __pyx_t_2); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyNumber_Add(__pyx_v_peak_length, __pyx_t_2); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = NULL;
@@ -14943,7 +14980,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_12 = 1;
}
}
- __pyx_t_13 = PyTuple_New(3+__pyx_t_12); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyTuple_New(3+__pyx_t_12); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
if (__pyx_t_2) {
PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = NULL;
@@ -14957,24 +14994,24 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
PyTuple_SET_ITEM(__pyx_t_13, 2+__pyx_t_12, __pyx_n_s_right);
__Pyx_GIVEREF(__pyx_n_s_right);
__pyx_t_14 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_13, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_13, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_n = __pyx_t_5;
- /* "MACS2/IO/CallPeakUnit.pyx":1172
+ /* "MACS2/IO/CallPeakUnit.pyx":1173
* m = np.searchsorted(summit_offsets, start_boundary)
* n = np.searchsorted(summit_offsets, peak_length + start_boundary, 'right')
* summit_offsets = summit_offsets[m:n] # <<<<<<<<<<<<<<
*
* summit_offsets = enforce_peakyness(peakdata, summit_offsets)
*/
- __pyx_t_1 = __Pyx_PyObject_GetSlice(((PyObject *)__pyx_v_summit_offsets), __pyx_v_m, __pyx_v_n, NULL, NULL, NULL, 1, 1, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetSlice(((PyObject *)__pyx_v_summit_offsets), __pyx_v_m, __pyx_v_n, NULL, NULL, NULL, 1, 1, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_11 = ((PyArrayObject *)__pyx_t_1);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -14990,21 +15027,21 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
__pyx_pybuffernd_summit_offsets.diminfo[0].strides = __pyx_pybuffernd_summit_offsets.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_summit_offsets.diminfo[0].shape = __pyx_pybuffernd_summit_offsets.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_11 = 0;
__Pyx_DECREF_SET(__pyx_v_summit_offsets, ((PyArrayObject *)__pyx_t_1));
__pyx_t_1 = 0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1174
+ /* "MACS2/IO/CallPeakUnit.pyx":1175
* summit_offsets = summit_offsets[m:n]
*
* summit_offsets = enforce_peakyness(peakdata, summit_offsets) # <<<<<<<<<<<<<<
* #print "enforced:",summit_offsets
* if summit_offsets.shape[0] == 0:
*/
- __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_enforce_peakyness); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_enforce_peakyness); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_13 = NULL;
__pyx_t_12 = 0;
@@ -15018,7 +15055,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_12 = 1;
}
}
- __pyx_t_14 = PyTuple_New(2+__pyx_t_12); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyTuple_New(2+__pyx_t_12); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
if (__pyx_t_13) {
PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_t_13); __Pyx_GIVEREF(__pyx_t_13); __pyx_t_13 = NULL;
@@ -15029,11 +15066,11 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_INCREF(((PyObject *)__pyx_v_summit_offsets));
PyTuple_SET_ITEM(__pyx_t_14, 1+__pyx_t_12, ((PyObject *)__pyx_v_summit_offsets));
__Pyx_GIVEREF(((PyObject *)__pyx_v_summit_offsets));
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_14, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_14, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_11 = ((PyArrayObject *)__pyx_t_1);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -15049,13 +15086,13 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
__pyx_pybuffernd_summit_offsets.diminfo[0].strides = __pyx_pybuffernd_summit_offsets.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_summit_offsets.diminfo[0].shape = __pyx_pybuffernd_summit_offsets.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_11 = 0;
__Pyx_DECREF_SET(__pyx_v_summit_offsets, ((PyArrayObject *)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1176
+ /* "MACS2/IO/CallPeakUnit.pyx":1177
* summit_offsets = enforce_peakyness(peakdata, summit_offsets)
* #print "enforced:",summit_offsets
* if summit_offsets.shape[0] == 0: # <<<<<<<<<<<<<<
@@ -15065,7 +15102,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_4 = (((__pyx_v_summit_offsets->dimensions[0]) == 0) != 0);
if (__pyx_t_4) {
- /* "MACS2/IO/CallPeakUnit.pyx":1178
+ /* "MACS2/IO/CallPeakUnit.pyx":1179
* if summit_offsets.shape[0] == 0:
* # **failsafe** if no summits, fall back on old approach #
* return self.__close_peak_wo_subpeaks(peak_content, peaks, min_length, chrom, smoothlen, score_array_s, score_cutoff_s) # <<<<<<<<<<<<<<
@@ -15075,38 +15112,38 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_XDECREF(((PyObject *)__pyx_r));
__pyx_t_22.__pyx_n = 1;
__pyx_t_22.score_cutoff_s = __pyx_v_score_cutoff_s;
- __pyx_t_1 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_wo_subpeaks(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, __pyx_v_smoothlen, __pyx_v_score_array_s, &__pyx_t_22)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_wo_subpeaks(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, __pyx_v_smoothlen, __pyx_v_score_array_s, &__pyx_t_22)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = ((PyBoolObject *)__pyx_t_1);
__pyx_t_1 = 0;
goto __pyx_L0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1180
+ /* "MACS2/IO/CallPeakUnit.pyx":1181
* return self.__close_peak_wo_subpeaks(peak_content, peaks, min_length, chrom, smoothlen, score_array_s, score_cutoff_s)
*
* summit_indices = peakindices[summit_offsets] # indices are those point to peak_content # <<<<<<<<<<<<<<
* summit_offsets -= start_boundary
*
*/
- __pyx_t_1 = PyObject_GetItem(((PyObject *)__pyx_v_peakindices), ((PyObject *)__pyx_v_summit_offsets)); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1180; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = PyObject_GetItem(((PyObject *)__pyx_v_peakindices), ((PyObject *)__pyx_v_summit_offsets)); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1181; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_summit_indices = __pyx_t_1;
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1181
+ /* "MACS2/IO/CallPeakUnit.pyx":1182
*
* summit_indices = peakindices[summit_offsets] # indices are those point to peak_content
* summit_offsets -= start_boundary # <<<<<<<<<<<<<<
*
* for summit_offset, summit_index in zip(summit_offsets, summit_indices):
*/
- __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_start_boundary); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_start_boundary); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyNumber_InPlaceSubtract(((PyObject *)__pyx_v_summit_offsets), __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_InPlaceSubtract(((PyObject *)__pyx_v_summit_offsets), __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_11 = ((PyArrayObject *)__pyx_t_3);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -15122,20 +15159,20 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
__pyx_pybuffernd_summit_offsets.diminfo[0].strides = __pyx_pybuffernd_summit_offsets.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_summit_offsets.diminfo[0].shape = __pyx_pybuffernd_summit_offsets.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_11 = 0;
__Pyx_DECREF_SET(__pyx_v_summit_offsets, ((PyArrayObject *)__pyx_t_3));
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1183
+ /* "MACS2/IO/CallPeakUnit.pyx":1184
* summit_offsets -= start_boundary
*
* for summit_offset, summit_index in zip(summit_offsets, summit_indices): # <<<<<<<<<<<<<<
*
* summit_treat = peak_content[ summit_index ][ 2 ]
*/
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(((PyObject *)__pyx_v_summit_offsets));
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_summit_offsets));
@@ -15143,16 +15180,16 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_INCREF(__pyx_v_summit_indices);
PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_summit_indices);
__Pyx_GIVEREF(__pyx_v_summit_indices);
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_zip, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_zip, __pyx_t_3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (likely(PyList_CheckExact(__pyx_t_1)) || PyTuple_CheckExact(__pyx_t_1)) {
__pyx_t_3 = __pyx_t_1; __Pyx_INCREF(__pyx_t_3); __pyx_t_12 = 0;
__pyx_t_23 = NULL;
} else {
- __pyx_t_12 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_23 = Py_TYPE(__pyx_t_3)->tp_iternext; if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_23 = Py_TYPE(__pyx_t_3)->tp_iternext; if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
for (;;) {
@@ -15160,16 +15197,16 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
if (likely(PyList_CheckExact(__pyx_t_3))) {
if (__pyx_t_12 >= PyList_GET_SIZE(__pyx_t_3)) break;
#if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_12); __Pyx_INCREF(__pyx_t_1); __pyx_t_12++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_12); __Pyx_INCREF(__pyx_t_1); __pyx_t_12++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_3, __pyx_t_12); __pyx_t_12++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_3, __pyx_t_12); __pyx_t_12++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
} else {
if (__pyx_t_12 >= PyTuple_GET_SIZE(__pyx_t_3)) break;
#if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_12); __Pyx_INCREF(__pyx_t_1); __pyx_t_12++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_12); __Pyx_INCREF(__pyx_t_1); __pyx_t_12++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_3, __pyx_t_12); __pyx_t_12++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_3, __pyx_t_12); __pyx_t_12++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
}
} else {
@@ -15178,7 +15215,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
PyObject* exc_type = PyErr_Occurred();
if (exc_type) {
if (likely(exc_type == PyExc_StopIteration || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -15194,7 +15231,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
if (unlikely(size != 2)) {
if (size > 2) __Pyx_RaiseTooManyValuesError(2);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
@@ -15207,15 +15244,15 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_INCREF(__pyx_t_14);
__Pyx_INCREF(__pyx_t_13);
#else
- __pyx_t_14 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
- __pyx_t_13 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
#endif
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
} else {
Py_ssize_t index = -1;
- __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_16 = Py_TYPE(__pyx_t_2)->tp_iternext;
@@ -15223,7 +15260,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_GOTREF(__pyx_t_14);
index = 1; __pyx_t_13 = __pyx_t_16(__pyx_t_2); if (unlikely(!__pyx_t_13)) goto __pyx_L13_unpacking_failed;
__Pyx_GOTREF(__pyx_t_13);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_16(__pyx_t_2), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_16(__pyx_t_2), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_16 = NULL;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
goto __pyx_L14_unpacking_done;
@@ -15231,17 +15268,17 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_16 = NULL;
if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L14_unpacking_done:;
}
- __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_14); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- __pyx_t_21 = __Pyx_PyInt_As_int(__pyx_t_13); if (unlikely((__pyx_t_21 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_21 = __Pyx_PyInt_As_int(__pyx_t_13); if (unlikely((__pyx_t_21 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
__pyx_v_summit_offset = __pyx_t_5;
__pyx_v_summit_index = __pyx_t_21;
- /* "MACS2/IO/CallPeakUnit.pyx":1185
+ /* "MACS2/IO/CallPeakUnit.pyx":1186
* for summit_offset, summit_index in zip(summit_offsets, summit_indices):
*
* summit_treat = peak_content[ summit_index ][ 2 ] # <<<<<<<<<<<<<<
@@ -15250,18 +15287,18 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_summit_index, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1185; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_summit_index, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1186; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_13 = __Pyx_GetItemInt(__pyx_t_1, 2, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_13 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1185; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_13 = __Pyx_GetItemInt(__pyx_t_1, 2, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_13 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1186; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_13);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_20 = __pyx_PyFloat_AsFloat(__pyx_t_13); if (unlikely((__pyx_t_20 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_20 = __pyx_PyFloat_AsFloat(__pyx_t_13); if (unlikely((__pyx_t_20 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
__pyx_v_summit_treat = __pyx_t_20;
- /* "MACS2/IO/CallPeakUnit.pyx":1186
+ /* "MACS2/IO/CallPeakUnit.pyx":1187
*
* summit_treat = peak_content[ summit_index ][ 2 ]
* summit_ctrl = peak_content[ summit_index ][ 3 ] # <<<<<<<<<<<<<<
@@ -15270,37 +15307,37 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_13 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_summit_index, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_13 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1186; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_13 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_summit_index, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_13 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_13);
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_13, 3, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1186; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_13, 3, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_t_20 = __pyx_PyFloat_AsFloat(__pyx_t_1); if (unlikely((__pyx_t_20 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_20 = __pyx_PyFloat_AsFloat(__pyx_t_1); if (unlikely((__pyx_t_20 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_summit_ctrl = __pyx_t_20;
- /* "MACS2/IO/CallPeakUnit.pyx":1188
+ /* "MACS2/IO/CallPeakUnit.pyx":1189
* summit_ctrl = peak_content[ summit_index ][ 3 ]
*
* summit_p_score = get_pscore( int(summit_treat), summit_ctrl ) # <<<<<<<<<<<<<<
* summit_q_score = self.pqtable[ summit_p_score ]
*
*/
- __pyx_t_13 = __Pyx_GetModuleGlobalName(__pyx_n_s_get_pscore); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_GetModuleGlobalName(__pyx_n_s_get_pscore); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- __pyx_t_14 = PyFloat_FromDouble(__pyx_v_summit_treat); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyFloat_FromDouble(__pyx_v_summit_treat); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_14);
__Pyx_GIVEREF(__pyx_t_14);
__pyx_t_14 = 0;
- __pyx_t_14 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_2, NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_2, NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyFloat_FromDouble(__pyx_v_summit_ctrl); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyFloat_FromDouble(__pyx_v_summit_ctrl); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_6 = NULL;
__pyx_t_24 = 0;
@@ -15314,7 +15351,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_24 = 1;
}
}
- __pyx_t_15 = PyTuple_New(2+__pyx_t_24); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = PyTuple_New(2+__pyx_t_24); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
if (__pyx_t_6) {
PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_6 = NULL;
@@ -15325,31 +15362,31 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_14 = 0;
__pyx_t_2 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_13, __pyx_t_15, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_13, __pyx_t_15, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_t_20 = __pyx_PyFloat_AsFloat(__pyx_t_1); if (unlikely((__pyx_t_20 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_20 = __pyx_PyFloat_AsFloat(__pyx_t_1); if (unlikely((__pyx_t_20 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_summit_p_score = __pyx_t_20;
- /* "MACS2/IO/CallPeakUnit.pyx":1189
+ /* "MACS2/IO/CallPeakUnit.pyx":1190
*
* summit_p_score = get_pscore( int(summit_treat), summit_ctrl )
* summit_q_score = self.pqtable[ summit_p_score ] # <<<<<<<<<<<<<<
*
* for i in range(len(score_cutoff_s)):
*/
- __pyx_t_1 = PyFloat_FromDouble(__pyx_v_summit_p_score); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_summit_p_score); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_13 = PyObject_GetItem(__pyx_v_self->pqtable, __pyx_t_1); if (unlikely(__pyx_t_13 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_13 = PyObject_GetItem(__pyx_v_self->pqtable, __pyx_t_1); if (unlikely(__pyx_t_13 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_13);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_20 = __pyx_PyFloat_AsFloat(__pyx_t_13); if (unlikely((__pyx_t_20 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_20 = __pyx_PyFloat_AsFloat(__pyx_t_13); if (unlikely((__pyx_t_20 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
__pyx_v_summit_q_score = __pyx_t_20;
- /* "MACS2/IO/CallPeakUnit.pyx":1191
+ /* "MACS2/IO/CallPeakUnit.pyx":1192
* summit_q_score = self.pqtable[ summit_p_score ]
*
* for i in range(len(score_cutoff_s)): # <<<<<<<<<<<<<<
@@ -15358,13 +15395,13 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_score_cutoff_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_24 = PyList_GET_SIZE(__pyx_v_score_cutoff_s); if (unlikely(__pyx_t_24 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_24 = PyList_GET_SIZE(__pyx_v_score_cutoff_s); if (unlikely(__pyx_t_24 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
for (__pyx_t_21 = 0; __pyx_t_21 < __pyx_t_24; __pyx_t_21+=1) {
__pyx_v_i = __pyx_t_21;
- /* "MACS2/IO/CallPeakUnit.pyx":1192
+ /* "MACS2/IO/CallPeakUnit.pyx":1193
*
* for i in range(len(score_cutoff_s)):
* if score_cutoff_s[i] > score_array_s[ i ][ peak_content[ summit_index ][ 4 ] ]: # <<<<<<<<<<<<<<
@@ -15373,37 +15410,37 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_score_cutoff_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_13 = __Pyx_GetItemInt_List(__pyx_v_score_cutoff_s, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_13 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_13 = __Pyx_GetItemInt_List(__pyx_v_score_cutoff_s, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_13 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_13);
if (unlikely(__pyx_v_score_array_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_score_array_s, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_score_array_s, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_15 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_summit_index, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_15 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_15 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_summit_index, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_15 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_15, 4, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_15, 4, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- __pyx_t_15 = PyObject_GetItem(__pyx_t_1, __pyx_t_2); if (unlikely(__pyx_t_15 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_15 = PyObject_GetItem(__pyx_t_1, __pyx_t_2); if (unlikely(__pyx_t_15 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_15);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_13, __pyx_t_15, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_13, __pyx_t_15, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_4) {
- /* "MACS2/IO/CallPeakUnit.pyx":1193
+ /* "MACS2/IO/CallPeakUnit.pyx":1194
* for i in range(len(score_cutoff_s)):
* if score_cutoff_s[i] > score_array_s[ i ][ peak_content[ summit_index ][ 4 ] ]:
* return False # not passed, then disgard this summit. # <<<<<<<<<<<<<<
@@ -15418,17 +15455,17 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
- /* "MACS2/IO/CallPeakUnit.pyx":1195
+ /* "MACS2/IO/CallPeakUnit.pyx":1196
* return False # not passed, then disgard this summit.
*
* peaks.add( chrom, # <<<<<<<<<<<<<<
* peak_content[ 0 ][ 0 ],
* peak_content[ -1 ][ 1 ],
*/
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_add); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_add); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- /* "MACS2/IO/CallPeakUnit.pyx":1196
+ /* "MACS2/IO/CallPeakUnit.pyx":1197
*
* peaks.add( chrom,
* peak_content[ 0 ][ 0 ], # <<<<<<<<<<<<<<
@@ -15437,15 +15474,15 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_15 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_15 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_15 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_15 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1197; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_13 = __Pyx_GetItemInt(__pyx_t_15, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_13 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_13 = __Pyx_GetItemInt(__pyx_t_15, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_13 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1197; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_13);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1197
+ /* "MACS2/IO/CallPeakUnit.pyx":1198
* peaks.add( chrom,
* peak_content[ 0 ][ 0 ],
* peak_content[ -1 ][ 1 ], # <<<<<<<<<<<<<<
@@ -15454,22 +15491,22 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1198; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_15 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_15 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1197; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_15 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_15 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1198; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_15, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1197; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_15, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1198; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1195
+ /* "MACS2/IO/CallPeakUnit.pyx":1196
* return False # not passed, then disgard this summit.
*
* peaks.add( chrom, # <<<<<<<<<<<<<<
* peak_content[ 0 ][ 0 ],
* peak_content[ -1 ][ 1 ],
*/
- __pyx_t_15 = PyTuple_New(3); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = PyTuple_New(3); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_v_chrom);
@@ -15480,58 +15517,58 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_13 = 0;
__pyx_t_1 = 0;
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- /* "MACS2/IO/CallPeakUnit.pyx":1198
+ /* "MACS2/IO/CallPeakUnit.pyx":1199
* peak_content[ 0 ][ 0 ],
* peak_content[ -1 ][ 1 ],
* summit = start + summit_offset, # <<<<<<<<<<<<<<
* peak_score = summit_q_score,
* pileup = summit_treat,
*/
- __pyx_t_13 = __Pyx_PyInt_From_int((__pyx_v_start + __pyx_v_summit_offset)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1198; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyInt_From_int((__pyx_v_start + __pyx_v_summit_offset)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_summit, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_summit, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1199
+ /* "MACS2/IO/CallPeakUnit.pyx":1200
* peak_content[ -1 ][ 1 ],
* summit = start + summit_offset,
* peak_score = summit_q_score, # <<<<<<<<<<<<<<
* pileup = summit_treat,
* pscore = summit_p_score,
*/
- __pyx_t_13 = PyFloat_FromDouble(__pyx_v_summit_q_score); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyFloat_FromDouble(__pyx_v_summit_q_score); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_peak_score, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_peak_score, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1200
+ /* "MACS2/IO/CallPeakUnit.pyx":1201
* summit = start + summit_offset,
* peak_score = summit_q_score,
* pileup = summit_treat, # <<<<<<<<<<<<<<
* pscore = summit_p_score,
* fold_change = float ( summit_treat + self.pseudocount ) / ( summit_ctrl + self.pseudocount ), # fold change
*/
- __pyx_t_13 = PyFloat_FromDouble(__pyx_v_summit_treat); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyFloat_FromDouble(__pyx_v_summit_treat); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_pileup, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_pileup, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1201
+ /* "MACS2/IO/CallPeakUnit.pyx":1202
* peak_score = summit_q_score,
* pileup = summit_treat,
* pscore = summit_p_score, # <<<<<<<<<<<<<<
* fold_change = float ( summit_treat + self.pseudocount ) / ( summit_ctrl + self.pseudocount ), # fold change
* qscore = summit_q_score
*/
- __pyx_t_13 = PyFloat_FromDouble(__pyx_v_summit_p_score); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyFloat_FromDouble(__pyx_v_summit_p_score); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_pscore, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_pscore, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1202
+ /* "MACS2/IO/CallPeakUnit.pyx":1203
* pileup = summit_treat,
* pscore = summit_p_score,
* fold_change = float ( summit_treat + self.pseudocount ) / ( summit_ctrl + self.pseudocount ), # fold change # <<<<<<<<<<<<<<
@@ -15547,40 +15584,40 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
#ifdef WITH_THREAD
PyGILState_Release(__pyx_gilstate_save);
#endif
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_13 = PyFloat_FromDouble((((double)(__pyx_v_summit_treat + __pyx_v_self->pseudocount)) / __pyx_t_20)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyFloat_FromDouble((((double)(__pyx_v_summit_treat + __pyx_v_self->pseudocount)) / __pyx_t_20)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_fold_change, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_fold_change, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1204
+ /* "MACS2/IO/CallPeakUnit.pyx":1205
* fold_change = float ( summit_treat + self.pseudocount ) / ( summit_ctrl + self.pseudocount ), # fold change
* qscore = summit_q_score
* ) # <<<<<<<<<<<<<<
* # start a new peak
* return True
*/
- __pyx_t_13 = PyFloat_FromDouble(__pyx_v_summit_q_score); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyFloat_FromDouble(__pyx_v_summit_q_score); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_qscore, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_qscore, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1195
+ /* "MACS2/IO/CallPeakUnit.pyx":1196
* return False # not passed, then disgard this summit.
*
* peaks.add( chrom, # <<<<<<<<<<<<<<
* peak_content[ 0 ][ 0 ],
* peak_content[ -1 ][ 1 ],
*/
- __pyx_t_13 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_15, __pyx_t_1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_15, __pyx_t_1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1183
+ /* "MACS2/IO/CallPeakUnit.pyx":1184
* summit_offsets -= start_boundary
*
* for summit_offset, summit_index in zip(summit_offsets, summit_indices): # <<<<<<<<<<<<<<
@@ -15590,7 +15627,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1206
+ /* "MACS2/IO/CallPeakUnit.pyx":1207
* )
* # start a new peak
* return True # <<<<<<<<<<<<<<
@@ -15602,7 +15639,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_r = ((PyBoolObject *)Py_True);
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":1122
+ /* "MACS2/IO/CallPeakUnit.pyx":1123
* return True
*
* cdef bool __close_peak_with_subpeaks (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<<
@@ -15643,7 +15680,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1208
+/* "MACS2/IO/CallPeakUnit.pyx":1209
* return True
*
* cdef np.ndarray __cal_pscore ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2 ): # <<<<<<<<<<<<<<
@@ -15699,16 +15736,16 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_pybuffernd_array2.rcbuffer = &__pyx_pybuffer_array2;
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array1.diminfo[0].strides = __pyx_pybuffernd_array1.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array1.diminfo[0].shape = __pyx_pybuffernd_array1.rcbuffer->pybuffer.shape[0];
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array2.diminfo[0].strides = __pyx_pybuffernd_array2.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array2.diminfo[0].shape = __pyx_pybuffernd_array2.rcbuffer->pybuffer.shape[0];
- /* "MACS2/IO/CallPeakUnit.pyx":1216
+ /* "MACS2/IO/CallPeakUnit.pyx":1217
* float32_t * s_ptr
*
* assert array1.shape[0] == array2.shape[0] # <<<<<<<<<<<<<<
@@ -15719,39 +15756,39 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
if (unlikely(!Py_OptimizeFlag)) {
if (unlikely(!(((__pyx_v_array1->dimensions[0]) == (__pyx_v_array2->dimensions[0])) != 0))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
}
#endif
- /* "MACS2/IO/CallPeakUnit.pyx":1217
+ /* "MACS2/IO/CallPeakUnit.pyx":1218
*
* assert array1.shape[0] == array2.shape[0]
* s = np.zeros(array1.shape[0], dtype="float32") # <<<<<<<<<<<<<<
*
* a1_ptr = <float32_t *> array1.data
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = ((PyArrayObject *)__pyx_t_4);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -15767,13 +15804,13 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
}
}
__pyx_pybuffernd_s.diminfo[0].strides = __pyx_pybuffernd_s.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_s.diminfo[0].shape = __pyx_pybuffernd_s.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = 0;
__pyx_v_s = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1219
+ /* "MACS2/IO/CallPeakUnit.pyx":1220
* s = np.zeros(array1.shape[0], dtype="float32")
*
* a1_ptr = <float32_t *> array1.data # <<<<<<<<<<<<<<
@@ -15782,7 +15819,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a1_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_array1->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1220
+ /* "MACS2/IO/CallPeakUnit.pyx":1221
*
* a1_ptr = <float32_t *> array1.data
* a2_ptr = <float32_t *> array2.data # <<<<<<<<<<<<<<
@@ -15791,7 +15828,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a2_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_array2->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1221
+ /* "MACS2/IO/CallPeakUnit.pyx":1222
* a1_ptr = <float32_t *> array1.data
* a2_ptr = <float32_t *> array2.data
* s_ptr = <float32_t *> s.data # <<<<<<<<<<<<<<
@@ -15800,7 +15837,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_s_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_s->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1223
+ /* "MACS2/IO/CallPeakUnit.pyx":1224
* s_ptr = <float32_t *> s.data
*
* array1_size = array1.shape[0] # <<<<<<<<<<<<<<
@@ -15809,7 +15846,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_array1_size = (__pyx_v_array1->dimensions[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1225
+ /* "MACS2/IO/CallPeakUnit.pyx":1226
* array1_size = array1.shape[0]
*
* for i in range(array1_size): # <<<<<<<<<<<<<<
@@ -15820,26 +15857,26 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) {
__pyx_v_i = __pyx_t_11;
- /* "MACS2/IO/CallPeakUnit.pyx":1226
+ /* "MACS2/IO/CallPeakUnit.pyx":1227
*
* for i in range(array1_size):
* s_ptr[0] = get_pscore( int(a1_ptr[0]), a2_ptr[0] ) # <<<<<<<<<<<<<<
* s_ptr += 1
* a1_ptr += 1
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_get_pscore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_get_pscore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyFloat_FromDouble((__pyx_v_a1_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble((__pyx_v_a1_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyFloat_FromDouble((__pyx_v_a2_ptr[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyFloat_FromDouble((__pyx_v_a2_ptr[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_12 = NULL;
__pyx_t_13 = 0;
@@ -15853,7 +15890,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_t_13 = 1;
}
}
- __pyx_t_14 = PyTuple_New(2+__pyx_t_13); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyTuple_New(2+__pyx_t_13); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
if (__pyx_t_12) {
PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_t_12); __Pyx_GIVEREF(__pyx_t_12); __pyx_t_12 = NULL;
@@ -15864,15 +15901,15 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_3 = 0;
__pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_14, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_14, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_4); if (unlikely((__pyx_t_15 == (npy_float32)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_4); if (unlikely((__pyx_t_15 == (npy_float32)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
(__pyx_v_s_ptr[0]) = __pyx_t_15;
- /* "MACS2/IO/CallPeakUnit.pyx":1227
+ /* "MACS2/IO/CallPeakUnit.pyx":1228
* for i in range(array1_size):
* s_ptr[0] = get_pscore( int(a1_ptr[0]), a2_ptr[0] )
* s_ptr += 1 # <<<<<<<<<<<<<<
@@ -15881,7 +15918,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_s_ptr = (__pyx_v_s_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1228
+ /* "MACS2/IO/CallPeakUnit.pyx":1229
* s_ptr[0] = get_pscore( int(a1_ptr[0]), a2_ptr[0] )
* s_ptr += 1
* a1_ptr += 1 # <<<<<<<<<<<<<<
@@ -15890,7 +15927,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a1_ptr = (__pyx_v_a1_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1229
+ /* "MACS2/IO/CallPeakUnit.pyx":1230
* s_ptr += 1
* a1_ptr += 1
* a2_ptr += 1 # <<<<<<<<<<<<<<
@@ -15900,7 +15937,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_v_a2_ptr = (__pyx_v_a2_ptr + 1);
}
- /* "MACS2/IO/CallPeakUnit.pyx":1230
+ /* "MACS2/IO/CallPeakUnit.pyx":1231
* a1_ptr += 1
* a2_ptr += 1
* return s # <<<<<<<<<<<<<<
@@ -15912,7 +15949,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_r = ((PyArrayObject *)__pyx_v_s);
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":1208
+ /* "MACS2/IO/CallPeakUnit.pyx":1209
* return True
*
* cdef np.ndarray __cal_pscore ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2 ): # <<<<<<<<<<<<<<
@@ -15948,7 +15985,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1232
+/* "MACS2/IO/CallPeakUnit.pyx":1233
* return s
*
* cdef np.ndarray __cal_qscore ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2 ): # <<<<<<<<<<<<<<
@@ -16003,16 +16040,16 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_pybuffernd_array2.rcbuffer = &__pyx_pybuffer_array2;
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array1.diminfo[0].strides = __pyx_pybuffernd_array1.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array1.diminfo[0].shape = __pyx_pybuffernd_array1.rcbuffer->pybuffer.shape[0];
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array2.diminfo[0].strides = __pyx_pybuffernd_array2.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array2.diminfo[0].shape = __pyx_pybuffernd_array2.rcbuffer->pybuffer.shape[0];
- /* "MACS2/IO/CallPeakUnit.pyx":1240
+ /* "MACS2/IO/CallPeakUnit.pyx":1241
* float32_t * s_ptr
*
* assert array1.shape[0] == array2.shape[0] # <<<<<<<<<<<<<<
@@ -16023,39 +16060,39 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
if (unlikely(!Py_OptimizeFlag)) {
if (unlikely(!(((__pyx_v_array1->dimensions[0]) == (__pyx_v_array2->dimensions[0])) != 0))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
}
#endif
- /* "MACS2/IO/CallPeakUnit.pyx":1241
+ /* "MACS2/IO/CallPeakUnit.pyx":1242
*
* assert array1.shape[0] == array2.shape[0]
* s = np.zeros(array1.shape[0], dtype="float32") # <<<<<<<<<<<<<<
*
* a1_ptr = <float32_t *> array1.data
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = ((PyArrayObject *)__pyx_t_4);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -16071,13 +16108,13 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
}
}
__pyx_pybuffernd_s.diminfo[0].strides = __pyx_pybuffernd_s.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_s.diminfo[0].shape = __pyx_pybuffernd_s.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = 0;
__pyx_v_s = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1243
+ /* "MACS2/IO/CallPeakUnit.pyx":1244
* s = np.zeros(array1.shape[0], dtype="float32")
*
* a1_ptr = <float32_t *> array1.data # <<<<<<<<<<<<<<
@@ -16086,7 +16123,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a1_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_array1->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1244
+ /* "MACS2/IO/CallPeakUnit.pyx":1245
*
* a1_ptr = <float32_t *> array1.data
* a2_ptr = <float32_t *> array2.data # <<<<<<<<<<<<<<
@@ -16095,7 +16132,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a2_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_array2->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1245
+ /* "MACS2/IO/CallPeakUnit.pyx":1246
* a1_ptr = <float32_t *> array1.data
* a2_ptr = <float32_t *> array2.data
* s_ptr = <float32_t *> s.data # <<<<<<<<<<<<<<
@@ -16104,7 +16141,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_s_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_s->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1247
+ /* "MACS2/IO/CallPeakUnit.pyx":1248
* s_ptr = <float32_t *> s.data
*
* for i in range(array1.shape[0]): # <<<<<<<<<<<<<<
@@ -16115,26 +16152,26 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) {
__pyx_v_i = __pyx_t_11;
- /* "MACS2/IO/CallPeakUnit.pyx":1248
+ /* "MACS2/IO/CallPeakUnit.pyx":1249
*
* for i in range(array1.shape[0]):
* s_ptr[0] = self.pqtable[ get_pscore( int(a1_ptr[0]), a2_ptr[0] ) ] # <<<<<<<<<<<<<<
* s_ptr += 1
* a1_ptr += 1
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_get_pscore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_get_pscore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyFloat_FromDouble((__pyx_v_a1_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble((__pyx_v_a1_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), __pyx_t_2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyFloat_FromDouble((__pyx_v_a2_ptr[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyFloat_FromDouble((__pyx_v_a2_ptr[0])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_12 = NULL;
__pyx_t_13 = 0;
@@ -16148,7 +16185,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_t_13 = 1;
}
}
- __pyx_t_14 = PyTuple_New(2+__pyx_t_13); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyTuple_New(2+__pyx_t_13); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
if (__pyx_t_12) {
PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_t_12); __Pyx_GIVEREF(__pyx_t_12); __pyx_t_12 = NULL;
@@ -16159,18 +16196,18 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_3 = 0;
__pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_14, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_14, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetItem(__pyx_v_self->pqtable, __pyx_t_4); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = PyObject_GetItem(__pyx_v_self->pqtable, __pyx_t_4); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_1); if (unlikely((__pyx_t_15 == (npy_float32)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_1); if (unlikely((__pyx_t_15 == (npy_float32)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
(__pyx_v_s_ptr[0]) = __pyx_t_15;
- /* "MACS2/IO/CallPeakUnit.pyx":1249
+ /* "MACS2/IO/CallPeakUnit.pyx":1250
* for i in range(array1.shape[0]):
* s_ptr[0] = self.pqtable[ get_pscore( int(a1_ptr[0]), a2_ptr[0] ) ]
* s_ptr += 1 # <<<<<<<<<<<<<<
@@ -16179,7 +16216,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_s_ptr = (__pyx_v_s_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1250
+ /* "MACS2/IO/CallPeakUnit.pyx":1251
* s_ptr[0] = self.pqtable[ get_pscore( int(a1_ptr[0]), a2_ptr[0] ) ]
* s_ptr += 1
* a1_ptr += 1 # <<<<<<<<<<<<<<
@@ -16188,7 +16225,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a1_ptr = (__pyx_v_a1_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1251
+ /* "MACS2/IO/CallPeakUnit.pyx":1252
* s_ptr += 1
* a1_ptr += 1
* a2_ptr += 1 # <<<<<<<<<<<<<<
@@ -16198,7 +16235,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_v_a2_ptr = (__pyx_v_a2_ptr + 1);
}
- /* "MACS2/IO/CallPeakUnit.pyx":1252
+ /* "MACS2/IO/CallPeakUnit.pyx":1253
* a1_ptr += 1
* a2_ptr += 1
* return s # <<<<<<<<<<<<<<
@@ -16210,7 +16247,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_r = ((PyArrayObject *)__pyx_v_s);
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":1232
+ /* "MACS2/IO/CallPeakUnit.pyx":1233
* return s
*
* cdef np.ndarray __cal_qscore ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2 ): # <<<<<<<<<<<<<<
@@ -16246,7 +16283,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1254
+/* "MACS2/IO/CallPeakUnit.pyx":1255
* return s
*
* cdef np.ndarray __cal_logLR ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2 ): # <<<<<<<<<<<<<<
@@ -16301,16 +16338,16 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_pybuffernd_array2.rcbuffer = &__pyx_pybuffer_array2;
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1255; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array1.diminfo[0].strides = __pyx_pybuffernd_array1.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array1.diminfo[0].shape = __pyx_pybuffernd_array1.rcbuffer->pybuffer.shape[0];
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1255; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array2.diminfo[0].strides = __pyx_pybuffernd_array2.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array2.diminfo[0].shape = __pyx_pybuffernd_array2.rcbuffer->pybuffer.shape[0];
- /* "MACS2/IO/CallPeakUnit.pyx":1262
+ /* "MACS2/IO/CallPeakUnit.pyx":1263
* float32_t * s_ptr
*
* assert array1.shape[0] == array2.shape[0] # <<<<<<<<<<<<<<
@@ -16321,39 +16358,39 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
if (unlikely(!Py_OptimizeFlag)) {
if (unlikely(!(((__pyx_v_array1->dimensions[0]) == (__pyx_v_array2->dimensions[0])) != 0))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
}
#endif
- /* "MACS2/IO/CallPeakUnit.pyx":1263
+ /* "MACS2/IO/CallPeakUnit.pyx":1264
*
* assert array1.shape[0] == array2.shape[0]
* s = np.zeros(array1.shape[0], dtype="float32") # <<<<<<<<<<<<<<
*
* a1_ptr = <float32_t *> array1.data
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = ((PyArrayObject *)__pyx_t_4);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -16369,13 +16406,13 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
}
}
__pyx_pybuffernd_s.diminfo[0].strides = __pyx_pybuffernd_s.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_s.diminfo[0].shape = __pyx_pybuffernd_s.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = 0;
__pyx_v_s = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1265
+ /* "MACS2/IO/CallPeakUnit.pyx":1266
* s = np.zeros(array1.shape[0], dtype="float32")
*
* a1_ptr = <float32_t *> array1.data # <<<<<<<<<<<<<<
@@ -16384,7 +16421,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a1_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_array1->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1266
+ /* "MACS2/IO/CallPeakUnit.pyx":1267
*
* a1_ptr = <float32_t *> array1.data
* a2_ptr = <float32_t *> array2.data # <<<<<<<<<<<<<<
@@ -16393,7 +16430,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a2_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_array2->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1267
+ /* "MACS2/IO/CallPeakUnit.pyx":1268
* a1_ptr = <float32_t *> array1.data
* a2_ptr = <float32_t *> array2.data
* s_ptr = <float32_t *> s.data # <<<<<<<<<<<<<<
@@ -16402,7 +16439,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_s_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_s->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1269
+ /* "MACS2/IO/CallPeakUnit.pyx":1270
* s_ptr = <float32_t *> s.data
*
* for i in range(array1.shape[0]): # <<<<<<<<<<<<<<
@@ -16413,18 +16450,18 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) {
__pyx_v_i = __pyx_t_11;
- /* "MACS2/IO/CallPeakUnit.pyx":1270
+ /* "MACS2/IO/CallPeakUnit.pyx":1271
*
* for i in range(array1.shape[0]):
* s_ptr[0] = get_logLR_asym( a1_ptr[0] + self.pseudocount, a2_ptr[0] + self.pseudocount ) # <<<<<<<<<<<<<<
* s_ptr += 1
* a1_ptr += 1
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_get_logLR_asym); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_get_logLR_asym); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyFloat_FromDouble(((__pyx_v_a1_ptr[0]) + __pyx_v_self->pseudocount)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(((__pyx_v_a1_ptr[0]) + __pyx_v_self->pseudocount)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyFloat_FromDouble(((__pyx_v_a2_ptr[0]) + __pyx_v_self->pseudocount)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyFloat_FromDouble(((__pyx_v_a2_ptr[0]) + __pyx_v_self->pseudocount)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_12 = NULL;
__pyx_t_13 = 0;
@@ -16438,7 +16475,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_t_13 = 1;
}
}
- __pyx_t_14 = PyTuple_New(2+__pyx_t_13); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyTuple_New(2+__pyx_t_13); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
if (__pyx_t_12) {
PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_t_12); __Pyx_GIVEREF(__pyx_t_12); __pyx_t_12 = NULL;
@@ -16449,15 +16486,15 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_3 = 0;
__pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_14, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_14, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_4); if (unlikely((__pyx_t_15 == (npy_float32)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_4); if (unlikely((__pyx_t_15 == (npy_float32)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
(__pyx_v_s_ptr[0]) = __pyx_t_15;
- /* "MACS2/IO/CallPeakUnit.pyx":1271
+ /* "MACS2/IO/CallPeakUnit.pyx":1272
* for i in range(array1.shape[0]):
* s_ptr[0] = get_logLR_asym( a1_ptr[0] + self.pseudocount, a2_ptr[0] + self.pseudocount )
* s_ptr += 1 # <<<<<<<<<<<<<<
@@ -16466,7 +16503,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_s_ptr = (__pyx_v_s_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1272
+ /* "MACS2/IO/CallPeakUnit.pyx":1273
* s_ptr[0] = get_logLR_asym( a1_ptr[0] + self.pseudocount, a2_ptr[0] + self.pseudocount )
* s_ptr += 1
* a1_ptr += 1 # <<<<<<<<<<<<<<
@@ -16475,7 +16512,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a1_ptr = (__pyx_v_a1_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1273
+ /* "MACS2/IO/CallPeakUnit.pyx":1274
* s_ptr += 1
* a1_ptr += 1
* a2_ptr += 1 # <<<<<<<<<<<<<<
@@ -16485,7 +16522,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_v_a2_ptr = (__pyx_v_a2_ptr + 1);
}
- /* "MACS2/IO/CallPeakUnit.pyx":1274
+ /* "MACS2/IO/CallPeakUnit.pyx":1275
* a1_ptr += 1
* a2_ptr += 1
* return s # <<<<<<<<<<<<<<
@@ -16497,7 +16534,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_r = ((PyArrayObject *)__pyx_v_s);
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":1254
+ /* "MACS2/IO/CallPeakUnit.pyx":1255
* return s
*
* cdef np.ndarray __cal_logLR ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2 ): # <<<<<<<<<<<<<<
@@ -16533,7 +16570,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1276
+/* "MACS2/IO/CallPeakUnit.pyx":1277
* return s
*
* cdef np.ndarray __cal_logFE ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2 ): # <<<<<<<<<<<<<<
@@ -16584,16 +16621,16 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_pybuffernd_array2.rcbuffer = &__pyx_pybuffer_array2;
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array1.diminfo[0].strides = __pyx_pybuffernd_array1.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array1.diminfo[0].shape = __pyx_pybuffernd_array1.rcbuffer->pybuffer.shape[0];
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array2.diminfo[0].strides = __pyx_pybuffernd_array2.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array2.diminfo[0].shape = __pyx_pybuffernd_array2.rcbuffer->pybuffer.shape[0];
- /* "MACS2/IO/CallPeakUnit.pyx":1284
+ /* "MACS2/IO/CallPeakUnit.pyx":1285
* float32_t * s_ptr
*
* assert array1.shape[0] == array2.shape[0] # <<<<<<<<<<<<<<
@@ -16604,39 +16641,39 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
if (unlikely(!Py_OptimizeFlag)) {
if (unlikely(!(((__pyx_v_array1->dimensions[0]) == (__pyx_v_array2->dimensions[0])) != 0))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
}
#endif
- /* "MACS2/IO/CallPeakUnit.pyx":1285
+ /* "MACS2/IO/CallPeakUnit.pyx":1286
*
* assert array1.shape[0] == array2.shape[0]
* s = np.zeros(array1.shape[0], dtype="float32") # <<<<<<<<<<<<<<
*
* a1_ptr = <float32_t *> array1.data
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = ((PyArrayObject *)__pyx_t_4);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -16652,13 +16689,13 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
}
}
__pyx_pybuffernd_s.diminfo[0].strides = __pyx_pybuffernd_s.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_s.diminfo[0].shape = __pyx_pybuffernd_s.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = 0;
__pyx_v_s = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1287
+ /* "MACS2/IO/CallPeakUnit.pyx":1288
* s = np.zeros(array1.shape[0], dtype="float32")
*
* a1_ptr = <float32_t *> array1.data # <<<<<<<<<<<<<<
@@ -16667,7 +16704,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a1_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_array1->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1288
+ /* "MACS2/IO/CallPeakUnit.pyx":1289
*
* a1_ptr = <float32_t *> array1.data
* a2_ptr = <float32_t *> array2.data # <<<<<<<<<<<<<<
@@ -16676,7 +16713,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a2_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_array2->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1289
+ /* "MACS2/IO/CallPeakUnit.pyx":1290
* a1_ptr = <float32_t *> array1.data
* a2_ptr = <float32_t *> array2.data
* s_ptr = <float32_t *> s.data # <<<<<<<<<<<<<<
@@ -16685,7 +16722,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_s_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_s->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1291
+ /* "MACS2/IO/CallPeakUnit.pyx":1292
* s_ptr = <float32_t *> s.data
*
* for i in range(array1.shape[0]): # <<<<<<<<<<<<<<
@@ -16696,7 +16733,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) {
__pyx_v_i = __pyx_t_11;
- /* "MACS2/IO/CallPeakUnit.pyx":1292
+ /* "MACS2/IO/CallPeakUnit.pyx":1293
*
* for i in range(array1.shape[0]):
* s_ptr[0] = get_logFE( a1_ptr[0] + self.pseudocount, a2_ptr[0] + self.pseudocount ) # <<<<<<<<<<<<<<
@@ -16705,7 +16742,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
(__pyx_v_s_ptr[0]) = __pyx_f_5MACS2_2IO_12CallPeakUnit_get_logFE(((__pyx_v_a1_ptr[0]) + __pyx_v_self->pseudocount), ((__pyx_v_a2_ptr[0]) + __pyx_v_self->pseudocount));
- /* "MACS2/IO/CallPeakUnit.pyx":1293
+ /* "MACS2/IO/CallPeakUnit.pyx":1294
* for i in range(array1.shape[0]):
* s_ptr[0] = get_logFE( a1_ptr[0] + self.pseudocount, a2_ptr[0] + self.pseudocount )
* s_ptr += 1 # <<<<<<<<<<<<<<
@@ -16714,7 +16751,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_s_ptr = (__pyx_v_s_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1294
+ /* "MACS2/IO/CallPeakUnit.pyx":1295
* s_ptr[0] = get_logFE( a1_ptr[0] + self.pseudocount, a2_ptr[0] + self.pseudocount )
* s_ptr += 1
* a1_ptr += 1 # <<<<<<<<<<<<<<
@@ -16723,7 +16760,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a1_ptr = (__pyx_v_a1_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1295
+ /* "MACS2/IO/CallPeakUnit.pyx":1296
* s_ptr += 1
* a1_ptr += 1
* a2_ptr += 1 # <<<<<<<<<<<<<<
@@ -16733,7 +16770,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_v_a2_ptr = (__pyx_v_a2_ptr + 1);
}
- /* "MACS2/IO/CallPeakUnit.pyx":1296
+ /* "MACS2/IO/CallPeakUnit.pyx":1297
* a1_ptr += 1
* a2_ptr += 1
* return s # <<<<<<<<<<<<<<
@@ -16745,7 +16782,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_r = ((PyArrayObject *)__pyx_v_s);
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":1276
+ /* "MACS2/IO/CallPeakUnit.pyx":1277
* return s
*
* cdef np.ndarray __cal_logFE ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2 ): # <<<<<<<<<<<<<<
@@ -16779,7 +16816,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1298
+/* "MACS2/IO/CallPeakUnit.pyx":1299
* return s
*
* cdef np.ndarray __cal_FE ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2 ): # <<<<<<<<<<<<<<
@@ -16832,16 +16869,16 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_pybuffernd_array2.rcbuffer = &__pyx_pybuffer_array2;
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array1.diminfo[0].strides = __pyx_pybuffernd_array1.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array1.diminfo[0].shape = __pyx_pybuffernd_array1.rcbuffer->pybuffer.shape[0];
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array2.diminfo[0].strides = __pyx_pybuffernd_array2.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array2.diminfo[0].shape = __pyx_pybuffernd_array2.rcbuffer->pybuffer.shape[0];
- /* "MACS2/IO/CallPeakUnit.pyx":1306
+ /* "MACS2/IO/CallPeakUnit.pyx":1307
* float32_t * s_ptr
*
* assert array1.shape[0] == array2.shape[0] # <<<<<<<<<<<<<<
@@ -16852,39 +16889,39 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
if (unlikely(!Py_OptimizeFlag)) {
if (unlikely(!(((__pyx_v_array1->dimensions[0]) == (__pyx_v_array2->dimensions[0])) != 0))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
}
#endif
- /* "MACS2/IO/CallPeakUnit.pyx":1307
+ /* "MACS2/IO/CallPeakUnit.pyx":1308
*
* assert array1.shape[0] == array2.shape[0]
* s = np.zeros(array1.shape[0], dtype="float32") # <<<<<<<<<<<<<<
*
* a1_ptr = <float32_t *> array1.data
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = ((PyArrayObject *)__pyx_t_4);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -16900,13 +16937,13 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
}
}
__pyx_pybuffernd_s.diminfo[0].strides = __pyx_pybuffernd_s.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_s.diminfo[0].shape = __pyx_pybuffernd_s.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = 0;
__pyx_v_s = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1309
+ /* "MACS2/IO/CallPeakUnit.pyx":1310
* s = np.zeros(array1.shape[0], dtype="float32")
*
* a1_ptr = <float32_t *> array1.data # <<<<<<<<<<<<<<
@@ -16915,7 +16952,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a1_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_array1->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1310
+ /* "MACS2/IO/CallPeakUnit.pyx":1311
*
* a1_ptr = <float32_t *> array1.data
* a2_ptr = <float32_t *> array2.data # <<<<<<<<<<<<<<
@@ -16924,7 +16961,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a2_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_array2->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1311
+ /* "MACS2/IO/CallPeakUnit.pyx":1312
* a1_ptr = <float32_t *> array1.data
* a2_ptr = <float32_t *> array2.data
* s_ptr = <float32_t *> s.data # <<<<<<<<<<<<<<
@@ -16933,7 +16970,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_s_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_s->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1313
+ /* "MACS2/IO/CallPeakUnit.pyx":1314
* s_ptr = <float32_t *> s.data
*
* for i in range(array1.shape[0]): # <<<<<<<<<<<<<<
@@ -16944,7 +16981,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) {
__pyx_v_i = __pyx_t_11;
- /* "MACS2/IO/CallPeakUnit.pyx":1314
+ /* "MACS2/IO/CallPeakUnit.pyx":1315
*
* for i in range(array1.shape[0]):
* s_ptr[0] = (a1_ptr[0] + self.pseudocount) / ( a2_ptr[0] + self.pseudocount ) # <<<<<<<<<<<<<<
@@ -16961,11 +16998,11 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
#ifdef WITH_THREAD
PyGILState_Release(__pyx_gilstate_save);
#endif
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
(__pyx_v_s_ptr[0]) = (__pyx_t_12 / __pyx_t_13);
- /* "MACS2/IO/CallPeakUnit.pyx":1315
+ /* "MACS2/IO/CallPeakUnit.pyx":1316
* for i in range(array1.shape[0]):
* s_ptr[0] = (a1_ptr[0] + self.pseudocount) / ( a2_ptr[0] + self.pseudocount )
* s_ptr += 1 # <<<<<<<<<<<<<<
@@ -16974,7 +17011,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_s_ptr = (__pyx_v_s_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1316
+ /* "MACS2/IO/CallPeakUnit.pyx":1317
* s_ptr[0] = (a1_ptr[0] + self.pseudocount) / ( a2_ptr[0] + self.pseudocount )
* s_ptr += 1
* a1_ptr += 1 # <<<<<<<<<<<<<<
@@ -16983,7 +17020,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a1_ptr = (__pyx_v_a1_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1317
+ /* "MACS2/IO/CallPeakUnit.pyx":1318
* s_ptr += 1
* a1_ptr += 1
* a2_ptr += 1 # <<<<<<<<<<<<<<
@@ -16993,7 +17030,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_v_a2_ptr = (__pyx_v_a2_ptr + 1);
}
- /* "MACS2/IO/CallPeakUnit.pyx":1318
+ /* "MACS2/IO/CallPeakUnit.pyx":1319
* a1_ptr += 1
* a2_ptr += 1
* return s # <<<<<<<<<<<<<<
@@ -17005,7 +17042,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_r = ((PyArrayObject *)__pyx_v_s);
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":1298
+ /* "MACS2/IO/CallPeakUnit.pyx":1299
* return s
*
* cdef np.ndarray __cal_FE ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2 ): # <<<<<<<<<<<<<<
@@ -17039,7 +17076,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1320
+/* "MACS2/IO/CallPeakUnit.pyx":1321
* return s
*
* cdef np.ndarray __cal_subtraction ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2 ): # <<<<<<<<<<<<<<
@@ -17090,16 +17127,16 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_pybuffernd_array2.rcbuffer = &__pyx_pybuffer_array2;
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array1.rcbuffer->pybuffer, (PyObject*)__pyx_v_array1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array1.diminfo[0].strides = __pyx_pybuffernd_array1.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array1.diminfo[0].shape = __pyx_pybuffernd_array1.rcbuffer->pybuffer.shape[0];
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_array2.rcbuffer->pybuffer, (PyObject*)__pyx_v_array2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_pybuffernd_array2.diminfo[0].strides = __pyx_pybuffernd_array2.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_array2.diminfo[0].shape = __pyx_pybuffernd_array2.rcbuffer->pybuffer.shape[0];
- /* "MACS2/IO/CallPeakUnit.pyx":1328
+ /* "MACS2/IO/CallPeakUnit.pyx":1329
* float32_t * s_ptr
*
* assert array1.shape[0] == array2.shape[0] # <<<<<<<<<<<<<<
@@ -17110,39 +17147,39 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
if (unlikely(!Py_OptimizeFlag)) {
if (unlikely(!(((__pyx_v_array1->dimensions[0]) == (__pyx_v_array2->dimensions[0])) != 0))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
}
#endif
- /* "MACS2/IO/CallPeakUnit.pyx":1329
+ /* "MACS2/IO/CallPeakUnit.pyx":1330
*
* assert array1.shape[0] == array2.shape[0]
* s = np.zeros(array1.shape[0], dtype="float32") # <<<<<<<<<<<<<<
*
* a1_ptr = <float32_t *> array1.data
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_array1->dimensions[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = ((PyArrayObject *)__pyx_t_4);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -17158,13 +17195,13 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
}
}
__pyx_pybuffernd_s.diminfo[0].strides = __pyx_pybuffernd_s.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_s.diminfo[0].shape = __pyx_pybuffernd_s.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = 0;
__pyx_v_s = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1331
+ /* "MACS2/IO/CallPeakUnit.pyx":1332
* s = np.zeros(array1.shape[0], dtype="float32")
*
* a1_ptr = <float32_t *> array1.data # <<<<<<<<<<<<<<
@@ -17173,7 +17210,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a1_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_array1->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1332
+ /* "MACS2/IO/CallPeakUnit.pyx":1333
*
* a1_ptr = <float32_t *> array1.data
* a2_ptr = <float32_t *> array2.data # <<<<<<<<<<<<<<
@@ -17182,7 +17219,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a2_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_array2->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1333
+ /* "MACS2/IO/CallPeakUnit.pyx":1334
* a1_ptr = <float32_t *> array1.data
* a2_ptr = <float32_t *> array2.data
* s_ptr = <float32_t *> s.data # <<<<<<<<<<<<<<
@@ -17191,7 +17228,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_s_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_s->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1335
+ /* "MACS2/IO/CallPeakUnit.pyx":1336
* s_ptr = <float32_t *> s.data
*
* for i in range(array1.shape[0]): # <<<<<<<<<<<<<<
@@ -17202,7 +17239,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
for (__pyx_t_11 = 0; __pyx_t_11 < __pyx_t_10; __pyx_t_11+=1) {
__pyx_v_i = __pyx_t_11;
- /* "MACS2/IO/CallPeakUnit.pyx":1336
+ /* "MACS2/IO/CallPeakUnit.pyx":1337
*
* for i in range(array1.shape[0]):
* s_ptr[0] = a1_ptr[0] - a2_ptr[0] # <<<<<<<<<<<<<<
@@ -17211,7 +17248,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
(__pyx_v_s_ptr[0]) = ((__pyx_v_a1_ptr[0]) - (__pyx_v_a2_ptr[0]));
- /* "MACS2/IO/CallPeakUnit.pyx":1337
+ /* "MACS2/IO/CallPeakUnit.pyx":1338
* for i in range(array1.shape[0]):
* s_ptr[0] = a1_ptr[0] - a2_ptr[0]
* s_ptr += 1 # <<<<<<<<<<<<<<
@@ -17220,7 +17257,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_s_ptr = (__pyx_v_s_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1338
+ /* "MACS2/IO/CallPeakUnit.pyx":1339
* s_ptr[0] = a1_ptr[0] - a2_ptr[0]
* s_ptr += 1
* a1_ptr += 1 # <<<<<<<<<<<<<<
@@ -17229,7 +17266,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
__pyx_v_a1_ptr = (__pyx_v_a1_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1339
+ /* "MACS2/IO/CallPeakUnit.pyx":1340
* s_ptr += 1
* a1_ptr += 1
* a2_ptr += 1 # <<<<<<<<<<<<<<
@@ -17239,7 +17276,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_v_a2_ptr = (__pyx_v_a2_ptr + 1);
}
- /* "MACS2/IO/CallPeakUnit.pyx":1340
+ /* "MACS2/IO/CallPeakUnit.pyx":1341
* a1_ptr += 1
* a2_ptr += 1
* return s # <<<<<<<<<<<<<<
@@ -17251,7 +17288,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_r = ((PyArrayObject *)__pyx_v_s);
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":1320
+ /* "MACS2/IO/CallPeakUnit.pyx":1321
* return s
*
* cdef np.ndarray __cal_subtraction ( self, np.ndarray[np.float32_t, ndim=1] array1, np.ndarray[np.float32_t, ndim=1] array2 ): # <<<<<<<<<<<<<<
@@ -17285,7 +17322,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1343
+/* "MACS2/IO/CallPeakUnit.pyx":1344
*
*
* cdef bool __write_bedGraph_for_a_chromosome ( self, str chrom ): # <<<<<<<<<<<<<<
@@ -17354,7 +17391,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_pybuffernd_ctrl_array.data = NULL;
__pyx_pybuffernd_ctrl_array.rcbuffer = &__pyx_pybuffer_ctrl_array;
- /* "MACS2/IO/CallPeakUnit.pyx":1362
+ /* "MACS2/IO/CallPeakUnit.pyx":1363
* bytes tmp_bytes
*
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl # <<<<<<<<<<<<<<
@@ -17373,7 +17410,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
if (unlikely(size != 3)) {
if (size > 3) __Pyx_RaiseTooManyValuesError(3);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
__pyx_t_2 = PyList_GET_ITEM(sequence, 0);
@@ -17383,20 +17420,20 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_INCREF(__pyx_t_3);
__Pyx_INCREF(__pyx_t_4);
#else
- __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
#endif
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
} else {
- __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = ((PyArrayObject *)__pyx_t_2);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -17412,7 +17449,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
__pyx_pybuffernd_pos_array.diminfo[0].strides = __pyx_pybuffernd_pos_array.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_pos_array.diminfo[0].shape = __pyx_pybuffernd_pos_array.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_5 = 0;
__pyx_v_pos_array = ((PyArrayObject *)__pyx_t_2);
@@ -17432,7 +17469,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
__pyx_pybuffernd_treat_array.diminfo[0].strides = __pyx_pybuffernd_treat_array.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_treat_array.diminfo[0].shape = __pyx_pybuffernd_treat_array.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_10 = 0;
__pyx_v_treat_array = ((PyArrayObject *)__pyx_t_3);
@@ -17452,13 +17489,13 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
__pyx_pybuffernd_ctrl_array.diminfo[0].strides = __pyx_pybuffernd_ctrl_array.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_ctrl_array.diminfo[0].shape = __pyx_pybuffernd_ctrl_array.rcbuffer->pybuffer.shape[0];
- if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_10 = 0;
__pyx_v_ctrl_array = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1363
+ /* "MACS2/IO/CallPeakUnit.pyx":1364
*
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl
* pos_array_ptr = <int32_t *> pos_array.data # <<<<<<<<<<<<<<
@@ -17467,7 +17504,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_pos_array_ptr = ((int32_t *)__pyx_v_pos_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1364
+ /* "MACS2/IO/CallPeakUnit.pyx":1365
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl
* pos_array_ptr = <int32_t *> pos_array.data
* treat_array_ptr = <float32_t *> treat_array.data # <<<<<<<<<<<<<<
@@ -17476,7 +17513,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_treat_array_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_treat_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1365
+ /* "MACS2/IO/CallPeakUnit.pyx":1366
* pos_array_ptr = <int32_t *> pos_array.data
* treat_array_ptr = <float32_t *> treat_array.data
* ctrl_array_ptr = <float32_t *> ctrl_array.data # <<<<<<<<<<<<<<
@@ -17485,17 +17522,17 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_ctrl_array_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_ctrl_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1367
+ /* "MACS2/IO/CallPeakUnit.pyx":1368
* ctrl_array_ptr = <float32_t *> ctrl_array.data
*
* if self.save_SPMR: # <<<<<<<<<<<<<<
* if self.treat_scaling_factor == 1:
* # in this case, control has been asked to be scaled to depth of treatment
*/
- __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->save_SPMR)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->save_SPMR)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1368
+ /* "MACS2/IO/CallPeakUnit.pyx":1369
*
* if self.save_SPMR:
* if self.treat_scaling_factor == 1: # <<<<<<<<<<<<<<
@@ -17505,38 +17542,38 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_11 = ((__pyx_v_self->treat_scaling_factor == 1.0) != 0);
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1370
+ /* "MACS2/IO/CallPeakUnit.pyx":1371
* if self.treat_scaling_factor == 1:
* # in this case, control has been asked to be scaled to depth of treatment
* denominator = self.treat.total/1e6 # <<<<<<<<<<<<<<
* else:
* # in this case, treatment has been asked to be scaled to depth of control
*/
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->treat, __pyx_n_s_total); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->treat, __pyx_n_s_total); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = __Pyx_PyNumber_Divide(__pyx_t_1, __pyx_float_1e6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyNumber_Divide(__pyx_t_1, __pyx_float_1e6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_12 = __pyx_PyFloat_AsFloat(__pyx_t_4); if (unlikely((__pyx_t_12 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __pyx_PyFloat_AsFloat(__pyx_t_4); if (unlikely((__pyx_t_12 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_v_denominator = __pyx_t_12;
goto __pyx_L4;
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1373
+ /* "MACS2/IO/CallPeakUnit.pyx":1374
* else:
* # in this case, treatment has been asked to be scaled to depth of control
* denominator = self.ctrl.total/1e6 # <<<<<<<<<<<<<<
* else:
* denominator = 1.0
*/
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->ctrl, __pyx_n_s_total); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->ctrl, __pyx_n_s_total); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_1 = __Pyx_PyNumber_Divide(__pyx_t_4, __pyx_float_1e6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyNumber_Divide(__pyx_t_4, __pyx_float_1e6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_12 = __pyx_PyFloat_AsFloat(__pyx_t_1); if (unlikely((__pyx_t_12 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __pyx_PyFloat_AsFloat(__pyx_t_1); if (unlikely((__pyx_t_12 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_denominator = __pyx_t_12;
}
@@ -17545,7 +17582,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1375
+ /* "MACS2/IO/CallPeakUnit.pyx":1376
* denominator = self.ctrl.total/1e6
* else:
* denominator = 1.0 # <<<<<<<<<<<<<<
@@ -17556,7 +17593,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
__pyx_L3:;
- /* "MACS2/IO/CallPeakUnit.pyx":1377
+ /* "MACS2/IO/CallPeakUnit.pyx":1378
* denominator = 1.0
*
* l = pos_array.shape[ 0 ] # <<<<<<<<<<<<<<
@@ -17565,7 +17602,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_l = (__pyx_v_pos_array->dimensions[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1379
+ /* "MACS2/IO/CallPeakUnit.pyx":1380
* l = pos_array.shape[ 0 ]
*
* if l == 0: # if there is no data, return # <<<<<<<<<<<<<<
@@ -17575,7 +17612,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_11 = ((__pyx_v_l == 0) != 0);
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1380
+ /* "MACS2/IO/CallPeakUnit.pyx":1381
*
* if l == 0: # if there is no data, return
* return False # <<<<<<<<<<<<<<
@@ -17588,7 +17625,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
goto __pyx_L0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1382
+ /* "MACS2/IO/CallPeakUnit.pyx":1383
* return False
*
* ft = self.bedGraph_treat_f # <<<<<<<<<<<<<<
@@ -17598,7 +17635,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_13 = __pyx_v_self->bedGraph_treat_f;
__pyx_v_ft = __pyx_t_13;
- /* "MACS2/IO/CallPeakUnit.pyx":1383
+ /* "MACS2/IO/CallPeakUnit.pyx":1384
*
* ft = self.bedGraph_treat_f
* fc = self.bedGraph_ctrl_f # <<<<<<<<<<<<<<
@@ -17608,7 +17645,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_13 = __pyx_v_self->bedGraph_ctrl_f;
__pyx_v_fc = __pyx_t_13;
- /* "MACS2/IO/CallPeakUnit.pyx":1387
+ /* "MACS2/IO/CallPeakUnit.pyx":1388
* #c_write_func = self.bedGraph_ctrl.write
*
* pre_p_t = 0 # <<<<<<<<<<<<<<
@@ -17617,7 +17654,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_pre_p_t = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1388
+ /* "MACS2/IO/CallPeakUnit.pyx":1389
*
* pre_p_t = 0
* pre_p_c = 0 # <<<<<<<<<<<<<<
@@ -17626,7 +17663,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_pre_p_c = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1389
+ /* "MACS2/IO/CallPeakUnit.pyx":1390
* pre_p_t = 0
* pre_p_c = 0
* pre_v_t = treat_array_ptr[ 0 ]/denominator # <<<<<<<<<<<<<<
@@ -17641,11 +17678,11 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
#ifdef WITH_THREAD
PyGILState_Release(__pyx_gilstate_save);
#endif
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_v_pre_v_t = ((__pyx_v_treat_array_ptr[0]) / __pyx_v_denominator);
- /* "MACS2/IO/CallPeakUnit.pyx":1390
+ /* "MACS2/IO/CallPeakUnit.pyx":1391
* pre_p_c = 0
* pre_v_t = treat_array_ptr[ 0 ]/denominator
* pre_v_c = ctrl_array_ptr [ 0 ]/denominator # <<<<<<<<<<<<<<
@@ -17660,11 +17697,11 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
#ifdef WITH_THREAD
PyGILState_Release(__pyx_gilstate_save);
#endif
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_v_pre_v_c = ((__pyx_v_ctrl_array_ptr[0]) / __pyx_v_denominator);
- /* "MACS2/IO/CallPeakUnit.pyx":1391
+ /* "MACS2/IO/CallPeakUnit.pyx":1392
* pre_v_t = treat_array_ptr[ 0 ]/denominator
* pre_v_c = ctrl_array_ptr [ 0 ]/denominator
* treat_array_ptr += 1 # <<<<<<<<<<<<<<
@@ -17673,7 +17710,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_treat_array_ptr = (__pyx_v_treat_array_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1392
+ /* "MACS2/IO/CallPeakUnit.pyx":1393
* pre_v_c = ctrl_array_ptr [ 0 ]/denominator
* treat_array_ptr += 1
* ctrl_array_ptr += 1 # <<<<<<<<<<<<<<
@@ -17682,7 +17719,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_ctrl_array_ptr = (__pyx_v_ctrl_array_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1394
+ /* "MACS2/IO/CallPeakUnit.pyx":1395
* ctrl_array_ptr += 1
*
* for i in range( 1, l ): # <<<<<<<<<<<<<<
@@ -17693,7 +17730,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
for (__pyx_t_14 = 1; __pyx_t_14 < __pyx_t_6; __pyx_t_14+=1) {
__pyx_v_i = __pyx_t_14;
- /* "MACS2/IO/CallPeakUnit.pyx":1395
+ /* "MACS2/IO/CallPeakUnit.pyx":1396
*
* for i in range( 1, l ):
* v_t = treat_array_ptr[ 0 ]/denominator # <<<<<<<<<<<<<<
@@ -17708,11 +17745,11 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
#ifdef WITH_THREAD
PyGILState_Release(__pyx_gilstate_save);
#endif
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_v_v_t = ((__pyx_v_treat_array_ptr[0]) / __pyx_v_denominator);
- /* "MACS2/IO/CallPeakUnit.pyx":1396
+ /* "MACS2/IO/CallPeakUnit.pyx":1397
* for i in range( 1, l ):
* v_t = treat_array_ptr[ 0 ]/denominator
* v_c = ctrl_array_ptr [ 0 ]/denominator # <<<<<<<<<<<<<<
@@ -17727,11 +17764,11 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
#ifdef WITH_THREAD
PyGILState_Release(__pyx_gilstate_save);
#endif
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_v_v_c = ((__pyx_v_ctrl_array_ptr[0]) / __pyx_v_denominator);
- /* "MACS2/IO/CallPeakUnit.pyx":1397
+ /* "MACS2/IO/CallPeakUnit.pyx":1398
* v_t = treat_array_ptr[ 0 ]/denominator
* v_c = ctrl_array_ptr [ 0 ]/denominator
* p = pos_array_ptr [ 0 ] # <<<<<<<<<<<<<<
@@ -17740,7 +17777,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_p = (__pyx_v_pos_array_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1398
+ /* "MACS2/IO/CallPeakUnit.pyx":1399
* v_c = ctrl_array_ptr [ 0 ]/denominator
* p = pos_array_ptr [ 0 ]
* pos_array_ptr += 1 # <<<<<<<<<<<<<<
@@ -17749,7 +17786,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_pos_array_ptr = (__pyx_v_pos_array_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1399
+ /* "MACS2/IO/CallPeakUnit.pyx":1400
* p = pos_array_ptr [ 0 ]
* pos_array_ptr += 1
* treat_array_ptr += 1 # <<<<<<<<<<<<<<
@@ -17758,7 +17795,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_treat_array_ptr = (__pyx_v_treat_array_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1400
+ /* "MACS2/IO/CallPeakUnit.pyx":1401
* pos_array_ptr += 1
* treat_array_ptr += 1
* ctrl_array_ptr += 1 # <<<<<<<<<<<<<<
@@ -17767,7 +17804,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_ctrl_array_ptr = (__pyx_v_ctrl_array_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1402
+ /* "MACS2/IO/CallPeakUnit.pyx":1403
* ctrl_array_ptr += 1
*
* if abs(pre_v_t - v_t) > 1e-5: # precision is 5 digits # <<<<<<<<<<<<<<
@@ -17777,20 +17814,20 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_11 = ((fabsf((__pyx_v_pre_v_t - __pyx_v_v_t)) > 1e-5) != 0);
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1403
+ /* "MACS2/IO/CallPeakUnit.pyx":1404
*
* if abs(pre_v_t - v_t) > 1e-5: # precision is 5 digits
* tmp_bytes = ("%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_t, p, pre_v_t )).encode() # <<<<<<<<<<<<<<
* #t_write_func( "%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_t, p, pre_v_t ) )
* fprintf( ft, tmp_bytes )
*/
- __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_pre_p_t); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_pre_p_t); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_p); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_p); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pre_v_t); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pre_v_t); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_v_chrom);
@@ -17804,10 +17841,10 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_4 = 0;
__pyx_t_3 = 0;
__pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_s_d_d_5f, __pyx_t_15); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_s_d_d_5f, __pyx_t_15); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- __pyx_t_15 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_encode); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_encode); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = NULL;
@@ -17821,28 +17858,28 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
if (__pyx_t_2) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_15, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_15, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_15); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_15); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_tmp_bytes, ((PyObject*)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1405
+ /* "MACS2/IO/CallPeakUnit.pyx":1406
* tmp_bytes = ("%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_t, p, pre_v_t )).encode()
* #t_write_func( "%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_t, p, pre_v_t ) )
* fprintf( ft, tmp_bytes ) # <<<<<<<<<<<<<<
* pre_v_t = v_t
* pre_p_t = p
*/
- __pyx_t_16 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_16) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1405; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_16) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1406; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
fprintf(__pyx_v_ft, __pyx_t_16);
- /* "MACS2/IO/CallPeakUnit.pyx":1406
+ /* "MACS2/IO/CallPeakUnit.pyx":1407
* #t_write_func( "%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_t, p, pre_v_t ) )
* fprintf( ft, tmp_bytes )
* pre_v_t = v_t # <<<<<<<<<<<<<<
@@ -17851,7 +17888,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_pre_v_t = __pyx_v_v_t;
- /* "MACS2/IO/CallPeakUnit.pyx":1407
+ /* "MACS2/IO/CallPeakUnit.pyx":1408
* fprintf( ft, tmp_bytes )
* pre_v_t = v_t
* pre_p_t = p # <<<<<<<<<<<<<<
@@ -17863,7 +17900,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
__pyx_L8:;
- /* "MACS2/IO/CallPeakUnit.pyx":1409
+ /* "MACS2/IO/CallPeakUnit.pyx":1410
* pre_p_t = p
*
* if abs(pre_v_c - v_c) > 1e-5: # precision is 5 digits # <<<<<<<<<<<<<<
@@ -17873,20 +17910,20 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_11 = ((fabsf((__pyx_v_pre_v_c - __pyx_v_v_c)) > 1e-5) != 0);
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1410
+ /* "MACS2/IO/CallPeakUnit.pyx":1411
*
* if abs(pre_v_c - v_c) > 1e-5: # precision is 5 digits
* tmp_bytes = ("%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_c, p, pre_v_c )).encode() # <<<<<<<<<<<<<<
* fprintf( fc, tmp_bytes )
* #c_write_func( "%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_c, p, pre_v_c ) )
*/
- __pyx_t_15 = __Pyx_PyInt_From_int(__pyx_v_pre_p_c); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_PyInt_From_int(__pyx_v_pre_p_c); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_p); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_p); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_pre_v_c); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_pre_v_c); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyTuple_New(4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyTuple_New(4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_chrom);
@@ -17900,10 +17937,10 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_15 = 0;
__pyx_t_2 = 0;
__pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyString_Format(__pyx_kp_s_s_d_d_5f, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyString_Format(__pyx_kp_s_s_d_d_5f, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_encode); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_encode); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_3 = NULL;
@@ -17917,28 +17954,28 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
if (__pyx_t_3) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_tmp_bytes, ((PyObject*)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1411
+ /* "MACS2/IO/CallPeakUnit.pyx":1412
* if abs(pre_v_c - v_c) > 1e-5: # precision is 5 digits
* tmp_bytes = ("%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_c, p, pre_v_c )).encode()
* fprintf( fc, tmp_bytes ) # <<<<<<<<<<<<<<
* #c_write_func( "%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_c, p, pre_v_c ) )
* pre_v_c = v_c
*/
- __pyx_t_16 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_16) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_16) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
fprintf(__pyx_v_fc, __pyx_t_16);
- /* "MACS2/IO/CallPeakUnit.pyx":1413
+ /* "MACS2/IO/CallPeakUnit.pyx":1414
* fprintf( fc, tmp_bytes )
* #c_write_func( "%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_c, p, pre_v_c ) )
* pre_v_c = v_c # <<<<<<<<<<<<<<
@@ -17947,7 +17984,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_pre_v_c = __pyx_v_v_c;
- /* "MACS2/IO/CallPeakUnit.pyx":1414
+ /* "MACS2/IO/CallPeakUnit.pyx":1415
* #c_write_func( "%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_c, p, pre_v_c ) )
* pre_v_c = v_c
* pre_p_c = p # <<<<<<<<<<<<<<
@@ -17960,7 +17997,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_L9:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1416
+ /* "MACS2/IO/CallPeakUnit.pyx":1417
* pre_p_c = p
*
* p = pos_array_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -17969,20 +18006,20 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_p = (__pyx_v_pos_array_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1418
+ /* "MACS2/IO/CallPeakUnit.pyx":1419
* p = pos_array_ptr[ 0 ]
* # last one
* tmp_bytes = ("%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_t, p, pre_v_t )).encode() # <<<<<<<<<<<<<<
* fprintf( ft, tmp_bytes )
* tmp_bytes = ("%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_c, p, pre_v_c )).encode()
*/
- __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_pre_p_t); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_pre_p_t); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_p); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_p); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pre_v_t); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pre_v_t); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = PyTuple_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_v_chrom);
@@ -17996,10 +18033,10 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_4 = 0;
__pyx_t_3 = 0;
__pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_s_d_d_5f, __pyx_t_15); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_s_d_d_5f, __pyx_t_15); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- __pyx_t_15 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_encode); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_encode); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = NULL;
@@ -18013,41 +18050,41 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
if (__pyx_t_2) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_15, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_15, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_15); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_15); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_tmp_bytes, ((PyObject*)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1419
+ /* "MACS2/IO/CallPeakUnit.pyx":1420
* # last one
* tmp_bytes = ("%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_t, p, pre_v_t )).encode()
* fprintf( ft, tmp_bytes ) # <<<<<<<<<<<<<<
* tmp_bytes = ("%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_c, p, pre_v_c )).encode()
* fprintf( fc, tmp_bytes )
*/
- __pyx_t_16 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_16) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_16) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
fprintf(__pyx_v_ft, __pyx_t_16);
- /* "MACS2/IO/CallPeakUnit.pyx":1420
+ /* "MACS2/IO/CallPeakUnit.pyx":1421
* tmp_bytes = ("%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_t, p, pre_v_t )).encode()
* fprintf( ft, tmp_bytes )
* tmp_bytes = ("%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_c, p, pre_v_c )).encode() # <<<<<<<<<<<<<<
* fprintf( fc, tmp_bytes )
* #t_write_func( "%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_t, p, pre_v_t ) )
*/
- __pyx_t_15 = __Pyx_PyInt_From_int(__pyx_v_pre_p_c); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_PyInt_From_int(__pyx_v_pre_p_c); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_p); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_p); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_pre_v_c); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_pre_v_c); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyTuple_New(4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyTuple_New(4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_chrom);
@@ -18061,10 +18098,10 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_t_15 = 0;
__pyx_t_2 = 0;
__pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyString_Format(__pyx_kp_s_s_d_d_5f, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyString_Format(__pyx_kp_s_s_d_d_5f, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_encode); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_encode); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_3 = NULL;
@@ -18078,28 +18115,28 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
if (__pyx_t_3) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "bytes", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF_SET(__pyx_v_tmp_bytes, ((PyObject*)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1421
+ /* "MACS2/IO/CallPeakUnit.pyx":1422
* fprintf( ft, tmp_bytes )
* tmp_bytes = ("%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_c, p, pre_v_c )).encode()
* fprintf( fc, tmp_bytes ) # <<<<<<<<<<<<<<
* #t_write_func( "%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_t, p, pre_v_t ) )
* #c_write_func( "%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_c, p, pre_v_c ) )
*/
- __pyx_t_16 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_16) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_16) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
fprintf(__pyx_v_fc, __pyx_t_16);
- /* "MACS2/IO/CallPeakUnit.pyx":1425
+ /* "MACS2/IO/CallPeakUnit.pyx":1426
* #c_write_func( "%s\t%d\t%d\t%.5f\n" % ( chrom, pre_p_c, p, pre_v_c ) )
*
* return True # <<<<<<<<<<<<<<
@@ -18111,7 +18148,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_r = ((PyBoolObject *)Py_True);
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":1343
+ /* "MACS2/IO/CallPeakUnit.pyx":1344
*
*
* cdef bool __write_bedGraph_for_a_chromosome ( self, str chrom ): # <<<<<<<<<<<<<<
@@ -18149,7 +18186,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1427
+/* "MACS2/IO/CallPeakUnit.pyx":1428
* return True
*
* cpdef call_broadpeaks (self, list scoring_function_symbols, list lvl1_cutoff_s, list lvl2_cutoff_s, int min_length=200, int lvl1_max_gap=50, int lvl2_max_gap=400, bool auto_cutoff = False): # <<<<<<<<<<<<<<
@@ -18221,15 +18258,15 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
if (unlikely(__pyx_skip_dispatch)) ;
/* Check if overridden in Python */
else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) {
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_call_broadpeaks); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_call_broadpeaks); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_11call_broadpeaks)) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_min_length); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_min_length); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_lvl1_max_gap); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_lvl1_max_gap); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_lvl2_max_gap); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_lvl2_max_gap); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_t_1);
__pyx_t_6 = __pyx_t_1; __pyx_t_7 = NULL;
@@ -18244,7 +18281,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
__pyx_t_8 = 1;
}
}
- __pyx_t_9 = PyTuple_New(7+__pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyTuple_New(7+__pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
if (__pyx_t_7) {
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); __pyx_t_7 = NULL;
@@ -18270,7 +18307,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
__pyx_t_3 = 0;
__pyx_t_4 = 0;
__pyx_t_5 = 0;
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_9, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_9, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
@@ -18282,14 +18319,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1453
+ /* "MACS2/IO/CallPeakUnit.pyx":1454
* #int tmp_n
*
* lvl1peaks = PeakIO() # <<<<<<<<<<<<<<
* lvl2peaks = PeakIO()
*
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_PeakIO); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_PeakIO); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_6 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) {
@@ -18302,24 +18339,24 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
}
if (__pyx_t_6) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_lvl1peaks = __pyx_t_1;
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1454
+ /* "MACS2/IO/CallPeakUnit.pyx":1455
*
* lvl1peaks = PeakIO()
* lvl2peaks = PeakIO() # <<<<<<<<<<<<<<
*
* # prepare p-q table
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_PeakIO); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_PeakIO); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_6 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) {
@@ -18332,72 +18369,72 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
}
if (__pyx_t_6) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_lvl2peaks = __pyx_t_1;
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1457
+ /* "MACS2/IO/CallPeakUnit.pyx":1458
*
* # prepare p-q table
* if not self.pqtable: # <<<<<<<<<<<<<<
* logging.info("#3 Pre-compute pvalue-qvalue table...")
* if auto_cutoff:
*/
- __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_self->pqtable); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_self->pqtable); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_11 = ((!__pyx_t_10) != 0);
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1458
+ /* "MACS2/IO/CallPeakUnit.pyx":1459
* # prepare p-q table
* if not self.pqtable:
* logging.info("#3 Pre-compute pvalue-qvalue table...") # <<<<<<<<<<<<<<
* if auto_cutoff:
* logging.info("#3 Cutoff for broad region will be automatically decided!")
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1459; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1459; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__28, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__28, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1459; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1459
+ /* "MACS2/IO/CallPeakUnit.pyx":1460
* if not self.pqtable:
* logging.info("#3 Pre-compute pvalue-qvalue table...")
* if auto_cutoff: # <<<<<<<<<<<<<<
* logging.info("#3 Cutoff for broad region will be automatically decided!")
* self.__pre_computes( max_gap = lvl2_max_gap, min_length = min_length )
*/
- __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_auto_cutoff)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1459; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_auto_cutoff)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1460
+ /* "MACS2/IO/CallPeakUnit.pyx":1461
* logging.info("#3 Pre-compute pvalue-qvalue table...")
* if auto_cutoff:
* logging.info("#3 Cutoff for broad region will be automatically decided!") # <<<<<<<<<<<<<<
* self.__pre_computes( max_gap = lvl2_max_gap, min_length = min_length )
* else:
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__29, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__29, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1461
+ /* "MACS2/IO/CallPeakUnit.pyx":1462
* if auto_cutoff:
* logging.info("#3 Cutoff for broad region will be automatically decided!")
* self.__pre_computes( max_gap = lvl2_max_gap, min_length = min_length ) # <<<<<<<<<<<<<<
@@ -18407,21 +18444,21 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
__pyx_t_12.__pyx_n = 2;
__pyx_t_12.max_gap = __pyx_v_lvl2_max_gap;
__pyx_t_12.min_length = __pyx_v_min_length;
- __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___pre_computes(__pyx_v_self, &__pyx_t_12); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___pre_computes(__pyx_v_self, &__pyx_t_12); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L4;
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1463
+ /* "MACS2/IO/CallPeakUnit.pyx":1464
* self.__pre_computes( max_gap = lvl2_max_gap, min_length = min_length )
* else:
* self.__cal_pvalue_qvalue_table() # <<<<<<<<<<<<<<
*
* # prepare bedGraph file
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_pvalue_qvalue_table(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1463; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_pvalue_qvalue_table(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
@@ -18430,17 +18467,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
__pyx_L3:;
- /* "MACS2/IO/CallPeakUnit.pyx":1466
+ /* "MACS2/IO/CallPeakUnit.pyx":1467
*
* # prepare bedGraph file
* if self.save_bedGraph: # <<<<<<<<<<<<<<
*
* self.bedGraph_treat_f = fopen( self.bedGraph_treat_filename, "w" )
*/
- __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->save_bedGraph)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->save_bedGraph)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1468
+ /* "MACS2/IO/CallPeakUnit.pyx":1469
* if self.save_bedGraph:
*
* self.bedGraph_treat_f = fopen( self.bedGraph_treat_filename, "w" ) # <<<<<<<<<<<<<<
@@ -18449,7 +18486,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
*/
__pyx_v_self->bedGraph_treat_f = fopen(__pyx_v_self->bedGraph_treat_filename, __pyx_k_w);
- /* "MACS2/IO/CallPeakUnit.pyx":1469
+ /* "MACS2/IO/CallPeakUnit.pyx":1470
*
* self.bedGraph_treat_f = fopen( self.bedGraph_treat_filename, "w" )
* self.bedGraph_ctrl_f = fopen( self.bedGraph_control_filename, "w" ) # <<<<<<<<<<<<<<
@@ -18458,38 +18495,38 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
*/
__pyx_v_self->bedGraph_ctrl_f = fopen(__pyx_v_self->bedGraph_control_filename, __pyx_k_w);
- /* "MACS2/IO/CallPeakUnit.pyx":1470
+ /* "MACS2/IO/CallPeakUnit.pyx":1471
* self.bedGraph_treat_f = fopen( self.bedGraph_treat_filename, "w" )
* self.bedGraph_ctrl_f = fopen( self.bedGraph_control_filename, "w" )
* logging.info ("#3 In the peak calling step, the following will be performed simultaneously:") # <<<<<<<<<<<<<<
* logging.info ("#3 Write bedGraph files for treatment pileup (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_treat_pileup.bdg")
* logging.info ("#3 Write bedGraph files for control lambda (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_control_lambda.bdg")
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__30, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__30, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1471
+ /* "MACS2/IO/CallPeakUnit.pyx":1472
* self.bedGraph_ctrl_f = fopen( self.bedGraph_control_filename, "w" )
* logging.info ("#3 In the peak calling step, the following will be performed simultaneously:")
* logging.info ("#3 Write bedGraph files for treatment pileup (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_treat_pileup.bdg") # <<<<<<<<<<<<<<
* logging.info ("#3 Write bedGraph files for control lambda (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_control_lambda.bdg")
*
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_info); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_info); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_3_Write_bedGraph_files_for_trea, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_3_Write_bedGraph_files_for_trea, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyNumber_Add(__pyx_t_2, __pyx_kp_s_treat_pileup_bdg); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyNumber_Add(__pyx_t_2, __pyx_kp_s_treat_pileup_bdg); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = NULL;
@@ -18503,38 +18540,38 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
}
if (!__pyx_t_2) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_GOTREF(__pyx_t_1);
} else {
- __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = NULL;
PyTuple_SET_ITEM(__pyx_t_5, 0+1, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_9 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1472
+ /* "MACS2/IO/CallPeakUnit.pyx":1473
* logging.info ("#3 In the peak calling step, the following will be performed simultaneously:")
* logging.info ("#3 Write bedGraph files for treatment pileup (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_treat_pileup.bdg")
* logging.info ("#3 Write bedGraph files for control lambda (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_control_lambda.bdg") # <<<<<<<<<<<<<<
*
* if self.trackline:
*/
- __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_info); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_info); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyString_Format(__pyx_kp_s_3_Write_bedGraph_files_for_cont, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyString_Format(__pyx_kp_s_3_Write_bedGraph_files_for_cont, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_9 = PyNumber_Add(__pyx_t_6, __pyx_kp_s_control_lambda_bdg); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyNumber_Add(__pyx_t_6, __pyx_kp_s_control_lambda_bdg); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_t_6 = NULL;
@@ -18548,43 +18585,43 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
}
if (!__pyx_t_6) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_GOTREF(__pyx_t_1);
} else {
- __pyx_t_2 = PyTuple_New(1+1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1+1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_6 = NULL;
PyTuple_SET_ITEM(__pyx_t_2, 0+1, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_9 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1474
+ /* "MACS2/IO/CallPeakUnit.pyx":1475
* logging.info ("#3 Write bedGraph files for control lambda (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_control_lambda.bdg")
*
* if self.trackline: # <<<<<<<<<<<<<<
* # this line is REQUIRED by the wiggle format for UCSC browser
* tmp_bytes = ("track type=bedGraph name=\"treatment pileup\" description=\"treatment pileup after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode()
*/
- __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->trackline)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->trackline)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1475; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1476
+ /* "MACS2/IO/CallPeakUnit.pyx":1477
* if self.trackline:
* # this line is REQUIRED by the wiggle format for UCSC browser
* tmp_bytes = ("track type=bedGraph name=\"treatment pileup\" description=\"treatment pileup after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode() # <<<<<<<<<<<<<<
* fprintf( self.bedGraph_treat_f, tmp_bytes )
* tmp_bytes = ("track type=bedGraph name=\"control lambda\" description=\"control lambda after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode()
*/
- __pyx_t_5 = __Pyx_PyString_Format(__pyx_kp_s_track_type_bedGraph_name_treatme, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyString_Format(__pyx_kp_s_track_type_bedGraph_name_treatme, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_5 = NULL;
@@ -18598,36 +18635,36 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
}
if (__pyx_t_5) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_tmp_bytes = __pyx_t_1;
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1477
+ /* "MACS2/IO/CallPeakUnit.pyx":1478
* # this line is REQUIRED by the wiggle format for UCSC browser
* tmp_bytes = ("track type=bedGraph name=\"treatment pileup\" description=\"treatment pileup after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode()
* fprintf( self.bedGraph_treat_f, tmp_bytes ) # <<<<<<<<<<<<<<
* tmp_bytes = ("track type=bedGraph name=\"control lambda\" description=\"control lambda after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode()
* fprintf( self.bedGraph_ctrl_f, tmp_bytes )
*/
- __pyx_t_13 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1478; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
fprintf(__pyx_v_self->bedGraph_treat_f, __pyx_t_13);
- /* "MACS2/IO/CallPeakUnit.pyx":1478
+ /* "MACS2/IO/CallPeakUnit.pyx":1479
* tmp_bytes = ("track type=bedGraph name=\"treatment pileup\" description=\"treatment pileup after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode()
* fprintf( self.bedGraph_treat_f, tmp_bytes )
* tmp_bytes = ("track type=bedGraph name=\"control lambda\" description=\"control lambda after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode() # <<<<<<<<<<<<<<
* fprintf( self.bedGraph_ctrl_f, tmp_bytes )
*
*/
- __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_track_type_bedGraph_name_control, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1478; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_track_type_bedGraph_name_control, __pyx_v_self->bedGraph_filename_prefix); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_encode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1478; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_encode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = NULL;
@@ -18641,24 +18678,24 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
}
if (__pyx_t_2) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1478; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1478; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF_SET(__pyx_v_tmp_bytes, __pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1479
+ /* "MACS2/IO/CallPeakUnit.pyx":1480
* fprintf( self.bedGraph_treat_f, tmp_bytes )
* tmp_bytes = ("track type=bedGraph name=\"control lambda\" description=\"control lambda after possible scaling for \'%s\'\"\n" % self.bedGraph_filename_prefix).encode()
* fprintf( self.bedGraph_ctrl_f, tmp_bytes ) # <<<<<<<<<<<<<<
*
*
*/
- __pyx_t_13 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyObject_AsString(__pyx_v_tmp_bytes); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
fprintf(__pyx_v_self->bedGraph_ctrl_f, __pyx_t_13);
goto __pyx_L6;
}
@@ -18667,24 +18704,24 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
__pyx_L5:;
- /* "MACS2/IO/CallPeakUnit.pyx":1482
+ /* "MACS2/IO/CallPeakUnit.pyx":1483
*
*
* logging.info("#3 Call peaks for each chromosome...") # <<<<<<<<<<<<<<
* for chrom in self.chromosomes:
* self.__chrom_call_broadpeak_using_certain_criteria ( lvl1peaks, lvl2peaks, chrom, scoring_function_symbols, lvl1_cutoff_s, lvl2_cutoff_s, min_length, lvl1_max_gap, lvl2_max_gap, self.save_bedGraph )
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_info); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_tuple__31, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_tuple__31, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1483
+ /* "MACS2/IO/CallPeakUnit.pyx":1484
*
* logging.info("#3 Call peaks for each chromosome...")
* for chrom in self.chromosomes: # <<<<<<<<<<<<<<
@@ -18693,21 +18730,21 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
*/
if (unlikely(__pyx_v_self->chromosomes == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_1 = __pyx_v_self->chromosomes; __Pyx_INCREF(__pyx_t_1); __pyx_t_8 = 0;
for (;;) {
if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_1)) break;
#if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_5 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_5); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_5); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_5 = PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
- if (!(likely(PyString_CheckExact(__pyx_t_5))||((__pyx_t_5) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_5)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_5))||((__pyx_t_5) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_5)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_chrom, ((PyObject*)__pyx_t_5));
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1484
+ /* "MACS2/IO/CallPeakUnit.pyx":1485
* logging.info("#3 Call peaks for each chromosome...")
* for chrom in self.chromosomes:
* self.__chrom_call_broadpeak_using_certain_criteria ( lvl1peaks, lvl2peaks, chrom, scoring_function_symbols, lvl1_cutoff_s, lvl2_cutoff_s, min_length, lvl1_max_gap, lvl2_max_gap, self.save_bedGraph ) # <<<<<<<<<<<<<<
@@ -18716,12 +18753,12 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
*/
__pyx_t_5 = ((PyObject *)__pyx_v_self->save_bedGraph);
__Pyx_INCREF(__pyx_t_5);
- __pyx_t_2 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___chrom_call_broadpeak_using_certain_criteria(__pyx_v_self, __pyx_v_lvl1peaks, __pyx_v_lvl2peaks, __pyx_v_chrom, __pyx_v_scoring_function_symbols, __pyx_v_lvl1_cutoff_s, __pyx_v_lvl2_cutoff_s, __pyx_v_min_length, __pyx_v_lvl1_max_gap, __pyx_v_lvl2_max_gap, ((PyBoolObject *)__pyx_t_5)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __py [...]
+ __pyx_t_2 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___chrom_call_broadpeak_using_certain_criteria(__pyx_v_self, __pyx_v_lvl1peaks, __pyx_v_lvl2peaks, __pyx_v_chrom, __pyx_v_scoring_function_symbols, __pyx_v_lvl1_cutoff_s, __pyx_v_lvl2_cutoff_s, __pyx_v_min_length, __pyx_v_lvl1_max_gap, __pyx_v_lvl2_max_gap, ((PyBoolObject *)__pyx_t_5)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1485; __py [...]
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1483
+ /* "MACS2/IO/CallPeakUnit.pyx":1484
*
* logging.info("#3 Call peaks for each chromosome...")
* for chrom in self.chromosomes: # <<<<<<<<<<<<<<
@@ -18731,17 +18768,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1487
+ /* "MACS2/IO/CallPeakUnit.pyx":1488
*
* # close bedGraph file
* if self.save_bedGraph: # <<<<<<<<<<<<<<
* fclose( self.bedGraph_treat_f )
* fclose( self.bedGraph_ctrl_f )
*/
- __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->save_bedGraph)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->save_bedGraph)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1488
+ /* "MACS2/IO/CallPeakUnit.pyx":1489
* # close bedGraph file
* if self.save_bedGraph:
* fclose( self.bedGraph_treat_f ) # <<<<<<<<<<<<<<
@@ -18750,7 +18787,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
*/
fclose(__pyx_v_self->bedGraph_treat_f);
- /* "MACS2/IO/CallPeakUnit.pyx":1489
+ /* "MACS2/IO/CallPeakUnit.pyx":1490
* if self.save_bedGraph:
* fclose( self.bedGraph_treat_f )
* fclose( self.bedGraph_ctrl_f ) # <<<<<<<<<<<<<<
@@ -18759,7 +18796,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
*/
fclose(__pyx_v_self->bedGraph_ctrl_f);
- /* "MACS2/IO/CallPeakUnit.pyx":1491
+ /* "MACS2/IO/CallPeakUnit.pyx":1492
* fclose( self.bedGraph_ctrl_f )
* #self.bedGraph_ctrl.close()
* self.save_bedGraph = False # <<<<<<<<<<<<<<
@@ -18775,14 +18812,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
__pyx_L9:;
- /* "MACS2/IO/CallPeakUnit.pyx":1494
+ /* "MACS2/IO/CallPeakUnit.pyx":1495
*
* # now combine lvl1 and lvl2 peaks
* chrs = lvl1peaks.get_chr_names() # <<<<<<<<<<<<<<
* broadpeaks = BroadPeakIO()
* # use lvl2_peaks as linking regions between lvl1_peaks
*/
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_lvl1peaks, __pyx_n_s_get_chr_names); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_lvl1peaks, __pyx_n_s_get_chr_names); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_5 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_2))) {
@@ -18795,25 +18832,25 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
}
if (__pyx_t_5) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (!(likely(PyList_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyList_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_chrs = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1495
+ /* "MACS2/IO/CallPeakUnit.pyx":1496
* # now combine lvl1 and lvl2 peaks
* chrs = lvl1peaks.get_chr_names()
* broadpeaks = BroadPeakIO() # <<<<<<<<<<<<<<
* # use lvl2_peaks as linking regions between lvl1_peaks
* for chrom in chrs:
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_BroadPeakIO); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_BroadPeakIO); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1496; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_5 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) {
@@ -18826,17 +18863,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
}
if (__pyx_t_5) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1496; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1496; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_broadpeaks = __pyx_t_1;
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1497
+ /* "MACS2/IO/CallPeakUnit.pyx":1498
* broadpeaks = BroadPeakIO()
* # use lvl2_peaks as linking regions between lvl1_peaks
* for chrom in chrs: # <<<<<<<<<<<<<<
@@ -18845,21 +18882,21 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
*/
if (unlikely(__pyx_v_chrs == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1497; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_1 = __pyx_v_chrs; __Pyx_INCREF(__pyx_t_1); __pyx_t_8 = 0;
for (;;) {
if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_1)) break;
#if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1497; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_8); __Pyx_INCREF(__pyx_t_2); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1497; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
- if (!(likely(PyString_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1497; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_chrom, ((PyObject*)__pyx_t_2));
__pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1498
+ /* "MACS2/IO/CallPeakUnit.pyx":1499
* # use lvl2_peaks as linking regions between lvl1_peaks
* for chrom in chrs:
* tmp_n = 0 # <<<<<<<<<<<<<<
@@ -18868,14 +18905,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
*/
__pyx_v_tmp_n = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1499
+ /* "MACS2/IO/CallPeakUnit.pyx":1500
* for chrom in chrs:
* tmp_n = 0
* lvl1peakschrom = lvl1peaks.get_data_from_chrom(chrom) # <<<<<<<<<<<<<<
* lvl2peakschrom = lvl2peaks.get_data_from_chrom(chrom)
* lvl1peakschrom_next = iter(lvl1peakschrom).next
*/
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_lvl1peaks, __pyx_n_s_get_data_from_chrom); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_lvl1peaks, __pyx_n_s_get_data_from_chrom); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_9 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_5))) {
@@ -18888,16 +18925,16 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
}
if (!__pyx_t_9) {
- __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_v_chrom); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_v_chrom); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
} else {
- __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_9); __Pyx_GIVEREF(__pyx_t_9); __pyx_t_9 = NULL;
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_6, 0+1, __pyx_v_chrom);
__Pyx_GIVEREF(__pyx_v_chrom);
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_6, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
}
@@ -18905,14 +18942,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
__Pyx_XDECREF_SET(__pyx_v_lvl1peakschrom, __pyx_t_2);
__pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1500
+ /* "MACS2/IO/CallPeakUnit.pyx":1501
* tmp_n = 0
* lvl1peakschrom = lvl1peaks.get_data_from_chrom(chrom)
* lvl2peakschrom = lvl2peaks.get_data_from_chrom(chrom) # <<<<<<<<<<<<<<
* lvl1peakschrom_next = iter(lvl1peakschrom).next
* tmppeakset = [] # to temporarily store lvl1 region inside a lvl2 region
*/
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_lvl2peaks, __pyx_n_s_get_data_from_chrom); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_lvl2peaks, __pyx_n_s_get_data_from_chrom); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_6 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_5))) {
@@ -18925,16 +18962,16 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
}
if (!__pyx_t_6) {
- __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_v_chrom); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_v_chrom); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
} else {
- __pyx_t_9 = PyTuple_New(1+1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyTuple_New(1+1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_6 = NULL;
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_9, 0+1, __pyx_v_chrom);
__Pyx_GIVEREF(__pyx_v_chrom);
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_9, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_9, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
}
@@ -18942,34 +18979,34 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
__Pyx_XDECREF_SET(__pyx_v_lvl2peakschrom, __pyx_t_2);
__pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1501
+ /* "MACS2/IO/CallPeakUnit.pyx":1502
* lvl1peakschrom = lvl1peaks.get_data_from_chrom(chrom)
* lvl2peakschrom = lvl2peaks.get_data_from_chrom(chrom)
* lvl1peakschrom_next = iter(lvl1peakschrom).next # <<<<<<<<<<<<<<
* tmppeakset = [] # to temporarily store lvl1 region inside a lvl2 region
* # our assumption is lvl1 regions should be included in lvl2 regions
*/
- __pyx_t_2 = PyObject_GetIter(__pyx_v_lvl1peakschrom); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetIter(__pyx_v_lvl1peakschrom); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_next); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_next); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF_SET(__pyx_v_lvl1peakschrom_next, __pyx_t_5);
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1502
+ /* "MACS2/IO/CallPeakUnit.pyx":1503
* lvl2peakschrom = lvl2peaks.get_data_from_chrom(chrom)
* lvl1peakschrom_next = iter(lvl1peakschrom).next
* tmppeakset = [] # to temporarily store lvl1 region inside a lvl2 region # <<<<<<<<<<<<<<
* # our assumption is lvl1 regions should be included in lvl2 regions
* try:
*/
- __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1503; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_XDECREF_SET(__pyx_v_tmppeakset, ((PyObject*)__pyx_t_5));
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1504
+ /* "MACS2/IO/CallPeakUnit.pyx":1505
* tmppeakset = [] # to temporarily store lvl1 region inside a lvl2 region
* # our assumption is lvl1 regions should be included in lvl2 regions
* try: # <<<<<<<<<<<<<<
@@ -18983,7 +19020,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
__Pyx_XGOTREF(__pyx_t_16);
/*try:*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1505
+ /* "MACS2/IO/CallPeakUnit.pyx":1506
* # our assumption is lvl1 regions should be included in lvl2 regions
* try:
* lvl1 = lvl1peakschrom_next() # <<<<<<<<<<<<<<
@@ -19002,40 +19039,40 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
}
if (__pyx_t_9) {
- __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_9); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1505; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
+ __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_9); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1506; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
} else {
- __pyx_t_5 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1505; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
+ __pyx_t_5 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1506; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF_SET(__pyx_v_lvl1, __pyx_t_5);
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1506
+ /* "MACS2/IO/CallPeakUnit.pyx":1507
* try:
* lvl1 = lvl1peakschrom_next()
* for i in range( len(lvl2peakschrom) ): # <<<<<<<<<<<<<<
* # for each lvl2 peak, find all lvl1 peaks inside
* # I assume lvl1 peaks can be ALL covered by lvl2 peaks.
*/
- __pyx_t_17 = PyObject_Length(__pyx_v_lvl2peakschrom); if (unlikely(__pyx_t_17 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1506; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
+ __pyx_t_17 = PyObject_Length(__pyx_v_lvl2peakschrom); if (unlikely(__pyx_t_17 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1507; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) {
__pyx_v_i = __pyx_t_18;
- /* "MACS2/IO/CallPeakUnit.pyx":1509
+ /* "MACS2/IO/CallPeakUnit.pyx":1510
* # for each lvl2 peak, find all lvl1 peaks inside
* # I assume lvl1 peaks can be ALL covered by lvl2 peaks.
* lvl2 = lvl2peakschrom[i] # <<<<<<<<<<<<<<
*
* while True:
*/
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_lvl2peakschrom, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1509; __pyx_clineno = __LINE__; goto __pyx_L12_error;};
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_lvl2peakschrom, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1510; __pyx_clineno = __LINE__; goto __pyx_L12_error;};
__Pyx_GOTREF(__pyx_t_5);
__Pyx_XDECREF_SET(__pyx_v_lvl2, __pyx_t_5);
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1511
+ /* "MACS2/IO/CallPeakUnit.pyx":1512
* lvl2 = lvl2peakschrom[i]
*
* while True: # <<<<<<<<<<<<<<
@@ -19044,50 +19081,50 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
*/
while (1) {
- /* "MACS2/IO/CallPeakUnit.pyx":1512
+ /* "MACS2/IO/CallPeakUnit.pyx":1513
*
* while True:
* if lvl2["start"] <= lvl1["start"] and lvl1["end"] <= lvl2["end"]: # <<<<<<<<<<<<<<
* tmppeakset.append(lvl1)
* lvl1 = lvl1peakschrom_next()
*/
- __pyx_t_5 = PyObject_GetItem(__pyx_v_lvl2, __pyx_n_s_start); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1512; __pyx_clineno = __LINE__; goto __pyx_L12_error;};
+ __pyx_t_5 = PyObject_GetItem(__pyx_v_lvl2, __pyx_n_s_start); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1513; __pyx_clineno = __LINE__; goto __pyx_L12_error;};
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyObject_GetItem(__pyx_v_lvl1, __pyx_n_s_start); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1512; __pyx_clineno = __LINE__; goto __pyx_L12_error;};
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_lvl1, __pyx_n_s_start); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1513; __pyx_clineno = __LINE__; goto __pyx_L12_error;};
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyObject_RichCompare(__pyx_t_5, __pyx_t_2, Py_LE); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1512; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
+ __pyx_t_9 = PyObject_RichCompare(__pyx_t_5, __pyx_t_2, Py_LE); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1513; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1512; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1513; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_10) {
} else {
__pyx_t_11 = __pyx_t_10;
goto __pyx_L25_bool_binop_done;
}
- __pyx_t_9 = PyObject_GetItem(__pyx_v_lvl1, __pyx_n_s_end); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1512; __pyx_clineno = __LINE__; goto __pyx_L12_error;};
+ __pyx_t_9 = PyObject_GetItem(__pyx_v_lvl1, __pyx_n_s_end); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1513; __pyx_clineno = __LINE__; goto __pyx_L12_error;};
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_2 = PyObject_GetItem(__pyx_v_lvl2, __pyx_n_s_end); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1512; __pyx_clineno = __LINE__; goto __pyx_L12_error;};
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_lvl2, __pyx_n_s_end); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1513; __pyx_clineno = __LINE__; goto __pyx_L12_error;};
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_9, __pyx_t_2, Py_LE); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1512; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_9, __pyx_t_2, Py_LE); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1513; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1512; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1513; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_11 = __pyx_t_10;
__pyx_L25_bool_binop_done:;
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1513
+ /* "MACS2/IO/CallPeakUnit.pyx":1514
* while True:
* if lvl2["start"] <= lvl1["start"] and lvl1["end"] <= lvl2["end"]:
* tmppeakset.append(lvl1) # <<<<<<<<<<<<<<
* lvl1 = lvl1peakschrom_next()
* else:
*/
- __pyx_t_19 = __Pyx_PyList_Append(__pyx_v_tmppeakset, __pyx_v_lvl1); if (unlikely(__pyx_t_19 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1513; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
+ __pyx_t_19 = __Pyx_PyList_Append(__pyx_v_tmppeakset, __pyx_v_lvl1); if (unlikely(__pyx_t_19 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1514; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
- /* "MACS2/IO/CallPeakUnit.pyx":1514
+ /* "MACS2/IO/CallPeakUnit.pyx":1515
* if lvl2["start"] <= lvl1["start"] and lvl1["end"] <= lvl2["end"]:
* tmppeakset.append(lvl1)
* lvl1 = lvl1peakschrom_next() # <<<<<<<<<<<<<<
@@ -19106,10 +19143,10 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
}
if (__pyx_t_9) {
- __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_9); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1514; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
+ __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_9); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1515; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
} else {
- __pyx_t_5 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1514; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
+ __pyx_t_5 = __Pyx_PyObject_CallNoArg(__pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1515; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -19119,30 +19156,30 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1518
+ /* "MACS2/IO/CallPeakUnit.pyx":1519
* # make a hierarchical broad peak
* #print lvl2["start"], lvl2["end"], lvl2["score"]
* self.__add_broadpeak ( broadpeaks, chrom, lvl2, tmppeakset) # <<<<<<<<<<<<<<
* #tmp_n += 1
* tmppeakset = []
*/
- __pyx_t_5 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___add_broadpeak(__pyx_v_self, __pyx_v_broadpeaks, __pyx_v_chrom, __pyx_v_lvl2, __pyx_v_tmppeakset); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1518; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
+ __pyx_t_5 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___add_broadpeak(__pyx_v_self, __pyx_v_broadpeaks, __pyx_v_chrom, __pyx_v_lvl2, __pyx_v_tmppeakset); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1519; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1520
+ /* "MACS2/IO/CallPeakUnit.pyx":1521
* self.__add_broadpeak ( broadpeaks, chrom, lvl2, tmppeakset)
* #tmp_n += 1
* tmppeakset = [] # <<<<<<<<<<<<<<
* break
* except StopIteration:
*/
- __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1520; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
+ __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1521; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF_SET(__pyx_v_tmppeakset, ((PyObject*)__pyx_t_5));
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1521
+ /* "MACS2/IO/CallPeakUnit.pyx":1522
* #tmp_n += 1
* tmppeakset = []
* break # <<<<<<<<<<<<<<
@@ -19169,7 +19206,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1522
+ /* "MACS2/IO/CallPeakUnit.pyx":1523
* tmppeakset = []
* break
* except StopIteration: # <<<<<<<<<<<<<<
@@ -19179,56 +19216,56 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
__pyx_t_18 = PyErr_ExceptionMatches(__pyx_builtin_StopIteration);
if (__pyx_t_18) {
__Pyx_AddTraceback("MACS2.IO.CallPeakUnit.CallerFromAlignments.call_broadpeaks", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_2, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1522; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;}
+ if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_2, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1523; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_9);
- /* "MACS2/IO/CallPeakUnit.pyx":1524
+ /* "MACS2/IO/CallPeakUnit.pyx":1525
* except StopIteration:
* # no more strong (aka lvl1) peaks left
* self.__add_broadpeak ( broadpeaks, chrom, lvl2, tmppeakset) # <<<<<<<<<<<<<<
* #tmp_n += 1
* tmppeakset = []
*/
- if (unlikely(!__pyx_v_lvl2)) { __Pyx_RaiseUnboundLocalError("lvl2"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1524; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;} }
- __pyx_t_6 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___add_broadpeak(__pyx_v_self, __pyx_v_broadpeaks, __pyx_v_chrom, __pyx_v_lvl2, __pyx_v_tmppeakset); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1524; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;}
+ if (unlikely(!__pyx_v_lvl2)) { __Pyx_RaiseUnboundLocalError("lvl2"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1525; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;} }
+ __pyx_t_6 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___add_broadpeak(__pyx_v_self, __pyx_v_broadpeaks, __pyx_v_chrom, __pyx_v_lvl2, __pyx_v_tmppeakset); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1525; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1526
+ /* "MACS2/IO/CallPeakUnit.pyx":1527
* self.__add_broadpeak ( broadpeaks, chrom, lvl2, tmppeakset)
* #tmp_n += 1
* tmppeakset = [] # <<<<<<<<<<<<<<
* # add the rest lvl2 peaks
* for j in range( i+1, len(lvl2peakschrom) ):
*/
- __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1526; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;}
+ __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1527; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF_SET(__pyx_v_tmppeakset, ((PyObject*)__pyx_t_6));
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1528
+ /* "MACS2/IO/CallPeakUnit.pyx":1529
* tmppeakset = []
* # add the rest lvl2 peaks
* for j in range( i+1, len(lvl2peakschrom) ): # <<<<<<<<<<<<<<
* self.__add_broadpeak( broadpeaks, chrom, lvl2peakschrom[j], tmppeakset )
* #tmp_n += 1
*/
- __pyx_t_17 = PyObject_Length(__pyx_v_lvl2peakschrom); if (unlikely(__pyx_t_17 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1528; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;}
+ __pyx_t_17 = PyObject_Length(__pyx_v_lvl2peakschrom); if (unlikely(__pyx_t_17 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1529; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;}
for (__pyx_t_18 = (__pyx_v_i + 1); __pyx_t_18 < __pyx_t_17; __pyx_t_18+=1) {
__pyx_v_j = __pyx_t_18;
- /* "MACS2/IO/CallPeakUnit.pyx":1529
+ /* "MACS2/IO/CallPeakUnit.pyx":1530
* # add the rest lvl2 peaks
* for j in range( i+1, len(lvl2peakschrom) ):
* self.__add_broadpeak( broadpeaks, chrom, lvl2peakschrom[j], tmppeakset ) # <<<<<<<<<<<<<<
* #tmp_n += 1
* #print len(lvl1peakschrom), len(lvl2peakschrom), tmp_n
*/
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_lvl2peakschrom, __pyx_v_j, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1529; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;};
+ __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_lvl2peakschrom, __pyx_v_j, int, 1, __Pyx_PyInt_From_int, 0, 1, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1530; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;};
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_4 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___add_broadpeak(__pyx_v_self, __pyx_v_broadpeaks, __pyx_v_chrom, __pyx_t_6, __pyx_v_tmppeakset); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1529; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;}
+ __pyx_t_4 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___add_broadpeak(__pyx_v_self, __pyx_v_broadpeaks, __pyx_v_chrom, __pyx_t_6, __pyx_v_tmppeakset); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1530; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -19253,7 +19290,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
__pyx_L19_try_end:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1497
+ /* "MACS2/IO/CallPeakUnit.pyx":1498
* broadpeaks = BroadPeakIO()
* # use lvl2_peaks as linking regions between lvl1_peaks
* for chrom in chrs: # <<<<<<<<<<<<<<
@@ -19263,7 +19300,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1533
+ /* "MACS2/IO/CallPeakUnit.pyx":1534
* #print len(lvl1peakschrom), len(lvl2peakschrom), tmp_n
*
* return broadpeaks # <<<<<<<<<<<<<<
@@ -19275,7 +19312,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
__pyx_r = __pyx_v_broadpeaks;
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":1427
+ /* "MACS2/IO/CallPeakUnit.pyx":1428
* return True
*
* cpdef call_broadpeaks (self, list scoring_function_symbols, list lvl1_cutoff_s, list lvl2_cutoff_s, int min_length=200, int lvl1_max_gap=50, int lvl2_max_gap=400, bool auto_cutoff = False): # <<<<<<<<<<<<<<
@@ -19356,12 +19393,12 @@ static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_11cal
case 1:
if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_lvl1_cutoff_s)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("call_broadpeaks", 0, 3, 7, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("call_broadpeaks", 0, 3, 7, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_lvl2_cutoff_s)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("call_broadpeaks", 0, 3, 7, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("call_broadpeaks", 0, 3, 7, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
if (kw_args > 0) {
@@ -19385,7 +19422,7 @@ static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_11cal
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "call_broadpeaks") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "call_broadpeaks") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -19404,17 +19441,17 @@ static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_11cal
__pyx_v_lvl1_cutoff_s = ((PyObject*)values[1]);
__pyx_v_lvl2_cutoff_s = ((PyObject*)values[2]);
if (values[3]) {
- __pyx_v_min_length = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_min_length == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_min_length = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_min_length == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_min_length = ((int)200);
}
if (values[4]) {
- __pyx_v_lvl1_max_gap = __Pyx_PyInt_As_int(values[4]); if (unlikely((__pyx_v_lvl1_max_gap == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_lvl1_max_gap = __Pyx_PyInt_As_int(values[4]); if (unlikely((__pyx_v_lvl1_max_gap == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_lvl1_max_gap = ((int)50);
}
if (values[5]) {
- __pyx_v_lvl2_max_gap = __Pyx_PyInt_As_int(values[5]); if (unlikely((__pyx_v_lvl2_max_gap == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_lvl2_max_gap = __Pyx_PyInt_As_int(values[5]); if (unlikely((__pyx_v_lvl2_max_gap == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_lvl2_max_gap = ((int)400);
}
@@ -19422,16 +19459,16 @@ static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_11cal
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("call_broadpeaks", 0, 3, 7, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("call_broadpeaks", 0, 3, 7, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("MACS2.IO.CallPeakUnit.CallerFromAlignments.call_broadpeaks", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_scoring_function_symbols), (&PyList_Type), 1, "scoring_function_symbols", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_lvl1_cutoff_s), (&PyList_Type), 1, "lvl1_cutoff_s", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_lvl2_cutoff_s), (&PyList_Type), 1, "lvl2_cutoff_s", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_auto_cutoff), __pyx_ptype_7cpython_4bool_bool, 1, "auto_cutoff", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_scoring_function_symbols), (&PyList_Type), 1, "scoring_function_symbols", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_lvl1_cutoff_s), (&PyList_Type), 1, "lvl1_cutoff_s", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_lvl2_cutoff_s), (&PyList_Type), 1, "lvl2_cutoff_s", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_auto_cutoff), __pyx_ptype_7cpython_4bool_bool, 1, "auto_cutoff", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = __pyx_pf_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_10call_broadpeaks(((struct __pyx_obj_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self), __pyx_v_scoring_function_symbols, __pyx_v_lvl1_cutoff_s, __pyx_v_lvl2_cutoff_s, __pyx_v_min_length, __pyx_v_lvl1_max_gap, __pyx_v_lvl2_max_gap, __pyx_v_auto_cutoff);
/* function exit code */
@@ -19458,7 +19495,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_10cal
__pyx_t_2.lvl1_max_gap = __pyx_v_lvl1_max_gap;
__pyx_t_2.lvl2_max_gap = __pyx_v_lvl2_max_gap;
__pyx_t_2.auto_cutoff = __pyx_v_auto_cutoff;
- __pyx_t_1 = __pyx_vtabptr_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments->call_broadpeaks(__pyx_v_self, __pyx_v_scoring_function_symbols, __pyx_v_lvl1_cutoff_s, __pyx_v_lvl2_cutoff_s, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_vtabptr_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments->call_broadpeaks(__pyx_v_self, __pyx_v_scoring_function_symbols, __pyx_v_lvl1_cutoff_s, __pyx_v_lvl2_cutoff_s, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -19475,7 +19512,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_10cal
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1535
+/* "MACS2/IO/CallPeakUnit.pyx":1536
* return broadpeaks
*
* cdef __chrom_call_broadpeak_using_certain_criteria ( self, lvl1peaks, lvl2peaks, str chrom, list scoring_function_s, list lvl1_cutoff_s, list lvl2_cutoff_s, # <<<<<<<<<<<<<<
@@ -19526,7 +19563,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__chrom_call_broadpeak_using_certain_criteria", 0);
- /* "MACS2/IO/CallPeakUnit.pyx":1559
+ /* "MACS2/IO/CallPeakUnit.pyx":1560
* float32_t * ctrl_array_ptr
*
* assert len(scoring_function_s) == len(lvl1_cutoff_s), "number of functions and cutoffs should be the same!" # <<<<<<<<<<<<<<
@@ -19537,22 +19574,22 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
if (unlikely(!Py_OptimizeFlag)) {
if (unlikely(__pyx_v_scoring_function_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = PyList_GET_SIZE(__pyx_v_scoring_function_s); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_GET_SIZE(__pyx_v_scoring_function_s); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(__pyx_v_lvl1_cutoff_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_2 = PyList_GET_SIZE(__pyx_v_lvl1_cutoff_s); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_GET_SIZE(__pyx_v_lvl1_cutoff_s); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(!((__pyx_t_1 == __pyx_t_2) != 0))) {
PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_number_of_functions_and_cutoffs);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
}
#endif
- /* "MACS2/IO/CallPeakUnit.pyx":1560
+ /* "MACS2/IO/CallPeakUnit.pyx":1561
*
* assert len(scoring_function_s) == len(lvl1_cutoff_s), "number of functions and cutoffs should be the same!"
* assert len(scoring_function_s) == len(lvl2_cutoff_s), "number of functions and cutoffs should be the same!" # <<<<<<<<<<<<<<
@@ -19563,33 +19600,33 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
if (unlikely(!Py_OptimizeFlag)) {
if (unlikely(__pyx_v_scoring_function_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_2 = PyList_GET_SIZE(__pyx_v_scoring_function_s); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_GET_SIZE(__pyx_v_scoring_function_s); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(__pyx_v_lvl2_cutoff_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = PyList_GET_SIZE(__pyx_v_lvl2_cutoff_s); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_GET_SIZE(__pyx_v_lvl2_cutoff_s); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(!((__pyx_t_2 == __pyx_t_1) != 0))) {
PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_number_of_functions_and_cutoffs);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
}
#endif
- /* "MACS2/IO/CallPeakUnit.pyx":1563
+ /* "MACS2/IO/CallPeakUnit.pyx":1564
*
* # first, build pileup, self.chr_pos_treat_ctrl
* self.__pileup_treat_ctrl_a_chromosome( chrom ) # <<<<<<<<<<<<<<
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl
*
*/
- __pyx_t_3 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___pileup_treat_ctrl_a_chromosome(__pyx_v_self, __pyx_v_chrom); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___pileup_treat_ctrl_a_chromosome(__pyx_v_self, __pyx_v_chrom); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1564
+ /* "MACS2/IO/CallPeakUnit.pyx":1565
* # first, build pileup, self.chr_pos_treat_ctrl
* self.__pileup_treat_ctrl_a_chromosome( chrom )
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl # <<<<<<<<<<<<<<
@@ -19608,7 +19645,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
if (unlikely(size != 3)) {
if (size > 3) __Pyx_RaiseTooManyValuesError(3);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
__pyx_t_4 = PyList_GET_ITEM(sequence, 0);
@@ -19618,20 +19655,20 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__Pyx_INCREF(__pyx_t_5);
__Pyx_INCREF(__pyx_t_6);
#else
- __pyx_t_4 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
#endif
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
} else {
- __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_pos_array = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
__pyx_v_treat_array = ((PyArrayObject *)__pyx_t_5);
@@ -19639,43 +19676,43 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_v_ctrl_array = ((PyArrayObject *)__pyx_t_6);
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1567
+ /* "MACS2/IO/CallPeakUnit.pyx":1568
*
* # while save_bedGraph is true, invoke __write_bedGraph_for_a_chromosome
* if save_bedGraph: # <<<<<<<<<<<<<<
* self.__write_bedGraph_for_a_chromosome ( chrom )
*
*/
- __pyx_t_7 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_save_bedGraph)); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_save_bedGraph)); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1568; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_7) {
- /* "MACS2/IO/CallPeakUnit.pyx":1568
+ /* "MACS2/IO/CallPeakUnit.pyx":1569
* # while save_bedGraph is true, invoke __write_bedGraph_for_a_chromosome
* if save_bedGraph:
* self.__write_bedGraph_for_a_chromosome ( chrom ) # <<<<<<<<<<<<<<
*
* # keep all types of scores needed
*/
- __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___write_bedGraph_for_a_chromosome(__pyx_v_self, __pyx_v_chrom)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1568; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___write_bedGraph_for_a_chromosome(__pyx_v_self, __pyx_v_chrom)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L3;
}
__pyx_L3:;
- /* "MACS2/IO/CallPeakUnit.pyx":1571
+ /* "MACS2/IO/CallPeakUnit.pyx":1572
*
* # keep all types of scores needed
* score_array_s = [] # <<<<<<<<<<<<<<
* for i in range(len(scoring_function_s)):
* s = scoring_function_s[i]
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1571; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_v_score_array_s = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1572
+ /* "MACS2/IO/CallPeakUnit.pyx":1573
* # keep all types of scores needed
* score_array_s = []
* for i in range(len(scoring_function_s)): # <<<<<<<<<<<<<<
@@ -19684,13 +19721,13 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
if (unlikely(__pyx_v_scoring_function_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = PyList_GET_SIZE(__pyx_v_scoring_function_s); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_GET_SIZE(__pyx_v_scoring_function_s); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_1; __pyx_t_8+=1) {
__pyx_v_i = __pyx_t_8;
- /* "MACS2/IO/CallPeakUnit.pyx":1573
+ /* "MACS2/IO/CallPeakUnit.pyx":1574
* score_array_s = []
* for i in range(len(scoring_function_s)):
* s = scoring_function_s[i] # <<<<<<<<<<<<<<
@@ -19699,141 +19736,141 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
if (unlikely(__pyx_v_scoring_function_s == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_scoring_function_s, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1573; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_scoring_function_s, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1574; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- if (!(likely(PyString_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_s, ((PyObject*)__pyx_t_3));
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1574
+ /* "MACS2/IO/CallPeakUnit.pyx":1575
* for i in range(len(scoring_function_s)):
* s = scoring_function_s[i]
* if s == 'p': # <<<<<<<<<<<<<<
* score_array_s.append( self.__cal_pscore( treat_array, ctrl_array ) )
* elif s == 'q':
*/
- __pyx_t_7 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_p, Py_EQ)); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_p, Py_EQ)); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1575; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_9 = (__pyx_t_7 != 0);
if (__pyx_t_9) {
- /* "MACS2/IO/CallPeakUnit.pyx":1575
+ /* "MACS2/IO/CallPeakUnit.pyx":1576
* s = scoring_function_s[i]
* if s == 'p':
* score_array_s.append( self.__cal_pscore( treat_array, ctrl_array ) ) # <<<<<<<<<<<<<<
* elif s == 'q':
* score_array_s.append( self.__cal_qscore( treat_array, ctrl_array ) )
*/
- __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_pscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1575; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_pscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1575; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L6;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1576
+ /* "MACS2/IO/CallPeakUnit.pyx":1577
* if s == 'p':
* score_array_s.append( self.__cal_pscore( treat_array, ctrl_array ) )
* elif s == 'q': # <<<<<<<<<<<<<<
* score_array_s.append( self.__cal_qscore( treat_array, ctrl_array ) )
* elif s == 'f':
*/
- __pyx_t_9 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_q, Py_EQ)); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_q, Py_EQ)); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1577; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = (__pyx_t_9 != 0);
if (__pyx_t_7) {
- /* "MACS2/IO/CallPeakUnit.pyx":1577
+ /* "MACS2/IO/CallPeakUnit.pyx":1578
* score_array_s.append( self.__cal_pscore( treat_array, ctrl_array ) )
* elif s == 'q':
* score_array_s.append( self.__cal_qscore( treat_array, ctrl_array ) ) # <<<<<<<<<<<<<<
* elif s == 'f':
* score_array_s.append( self.__cal_FE( treat_array, ctrl_array ) )
*/
- __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_qscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1577; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_qscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1577; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L6;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1578
+ /* "MACS2/IO/CallPeakUnit.pyx":1579
* elif s == 'q':
* score_array_s.append( self.__cal_qscore( treat_array, ctrl_array ) )
* elif s == 'f': # <<<<<<<<<<<<<<
* score_array_s.append( self.__cal_FE( treat_array, ctrl_array ) )
* elif s == 's':
*/
- __pyx_t_7 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_f, Py_EQ)); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_f, Py_EQ)); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_9 = (__pyx_t_7 != 0);
if (__pyx_t_9) {
- /* "MACS2/IO/CallPeakUnit.pyx":1579
+ /* "MACS2/IO/CallPeakUnit.pyx":1580
* score_array_s.append( self.__cal_qscore( treat_array, ctrl_array ) )
* elif s == 'f':
* score_array_s.append( self.__cal_FE( treat_array, ctrl_array ) ) # <<<<<<<<<<<<<<
* elif s == 's':
* score_array_s.append( self.__cal_subtraction( treat_array, ctrl_array ) )
*/
- __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_FE(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_FE(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1580; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1580; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L6;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1580
+ /* "MACS2/IO/CallPeakUnit.pyx":1581
* elif s == 'f':
* score_array_s.append( self.__cal_FE( treat_array, ctrl_array ) )
* elif s == 's': # <<<<<<<<<<<<<<
* score_array_s.append( self.__cal_subtraction( treat_array, ctrl_array ) )
*
*/
- __pyx_t_9 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_s, Py_EQ)); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1580; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = (__Pyx_PyString_Equals(__pyx_v_s, __pyx_n_s_s, Py_EQ)); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = (__pyx_t_9 != 0);
if (__pyx_t_7) {
- /* "MACS2/IO/CallPeakUnit.pyx":1581
+ /* "MACS2/IO/CallPeakUnit.pyx":1582
* score_array_s.append( self.__cal_FE( treat_array, ctrl_array ) )
* elif s == 's':
* score_array_s.append( self.__cal_subtraction( treat_array, ctrl_array ) ) # <<<<<<<<<<<<<<
*
* # lvl1 : strong peaks
*/
- __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_subtraction(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_subtraction(__pyx_v_self, ((PyArrayObject *)__pyx_v_treat_array), ((PyArrayObject *)__pyx_v_ctrl_array))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_score_array_s, __pyx_t_3); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L6;
}
__pyx_L6:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1584
+ /* "MACS2/IO/CallPeakUnit.pyx":1585
*
* # lvl1 : strong peaks
* peak_content = [] # to store points above cutoff # <<<<<<<<<<<<<<
*
* # get the regions with scores above cutoffs
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_v_peak_content = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1587
+ /* "MACS2/IO/CallPeakUnit.pyx":1588
*
* # get the regions with scores above cutoffs
* above_cutoff = np.nonzero( apply_multiple_cutoffs(score_array_s,lvl1_cutoff_s) )[0] # this is not an optimized method. It would be better to store score array in a 2-D ndarray? # <<<<<<<<<<<<<<
- * above_cutoff_index_array = np.arange(pos_array.shape[0])[above_cutoff] # indices
+ * above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff
*/
- __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_nonzero); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_nonzero); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = ((PyObject *)__pyx_f_5MACS2_2IO_12CallPeakUnit_apply_multiple_cutoffs(__pyx_v_score_array_s, __pyx_v_lvl1_cutoff_s)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = ((PyObject *)__pyx_f_5MACS2_2IO_12CallPeakUnit_apply_multiple_cutoffs(__pyx_v_score_array_s, __pyx_v_lvl1_cutoff_s)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_4 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_5))) {
@@ -19846,120 +19883,107 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
}
if (!__pyx_t_4) {
- __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_GOTREF(__pyx_t_3);
} else {
- __pyx_t_11 = PyTuple_New(1+1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyTuple_New(1+1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); __pyx_t_4 = NULL;
PyTuple_SET_ITEM(__pyx_t_11, 0+1, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_11, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_11, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1587; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_above_cutoff = ((PyArrayObject *)__pyx_t_5);
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1588
+ /* "MACS2/IO/CallPeakUnit.pyx":1589
* # get the regions with scores above cutoffs
* above_cutoff = np.nonzero( apply_multiple_cutoffs(score_array_s,lvl1_cutoff_s) )[0] # this is not an optimized method. It would be better to store score array in a 2-D ndarray?
- * above_cutoff_index_array = np.arange(pos_array.shape[0])[above_cutoff] # indices # <<<<<<<<<<<<<<
+ * above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices # <<<<<<<<<<<<<<
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
*/
- __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_arange); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_arange); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_5 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_pos_array->dimensions[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
+ PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_11, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_pos_array->dimensions[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = NULL;
- if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_11))) {
- __pyx_t_6 = PyMethod_GET_SELF(__pyx_t_11);
- if (likely(__pyx_t_6)) {
- PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_11);
- __Pyx_INCREF(__pyx_t_6);
- __Pyx_INCREF(function);
- __Pyx_DECREF_SET(__pyx_t_11, function);
- }
- }
- if (!__pyx_t_6) {
- __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_t_11, __pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_GOTREF(__pyx_t_5);
- } else {
- __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_6 = NULL;
- PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_4, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- }
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __pyx_t_11 = PyObject_GetItem(__pyx_t_5, ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_11 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (!(likely(((__pyx_t_11) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_11, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_above_cutoff_index_array = ((PyArrayObject *)__pyx_t_11);
- __pyx_t_11 = 0;
+ __pyx_t_5 = PyObject_GetItem(__pyx_t_6, ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1589; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_above_cutoff_index_array = ((PyArrayObject *)__pyx_t_5);
+ __pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1589
+ /* "MACS2/IO/CallPeakUnit.pyx":1590
* above_cutoff = np.nonzero( apply_multiple_cutoffs(score_array_s,lvl1_cutoff_s) )[0] # this is not an optimized method. It would be better to store score array in a 2-D ndarray?
- * above_cutoff_index_array = np.arange(pos_array.shape[0])[above_cutoff] # indices
+ * above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff # <<<<<<<<<<<<<<
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
*
*/
- __pyx_t_11 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_11 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1589; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_11);
- if (!(likely(((__pyx_t_11) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_11, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_above_cutoff_endpos = ((PyArrayObject *)__pyx_t_11);
- __pyx_t_11 = 0;
+ __pyx_t_5 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1590; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_5);
+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_above_cutoff_endpos = ((PyArrayObject *)__pyx_t_5);
+ __pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1590
- * above_cutoff_index_array = np.arange(pos_array.shape[0])[above_cutoff] # indices
+ /* "MACS2/IO/CallPeakUnit.pyx":1591
+ * above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff # <<<<<<<<<<<<<<
*
* if above_cutoff.size == 0:
*/
- __pyx_t_11 = PyNumber_Subtract(((PyObject *)__pyx_v_above_cutoff), __pyx_int_1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_11);
- __pyx_t_5 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), __pyx_t_11); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1590; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_5 = PyNumber_Subtract(((PyObject *)__pyx_v_above_cutoff), __pyx_int_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_above_cutoff_startpos = ((PyArrayObject *)__pyx_t_5);
- __pyx_t_5 = 0;
+ __pyx_t_6 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), __pyx_t_5); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1591; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_above_cutoff_startpos = ((PyArrayObject *)__pyx_t_6);
+ __pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1592
+ /* "MACS2/IO/CallPeakUnit.pyx":1593
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
*
* if above_cutoff.size == 0: # <<<<<<<<<<<<<<
* # nothing above cutoff
* return
*/
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff), __pyx_n_s_size); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_11 = PyObject_RichCompare(__pyx_t_5, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_11); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff), __pyx_n_s_size); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_6, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_11); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
if (__pyx_t_7) {
- /* "MACS2/IO/CallPeakUnit.pyx":1594
+ /* "MACS2/IO/CallPeakUnit.pyx":1595
* if above_cutoff.size == 0:
* # nothing above cutoff
* return # <<<<<<<<<<<<<<
@@ -19971,34 +19995,34 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
goto __pyx_L0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1596
+ /* "MACS2/IO/CallPeakUnit.pyx":1597
* return
*
* if above_cutoff[0] == 0: # <<<<<<<<<<<<<<
* # first element > cutoff, fix the first point as 0. otherwise it would be the last item in data[chrom]['pos']
* above_cutoff_startpos[0] = 0
*/
- __pyx_t_11 = __Pyx_GetItemInt(((PyObject *)__pyx_v_above_cutoff), 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_11 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_11);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_11, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetItemInt(((PyObject *)__pyx_v_above_cutoff), 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1597; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_5, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (__pyx_t_7) {
- /* "MACS2/IO/CallPeakUnit.pyx":1598
+ /* "MACS2/IO/CallPeakUnit.pyx":1599
* if above_cutoff[0] == 0:
* # first element > cutoff, fix the first point as 0. otherwise it would be the last item in data[chrom]['pos']
* above_cutoff_startpos[0] = 0 # <<<<<<<<<<<<<<
*
* # first bit of region above cutoff
*/
- if (unlikely(__Pyx_SetItemInt(((PyObject *)__pyx_v_above_cutoff_startpos), 0, __pyx_int_0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_SetItemInt(((PyObject *)__pyx_v_above_cutoff_startpos), 0, __pyx_int_0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1599; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L8;
}
__pyx_L8:;
- /* "MACS2/IO/CallPeakUnit.pyx":1601
+ /* "MACS2/IO/CallPeakUnit.pyx":1602
*
* # first bit of region above cutoff
* acs_ptr = <int32_t *>above_cutoff_startpos.data # <<<<<<<<<<<<<<
@@ -20007,7 +20031,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_acs_ptr = ((int32_t *)__pyx_v_above_cutoff_startpos->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1602
+ /* "MACS2/IO/CallPeakUnit.pyx":1603
* # first bit of region above cutoff
* acs_ptr = <int32_t *>above_cutoff_startpos.data
* ace_ptr = <int32_t *>above_cutoff_endpos.data # <<<<<<<<<<<<<<
@@ -20016,7 +20040,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ace_ptr = ((int32_t *)__pyx_v_above_cutoff_endpos->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1603
+ /* "MACS2/IO/CallPeakUnit.pyx":1604
* acs_ptr = <int32_t *>above_cutoff_startpos.data
* ace_ptr = <int32_t *>above_cutoff_endpos.data
* acia_ptr= <int32_t *>above_cutoff_index_array.data # <<<<<<<<<<<<<<
@@ -20025,7 +20049,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_acia_ptr = ((int32_t *)__pyx_v_above_cutoff_index_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1604
+ /* "MACS2/IO/CallPeakUnit.pyx":1605
* ace_ptr = <int32_t *>above_cutoff_endpos.data
* acia_ptr= <int32_t *>above_cutoff_index_array.data
* treat_array_ptr = <float32_t *> treat_array.data # <<<<<<<<<<<<<<
@@ -20034,7 +20058,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_treat_array_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_treat_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1605
+ /* "MACS2/IO/CallPeakUnit.pyx":1606
* acia_ptr= <int32_t *>above_cutoff_index_array.data
* treat_array_ptr = <float32_t *> treat_array.data
* ctrl_array_ptr = <float32_t *> ctrl_array.data # <<<<<<<<<<<<<<
@@ -20043,19 +20067,19 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ctrl_array_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_ctrl_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1607
+ /* "MACS2/IO/CallPeakUnit.pyx":1608
* ctrl_array_ptr = <float32_t *> ctrl_array.data
*
* ts = acs_ptr[ 0 ] # <<<<<<<<<<<<<<
* te = ace_ptr[ 0 ]
* ti = acia_ptr[ 0 ]
*/
- __pyx_t_5 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1607; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_v_ts = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_v_ts = __pyx_t_6;
+ __pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1608
+ /* "MACS2/IO/CallPeakUnit.pyx":1609
*
* ts = acs_ptr[ 0 ]
* te = ace_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -20064,7 +20088,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_te = (__pyx_v_ace_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1609
+ /* "MACS2/IO/CallPeakUnit.pyx":1610
* ts = acs_ptr[ 0 ]
* te = ace_ptr[ 0 ]
* ti = acia_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -20073,100 +20097,127 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ti = (__pyx_v_acia_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1610
+ /* "MACS2/IO/CallPeakUnit.pyx":1611
* te = ace_ptr[ 0 ]
* ti = acia_ptr[ 0 ]
* tp = treat_array_ptr[ ti ] # <<<<<<<<<<<<<<
* cp = ctrl_array_ptr[ ti ]
*
*/
- __pyx_t_5 = PyFloat_FromDouble((__pyx_v_treat_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_v_tp = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_t_6 = PyFloat_FromDouble((__pyx_v_treat_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_v_tp = __pyx_t_6;
+ __pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1611
+ /* "MACS2/IO/CallPeakUnit.pyx":1612
* ti = acia_ptr[ 0 ]
* tp = treat_array_ptr[ ti ]
* cp = ctrl_array_ptr[ ti ] # <<<<<<<<<<<<<<
*
* peak_content.append( ( ts, te, tp, cp, ti ) )
*/
- __pyx_t_5 = PyFloat_FromDouble((__pyx_v_ctrl_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_v_cp = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_t_6 = PyFloat_FromDouble((__pyx_v_ctrl_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_v_cp = __pyx_t_6;
+ __pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1613
+ /* "MACS2/IO/CallPeakUnit.pyx":1614
* cp = ctrl_array_ptr[ ti ]
*
* peak_content.append( ( ts, te, tp, cp, ti ) ) # <<<<<<<<<<<<<<
- * lastp = te
- *
+ * acs_ptr += 1 # move ptr
+ * ace_ptr += 1
*/
- __pyx_t_5 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_5 = __Pyx_PyInt_From_int32_t(__pyx_v_ti); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_11 = __Pyx_PyInt_From_int32_t(__pyx_v_ti); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyTuple_New(5); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_4 = PyTuple_New(5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(__pyx_v_ts);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_ts);
+ PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_v_ts);
__Pyx_GIVEREF(__pyx_v_ts);
- PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_11, 1, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
__Pyx_INCREF(__pyx_v_tp);
- PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_tp);
+ PyTuple_SET_ITEM(__pyx_t_11, 2, __pyx_v_tp);
__Pyx_GIVEREF(__pyx_v_tp);
__Pyx_INCREF(__pyx_v_cp);
- PyTuple_SET_ITEM(__pyx_t_4, 3, __pyx_v_cp);
+ PyTuple_SET_ITEM(__pyx_t_11, 3, __pyx_v_cp);
__Pyx_GIVEREF(__pyx_v_cp);
- PyTuple_SET_ITEM(__pyx_t_4, 4, __pyx_t_11);
- __Pyx_GIVEREF(__pyx_t_11);
+ PyTuple_SET_ITEM(__pyx_t_11, 4, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_6 = 0;
__pyx_t_5 = 0;
- __pyx_t_11 = 0;
- __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_4); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_11); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1614
+ /* "MACS2/IO/CallPeakUnit.pyx":1615
*
* peak_content.append( ( ts, te, tp, cp, ti ) )
+ * acs_ptr += 1 # move ptr # <<<<<<<<<<<<<<
+ * ace_ptr += 1
+ * acia_ptr+= 1
+ */
+ __pyx_v_acs_ptr = (__pyx_v_acs_ptr + 1);
+
+ /* "MACS2/IO/CallPeakUnit.pyx":1616
+ * peak_content.append( ( ts, te, tp, cp, ti ) )
+ * acs_ptr += 1 # move ptr
+ * ace_ptr += 1 # <<<<<<<<<<<<<<
+ * acia_ptr+= 1
+ * lastp = te
+ */
+ __pyx_v_ace_ptr = (__pyx_v_ace_ptr + 1);
+
+ /* "MACS2/IO/CallPeakUnit.pyx":1617
+ * acs_ptr += 1 # move ptr
+ * ace_ptr += 1
+ * acia_ptr+= 1 # <<<<<<<<<<<<<<
+ * lastp = te
+ *
+ */
+ __pyx_v_acia_ptr = (__pyx_v_acia_ptr + 1);
+
+ /* "MACS2/IO/CallPeakUnit.pyx":1618
+ * ace_ptr += 1
+ * acia_ptr+= 1
* lastp = te # <<<<<<<<<<<<<<
*
* #peak_content.append( (above_cutoff_startpos[0], above_cutoff_endpos[0], treat_array[above_cutoff_index_array[0]], ctrl_array[above_cutoff_index_array[0]], score_array_s, above_cutoff_index_array[0] ) )
*/
- __pyx_t_4 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_v_lastp = __pyx_t_4;
- __pyx_t_4 = 0;
+ __pyx_t_11 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __pyx_v_lastp = __pyx_t_11;
+ __pyx_t_11 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1617
+ /* "MACS2/IO/CallPeakUnit.pyx":1621
*
* #peak_content.append( (above_cutoff_startpos[0], above_cutoff_endpos[0], treat_array[above_cutoff_index_array[0]], ctrl_array[above_cutoff_index_array[0]], score_array_s, above_cutoff_index_array[0] ) )
* for i in range( 1, above_cutoff_startpos.size ): # <<<<<<<<<<<<<<
* ts = acs_ptr[ 0 ]
* te = ace_ptr[ 0 ]
*/
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff_startpos), __pyx_n_s_size); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_12 = __Pyx_PyInt_As_long(__pyx_t_4); if (unlikely((__pyx_t_12 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_11 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff_startpos), __pyx_n_s_size); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_12 = __Pyx_PyInt_As_long(__pyx_t_11); if (unlikely((__pyx_t_12 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
for (__pyx_t_8 = 1; __pyx_t_8 < __pyx_t_12; __pyx_t_8+=1) {
__pyx_v_i = __pyx_t_8;
- /* "MACS2/IO/CallPeakUnit.pyx":1618
+ /* "MACS2/IO/CallPeakUnit.pyx":1622
* #peak_content.append( (above_cutoff_startpos[0], above_cutoff_endpos[0], treat_array[above_cutoff_index_array[0]], ctrl_array[above_cutoff_index_array[0]], score_array_s, above_cutoff_index_array[0] ) )
* for i in range( 1, above_cutoff_startpos.size ):
* ts = acs_ptr[ 0 ] # <<<<<<<<<<<<<<
* te = ace_ptr[ 0 ]
* ti = acia_ptr[ 0 ]
*/
- __pyx_t_4 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF_SET(__pyx_v_ts, __pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_11 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF_SET(__pyx_v_ts, __pyx_t_11);
+ __pyx_t_11 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1619
+ /* "MACS2/IO/CallPeakUnit.pyx":1623
* for i in range( 1, above_cutoff_startpos.size ):
* ts = acs_ptr[ 0 ]
* te = ace_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -20175,7 +20226,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_te = (__pyx_v_ace_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1620
+ /* "MACS2/IO/CallPeakUnit.pyx":1624
* ts = acs_ptr[ 0 ]
* te = ace_ptr[ 0 ]
* ti = acia_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -20184,7 +20235,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ti = (__pyx_v_acia_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1621
+ /* "MACS2/IO/CallPeakUnit.pyx":1625
* te = ace_ptr[ 0 ]
* ti = acia_ptr[ 0 ]
* acs_ptr += 1 # <<<<<<<<<<<<<<
@@ -20193,7 +20244,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_acs_ptr = (__pyx_v_acs_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1622
+ /* "MACS2/IO/CallPeakUnit.pyx":1626
* ti = acia_ptr[ 0 ]
* acs_ptr += 1
* ace_ptr += 1 # <<<<<<<<<<<<<<
@@ -20202,7 +20253,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ace_ptr = (__pyx_v_ace_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1623
+ /* "MACS2/IO/CallPeakUnit.pyx":1627
* acs_ptr += 1
* ace_ptr += 1
* acia_ptr+= 1 # <<<<<<<<<<<<<<
@@ -20211,166 +20262,166 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_acia_ptr = (__pyx_v_acia_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1624
+ /* "MACS2/IO/CallPeakUnit.pyx":1628
* ace_ptr += 1
* acia_ptr+= 1
* tp = treat_array_ptr[ ti ] # <<<<<<<<<<<<<<
* cp = ctrl_array_ptr[ ti ]
* tl = ts - lastp
*/
- __pyx_t_4 = PyFloat_FromDouble((__pyx_v_treat_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF_SET(__pyx_v_tp, __pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_11 = PyFloat_FromDouble((__pyx_v_treat_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF_SET(__pyx_v_tp, __pyx_t_11);
+ __pyx_t_11 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1625
+ /* "MACS2/IO/CallPeakUnit.pyx":1629
* acia_ptr+= 1
* tp = treat_array_ptr[ ti ]
* cp = ctrl_array_ptr[ ti ] # <<<<<<<<<<<<<<
* tl = ts - lastp
* if tl <= lvl1_max_gap:
*/
- __pyx_t_4 = PyFloat_FromDouble((__pyx_v_ctrl_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF_SET(__pyx_v_cp, __pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_11 = PyFloat_FromDouble((__pyx_v_ctrl_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF_SET(__pyx_v_cp, __pyx_t_11);
+ __pyx_t_11 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1626
+ /* "MACS2/IO/CallPeakUnit.pyx":1630
* tp = treat_array_ptr[ ti ]
* cp = ctrl_array_ptr[ ti ]
* tl = ts - lastp # <<<<<<<<<<<<<<
* if tl <= lvl1_max_gap:
* # append
*/
- __pyx_t_4 = PyNumber_Subtract(__pyx_v_ts, __pyx_v_lastp); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_XDECREF_SET(__pyx_v_tl, __pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_11 = PyNumber_Subtract(__pyx_v_ts, __pyx_v_lastp); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_XDECREF_SET(__pyx_v_tl, __pyx_t_11);
+ __pyx_t_11 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1627
+ /* "MACS2/IO/CallPeakUnit.pyx":1631
* cp = ctrl_array_ptr[ ti ]
* tl = ts - lastp
* if tl <= lvl1_max_gap: # <<<<<<<<<<<<<<
* # append
* #peak_content.append( (above_cutoff_startpos[i], above_cutoff_endpos[i], treat_array[above_cutoff_index_array[i]], ctrl_array[above_cutoff_index_array[i]], score_array_s, above_cutoff_index_array[i] ) )
*/
- __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_lvl1_max_gap); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_11 = PyObject_RichCompare(__pyx_v_tl, __pyx_t_4, Py_LE); __Pyx_XGOTREF(__pyx_t_11); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_11); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyInt_From_int(__pyx_v_lvl1_max_gap); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_tl, __pyx_t_11, Py_LE); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_7) {
- /* "MACS2/IO/CallPeakUnit.pyx":1630
+ /* "MACS2/IO/CallPeakUnit.pyx":1634
* # append
* #peak_content.append( (above_cutoff_startpos[i], above_cutoff_endpos[i], treat_array[above_cutoff_index_array[i]], ctrl_array[above_cutoff_index_array[i]], score_array_s, above_cutoff_index_array[i] ) )
* peak_content.append( ( ts, te, tp, cp, ti ) ) # <<<<<<<<<<<<<<
* lastp = te
* else:
*/
- __pyx_t_11 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_11);
- __pyx_t_4 = __Pyx_PyInt_From_int32_t(__pyx_v_ti); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyTuple_New(5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_11 = __Pyx_PyInt_From_int32_t(__pyx_v_ti); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_6 = PyTuple_New(5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_INCREF(__pyx_v_ts);
- PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_ts);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_ts);
__Pyx_GIVEREF(__pyx_v_ts);
- PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_11);
- __Pyx_GIVEREF(__pyx_t_11);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
__Pyx_INCREF(__pyx_v_tp);
- PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_v_tp);
+ PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_v_tp);
__Pyx_GIVEREF(__pyx_v_tp);
__Pyx_INCREF(__pyx_v_cp);
- PyTuple_SET_ITEM(__pyx_t_5, 3, __pyx_v_cp);
+ PyTuple_SET_ITEM(__pyx_t_6, 3, __pyx_v_cp);
__Pyx_GIVEREF(__pyx_v_cp);
- PyTuple_SET_ITEM(__pyx_t_5, 4, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_6, 4, __pyx_t_11);
+ __Pyx_GIVEREF(__pyx_t_11);
+ __pyx_t_5 = 0;
__pyx_t_11 = 0;
- __pyx_t_4 = 0;
- __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_5); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_6); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1631
+ /* "MACS2/IO/CallPeakUnit.pyx":1635
* #peak_content.append( (above_cutoff_startpos[i], above_cutoff_endpos[i], treat_array[above_cutoff_index_array[i]], ctrl_array[above_cutoff_index_array[i]], score_array_s, above_cutoff_index_array[i] ) )
* peak_content.append( ( ts, te, tp, cp, ti ) )
* lastp = te # <<<<<<<<<<<<<<
* else:
* # close
*/
- __pyx_t_5 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF_SET(__pyx_v_lastp, __pyx_t_5);
- __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1635; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF_SET(__pyx_v_lastp, __pyx_t_6);
+ __pyx_t_6 = 0;
goto __pyx_L11;
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1634
+ /* "MACS2/IO/CallPeakUnit.pyx":1638
* else:
* # close
* self.__close_peak_for_broad_region (peak_content, lvl1peaks, min_length, chrom, lvl1_max_gap/2, score_array_s ) # <<<<<<<<<<<<<<
* #peak_content = [ (above_cutoff_startpos[i], above_cutoff_endpos[i], treat_array[above_cutoff_index_array[i]], ctrl_array[above_cutoff_index_array[i]], score_array_s, above_cutoff_index_array[i]) , ]
* peak_content = [ ( ts, te, tp, cp, ti ), ]
*/
- __pyx_t_5 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_for_broad_region(__pyx_v_self, __pyx_v_peak_content, __pyx_v_lvl1peaks, __pyx_v_min_length, __pyx_v_chrom, __Pyx_div_long(__pyx_v_lvl1_max_gap, 2), __pyx_v_score_array_s, NULL)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_for_broad_region(__pyx_v_self, __pyx_v_peak_content, __pyx_v_lvl1peaks, __pyx_v_min_length, __pyx_v_chrom, __Pyx_div_long(__pyx_v_lvl1_max_gap, 2), __pyx_v_score_array_s, NULL)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1638; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1636
+ /* "MACS2/IO/CallPeakUnit.pyx":1640
* self.__close_peak_for_broad_region (peak_content, lvl1peaks, min_length, chrom, lvl1_max_gap/2, score_array_s )
* #peak_content = [ (above_cutoff_startpos[i], above_cutoff_endpos[i], treat_array[above_cutoff_index_array[i]], ctrl_array[above_cutoff_index_array[i]], score_array_s, above_cutoff_index_array[i]) , ]
* peak_content = [ ( ts, te, tp, cp, ti ), ] # <<<<<<<<<<<<<<
* lastp = te #above_cutoff_endpos[i]
*
*/
- __pyx_t_5 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_4 = __Pyx_PyInt_From_int32_t(__pyx_v_ti); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_11 = PyTuple_New(5); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1640; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_11 = __Pyx_PyInt_From_int32_t(__pyx_v_ti); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1640; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_5 = PyTuple_New(5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1640; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_v_ts);
- PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_v_ts);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_ts);
__Pyx_GIVEREF(__pyx_v_ts);
- PyTuple_SET_ITEM(__pyx_t_11, 1, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
__Pyx_INCREF(__pyx_v_tp);
- PyTuple_SET_ITEM(__pyx_t_11, 2, __pyx_v_tp);
+ PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_v_tp);
__Pyx_GIVEREF(__pyx_v_tp);
__Pyx_INCREF(__pyx_v_cp);
- PyTuple_SET_ITEM(__pyx_t_11, 3, __pyx_v_cp);
+ PyTuple_SET_ITEM(__pyx_t_5, 3, __pyx_v_cp);
__Pyx_GIVEREF(__pyx_v_cp);
- PyTuple_SET_ITEM(__pyx_t_11, 4, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_5 = 0;
- __pyx_t_4 = 0;
- __pyx_t_4 = PyList_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyList_SET_ITEM(__pyx_t_4, 0, __pyx_t_11);
+ PyTuple_SET_ITEM(__pyx_t_5, 4, __pyx_t_11);
__Pyx_GIVEREF(__pyx_t_11);
+ __pyx_t_6 = 0;
+ __pyx_t_11 = 0;
+ __pyx_t_11 = PyList_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1640; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ PyList_SET_ITEM(__pyx_t_11, 0, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_5 = 0;
+ __Pyx_DECREF_SET(__pyx_v_peak_content, ((PyObject*)__pyx_t_11));
__pyx_t_11 = 0;
- __Pyx_DECREF_SET(__pyx_v_peak_content, ((PyObject*)__pyx_t_4));
- __pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1637
+ /* "MACS2/IO/CallPeakUnit.pyx":1641
* #peak_content = [ (above_cutoff_startpos[i], above_cutoff_endpos[i], treat_array[above_cutoff_index_array[i]], ctrl_array[above_cutoff_index_array[i]], score_array_s, above_cutoff_index_array[i]) , ]
* peak_content = [ ( ts, te, tp, cp, ti ), ]
* lastp = te #above_cutoff_endpos[i] # <<<<<<<<<<<<<<
*
* # save the last peak
*/
- __pyx_t_4 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1637; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF_SET(__pyx_v_lastp, __pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_11 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF_SET(__pyx_v_lastp, __pyx_t_11);
+ __pyx_t_11 = 0;
}
__pyx_L11:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1640
+ /* "MACS2/IO/CallPeakUnit.pyx":1644
*
* # save the last peak
* if peak_content: # <<<<<<<<<<<<<<
@@ -20380,171 +20431,158 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_t_7 = (__pyx_v_peak_content != Py_None) && (PyList_GET_SIZE(__pyx_v_peak_content) != 0);
if (__pyx_t_7) {
- /* "MACS2/IO/CallPeakUnit.pyx":1641
+ /* "MACS2/IO/CallPeakUnit.pyx":1645
* # save the last peak
* if peak_content:
* self.__close_peak_for_broad_region (peak_content, lvl1peaks, min_length, chrom, lvl1_max_gap/2, score_array_s ) # <<<<<<<<<<<<<<
*
* # lvl2 : weak peaks
*/
- __pyx_t_4 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_for_broad_region(__pyx_v_self, __pyx_v_peak_content, __pyx_v_lvl1peaks, __pyx_v_min_length, __pyx_v_chrom, __Pyx_div_long(__pyx_v_lvl1_max_gap, 2), __pyx_v_score_array_s, NULL)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_11 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_for_broad_region(__pyx_v_self, __pyx_v_peak_content, __pyx_v_lvl1peaks, __pyx_v_min_length, __pyx_v_chrom, __Pyx_div_long(__pyx_v_lvl1_max_gap, 2), __pyx_v_score_array_s, NULL)); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1645; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
goto __pyx_L12;
}
__pyx_L12:;
- /* "MACS2/IO/CallPeakUnit.pyx":1644
+ /* "MACS2/IO/CallPeakUnit.pyx":1648
*
* # lvl2 : weak peaks
* peak_content = [] # to store points above cutoff # <<<<<<<<<<<<<<
*
* # get the regions with scores above cutoffs
*/
- __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF_SET(__pyx_v_peak_content, ((PyObject*)__pyx_t_4));
- __pyx_t_4 = 0;
+ __pyx_t_11 = PyList_New(0); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF_SET(__pyx_v_peak_content, ((PyObject*)__pyx_t_11));
+ __pyx_t_11 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1647
+ /* "MACS2/IO/CallPeakUnit.pyx":1651
*
* # get the regions with scores above cutoffs
* above_cutoff = np.nonzero( apply_multiple_cutoffs(score_array_s,lvl2_cutoff_s) )[0] # this is not an optimized method. It would be better to store score array in a 2-D ndarray? # <<<<<<<<<<<<<<
- * above_cutoff_index_array = np.arange(pos_array.shape[0])[above_cutoff] # indices
+ * above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff
*/
- __pyx_t_11 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_11);
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_11, __pyx_n_s_nonzero); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_nonzero); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_5 = ((PyObject *)__pyx_f_5MACS2_2IO_12CallPeakUnit_apply_multiple_cutoffs(__pyx_v_score_array_s, __pyx_v_lvl2_cutoff_s)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __pyx_t_11 = ((PyObject *)__pyx_f_5MACS2_2IO_12CallPeakUnit_apply_multiple_cutoffs(__pyx_v_score_array_s, __pyx_v_lvl2_cutoff_s)); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_11);
__pyx_t_3 = NULL;
- if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_5))) {
- __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_5);
+ if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_6))) {
+ __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_6);
if (likely(__pyx_t_3)) {
- PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_5);
+ PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
__Pyx_INCREF(__pyx_t_3);
__Pyx_INCREF(function);
- __Pyx_DECREF_SET(__pyx_t_5, function);
+ __Pyx_DECREF_SET(__pyx_t_6, function);
}
}
if (!__pyx_t_3) {
- __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_11); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_11 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_5); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_GOTREF(__pyx_t_11);
} else {
- __pyx_t_6 = PyTuple_New(1+1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = NULL;
- PyTuple_SET_ITEM(__pyx_t_6, 0+1, __pyx_t_11);
- __Pyx_GIVEREF(__pyx_t_11);
- __pyx_t_11 = 0;
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_6, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = NULL;
+ PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_5 = 0;
+ __pyx_t_11 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_4, NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_4, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF_SET(__pyx_v_above_cutoff, ((PyArrayObject *)__pyx_t_5));
- __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_11, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1651; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF_SET(__pyx_v_above_cutoff, ((PyArrayObject *)__pyx_t_6));
+ __pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1648
+ /* "MACS2/IO/CallPeakUnit.pyx":1652
* # get the regions with scores above cutoffs
* above_cutoff = np.nonzero( apply_multiple_cutoffs(score_array_s,lvl2_cutoff_s) )[0] # this is not an optimized method. It would be better to store score array in a 2-D ndarray?
- * above_cutoff_index_array = np.arange(pos_array.shape[0])[above_cutoff] # indices # <<<<<<<<<<<<<<
+ * above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices # <<<<<<<<<<<<<<
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
*/
- __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_arange); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_pos_array->dimensions[0])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_11 = NULL;
- if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_6))) {
- __pyx_t_11 = PyMethod_GET_SELF(__pyx_t_6);
- if (likely(__pyx_t_11)) {
- PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
- __Pyx_INCREF(__pyx_t_11);
- __Pyx_INCREF(function);
- __Pyx_DECREF_SET(__pyx_t_6, function);
- }
- }
- if (!__pyx_t_11) {
- __pyx_t_5 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_GOTREF(__pyx_t_5);
- } else {
- __pyx_t_3 = PyTuple_New(1+1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_11); __Pyx_GIVEREF(__pyx_t_11); __pyx_t_11 = NULL;
- PyTuple_SET_ITEM(__pyx_t_3, 0+1, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_4 = 0;
- __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_3, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- }
+ __pyx_t_11 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_arange); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_6 = __Pyx_PyInt_From_Py_intptr_t((__pyx_v_pos_array->dimensions[0])); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_6 = 0;
+ __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_11, __pyx_t_4, __pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_GetItem(__pyx_t_5, ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1648; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_6 = PyObject_GetItem(__pyx_t_5, ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF_SET(__pyx_v_above_cutoff_index_array, ((PyArrayObject *)__pyx_t_6));
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1649
+ /* "MACS2/IO/CallPeakUnit.pyx":1653
* above_cutoff = np.nonzero( apply_multiple_cutoffs(score_array_s,lvl2_cutoff_s) )[0] # this is not an optimized method. It would be better to store score array in a 2-D ndarray?
- * above_cutoff_index_array = np.arange(pos_array.shape[0])[above_cutoff] # indices
+ * above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff # <<<<<<<<<<<<<<
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
*
*/
- __pyx_t_6 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_6 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), ((PyObject *)__pyx_v_above_cutoff)); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_6);
- if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF_SET(__pyx_v_above_cutoff_endpos, ((PyArrayObject *)__pyx_t_6));
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1650
- * above_cutoff_index_array = np.arange(pos_array.shape[0])[above_cutoff] # indices
+ /* "MACS2/IO/CallPeakUnit.pyx":1654
+ * above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices
* above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff # <<<<<<<<<<<<<<
*
* if above_cutoff.size == 0:
*/
- __pyx_t_6 = PyNumber_Subtract(((PyObject *)__pyx_v_above_cutoff), __pyx_int_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Subtract(((PyObject *)__pyx_v_above_cutoff), __pyx_int_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), __pyx_t_6); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_5 = PyObject_GetItem(((PyObject *)__pyx_v_pos_array), __pyx_t_6); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1654; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF_SET(__pyx_v_above_cutoff_startpos, ((PyArrayObject *)__pyx_t_5));
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1652
+ /* "MACS2/IO/CallPeakUnit.pyx":1656
* above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
*
* if above_cutoff.size == 0: # <<<<<<<<<<<<<<
* # nothing above cutoff
* return
*/
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff), __pyx_n_s_size); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff), __pyx_n_s_size); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyObject_RichCompare(__pyx_t_5, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_5, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (__pyx_t_7) {
- /* "MACS2/IO/CallPeakUnit.pyx":1654
+ /* "MACS2/IO/CallPeakUnit.pyx":1658
* if above_cutoff.size == 0:
* # nothing above cutoff
* return # <<<<<<<<<<<<<<
@@ -20556,34 +20594,34 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
goto __pyx_L0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1656
+ /* "MACS2/IO/CallPeakUnit.pyx":1660
* return
*
* if above_cutoff[0] == 0: # <<<<<<<<<<<<<<
* # first element > cutoff, fix the first point as 0. otherwise it would be the last item in data[chrom]['pos']
* above_cutoff_startpos[0] = 0
*/
- __pyx_t_6 = __Pyx_GetItemInt(((PyObject *)__pyx_v_above_cutoff), 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1656; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_6 = __Pyx_GetItemInt(((PyObject *)__pyx_v_above_cutoff), 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1660; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_6, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_6, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_7) {
- /* "MACS2/IO/CallPeakUnit.pyx":1658
+ /* "MACS2/IO/CallPeakUnit.pyx":1662
* if above_cutoff[0] == 0:
* # first element > cutoff, fix the first point as 0. otherwise it would be the last item in data[chrom]['pos']
* above_cutoff_startpos[0] = 0 # <<<<<<<<<<<<<<
*
* # first bit of region above cutoff
*/
- if (unlikely(__Pyx_SetItemInt(((PyObject *)__pyx_v_above_cutoff_startpos), 0, __pyx_int_0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_SetItemInt(((PyObject *)__pyx_v_above_cutoff_startpos), 0, __pyx_int_0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L14;
}
__pyx_L14:;
- /* "MACS2/IO/CallPeakUnit.pyx":1661
+ /* "MACS2/IO/CallPeakUnit.pyx":1665
*
* # first bit of region above cutoff
* acs_ptr = <int32_t *>above_cutoff_startpos.data # <<<<<<<<<<<<<<
@@ -20592,7 +20630,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_acs_ptr = ((int32_t *)__pyx_v_above_cutoff_startpos->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1662
+ /* "MACS2/IO/CallPeakUnit.pyx":1666
* # first bit of region above cutoff
* acs_ptr = <int32_t *>above_cutoff_startpos.data
* ace_ptr = <int32_t *>above_cutoff_endpos.data # <<<<<<<<<<<<<<
@@ -20601,7 +20639,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ace_ptr = ((int32_t *)__pyx_v_above_cutoff_endpos->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1663
+ /* "MACS2/IO/CallPeakUnit.pyx":1667
* acs_ptr = <int32_t *>above_cutoff_startpos.data
* ace_ptr = <int32_t *>above_cutoff_endpos.data
* acia_ptr= <int32_t *>above_cutoff_index_array.data # <<<<<<<<<<<<<<
@@ -20610,7 +20648,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_acia_ptr = ((int32_t *)__pyx_v_above_cutoff_index_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1664
+ /* "MACS2/IO/CallPeakUnit.pyx":1668
* ace_ptr = <int32_t *>above_cutoff_endpos.data
* acia_ptr= <int32_t *>above_cutoff_index_array.data
* treat_array_ptr = <float32_t *> treat_array.data # <<<<<<<<<<<<<<
@@ -20619,7 +20657,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_treat_array_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_treat_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1665
+ /* "MACS2/IO/CallPeakUnit.pyx":1669
* acia_ptr= <int32_t *>above_cutoff_index_array.data
* treat_array_ptr = <float32_t *> treat_array.data
* ctrl_array_ptr = <float32_t *> ctrl_array.data # <<<<<<<<<<<<<<
@@ -20628,19 +20666,19 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ctrl_array_ptr = ((__pyx_t_5MACS2_2IO_12CallPeakUnit_float32_t *)__pyx_v_ctrl_array->data);
- /* "MACS2/IO/CallPeakUnit.pyx":1667
+ /* "MACS2/IO/CallPeakUnit.pyx":1671
* ctrl_array_ptr = <float32_t *> ctrl_array.data
*
* ts = acs_ptr[ 0 ] # <<<<<<<<<<<<<<
* te = ace_ptr[ 0 ]
* ti = acia_ptr[ 0 ]
*/
- __pyx_t_5 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF_SET(__pyx_v_ts, __pyx_t_5);
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1668
+ /* "MACS2/IO/CallPeakUnit.pyx":1672
*
* ts = acs_ptr[ 0 ]
* te = ace_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -20649,7 +20687,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_te = (__pyx_v_ace_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1669
+ /* "MACS2/IO/CallPeakUnit.pyx":1673
* ts = acs_ptr[ 0 ]
* te = ace_ptr[ 0 ]
* ti = acia_ptr[ 0 ] # <<<<<<<<<<<<<<
@@ -20658,207 +20696,234 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ti = (__pyx_v_acia_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1670
+ /* "MACS2/IO/CallPeakUnit.pyx":1674
* te = ace_ptr[ 0 ]
* ti = acia_ptr[ 0 ]
* tp = treat_array_ptr[ ti ] # <<<<<<<<<<<<<<
* cp = ctrl_array_ptr[ ti ]
- *
+ * peak_content.append( ( ts, te, tp, cp, ti ) )
*/
- __pyx_t_5 = PyFloat_FromDouble((__pyx_v_treat_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyFloat_FromDouble((__pyx_v_treat_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF_SET(__pyx_v_tp, __pyx_t_5);
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1671
+ /* "MACS2/IO/CallPeakUnit.pyx":1675
* ti = acia_ptr[ 0 ]
* tp = treat_array_ptr[ ti ]
* cp = ctrl_array_ptr[ ti ] # <<<<<<<<<<<<<<
- *
* peak_content.append( ( ts, te, tp, cp, ti ) )
+ * acs_ptr += 1 # move ptr
*/
- __pyx_t_5 = PyFloat_FromDouble((__pyx_v_ctrl_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyFloat_FromDouble((__pyx_v_ctrl_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF_SET(__pyx_v_cp, __pyx_t_5);
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1673
+ /* "MACS2/IO/CallPeakUnit.pyx":1676
+ * tp = treat_array_ptr[ ti ]
* cp = ctrl_array_ptr[ ti ]
- *
* peak_content.append( ( ts, te, tp, cp, ti ) ) # <<<<<<<<<<<<<<
- * lastp = te
- * for i in range( 1, above_cutoff_startpos.size ):
+ * acs_ptr += 1 # move ptr
+ * ace_ptr += 1
*/
- __pyx_t_5 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = __Pyx_PyInt_From_int32_t(__pyx_v_ti); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_From_int32_t(__pyx_v_ti); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_3 = PyTuple_New(5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = PyTuple_New(5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(__pyx_v_ts);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_ts);
+ PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_ts);
__Pyx_GIVEREF(__pyx_v_ts);
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__Pyx_INCREF(__pyx_v_tp);
- PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_v_tp);
+ PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_tp);
__Pyx_GIVEREF(__pyx_v_tp);
__Pyx_INCREF(__pyx_v_cp);
- PyTuple_SET_ITEM(__pyx_t_3, 3, __pyx_v_cp);
+ PyTuple_SET_ITEM(__pyx_t_4, 3, __pyx_v_cp);
__Pyx_GIVEREF(__pyx_v_cp);
- PyTuple_SET_ITEM(__pyx_t_3, 4, __pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_4, 4, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_5 = 0;
__pyx_t_6 = 0;
- __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_3); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_4); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1674
- *
+ /* "MACS2/IO/CallPeakUnit.pyx":1677
+ * cp = ctrl_array_ptr[ ti ]
* peak_content.append( ( ts, te, tp, cp, ti ) )
+ * acs_ptr += 1 # move ptr # <<<<<<<<<<<<<<
+ * ace_ptr += 1
+ * acia_ptr+= 1
+ */
+ __pyx_v_acs_ptr = (__pyx_v_acs_ptr + 1);
+
+ /* "MACS2/IO/CallPeakUnit.pyx":1678
+ * peak_content.append( ( ts, te, tp, cp, ti ) )
+ * acs_ptr += 1 # move ptr
+ * ace_ptr += 1 # <<<<<<<<<<<<<<
+ * acia_ptr+= 1
+ *
+ */
+ __pyx_v_ace_ptr = (__pyx_v_ace_ptr + 1);
+
+ /* "MACS2/IO/CallPeakUnit.pyx":1679
+ * acs_ptr += 1 # move ptr
+ * ace_ptr += 1
+ * acia_ptr+= 1 # <<<<<<<<<<<<<<
+ *
+ * lastp = te
+ */
+ __pyx_v_acia_ptr = (__pyx_v_acia_ptr + 1);
+
+ /* "MACS2/IO/CallPeakUnit.pyx":1681
+ * acia_ptr+= 1
+ *
* lastp = te # <<<<<<<<<<<<<<
* for i in range( 1, above_cutoff_startpos.size ):
- * ts = acs_ptr[ 0 ]
+ * # for everything above cutoff
*/
- __pyx_t_3 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF_SET(__pyx_v_lastp, __pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_4 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF_SET(__pyx_v_lastp, __pyx_t_4);
+ __pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1675
- * peak_content.append( ( ts, te, tp, cp, ti ) )
+ /* "MACS2/IO/CallPeakUnit.pyx":1682
+ *
* lastp = te
* for i in range( 1, above_cutoff_startpos.size ): # <<<<<<<<<<<<<<
- * ts = acs_ptr[ 0 ]
- * te = ace_ptr[ 0 ]
+ * # for everything above cutoff
+ * ts = acs_ptr[ 0 ] # get the start
*/
- __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff_startpos), __pyx_n_s_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_12 = __Pyx_PyInt_As_long(__pyx_t_3); if (unlikely((__pyx_t_12 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_above_cutoff_startpos), __pyx_n_s_size); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_12 = __Pyx_PyInt_As_long(__pyx_t_4); if (unlikely((__pyx_t_12 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
for (__pyx_t_8 = 1; __pyx_t_8 < __pyx_t_12; __pyx_t_8+=1) {
__pyx_v_i = __pyx_t_8;
- /* "MACS2/IO/CallPeakUnit.pyx":1676
- * lastp = te
+ /* "MACS2/IO/CallPeakUnit.pyx":1684
* for i in range( 1, above_cutoff_startpos.size ):
- * ts = acs_ptr[ 0 ] # <<<<<<<<<<<<<<
- * te = ace_ptr[ 0 ]
- * ti = acia_ptr[ 0 ]
+ * # for everything above cutoff
+ * ts = acs_ptr[ 0 ] # get the start # <<<<<<<<<<<<<<
+ * te = ace_ptr[ 0 ] # get the end
+ * ti = acia_ptr[ 0 ]# get the index
*/
- __pyx_t_3 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF_SET(__pyx_v_ts, __pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_4 = __Pyx_PyInt_From_int32_t((__pyx_v_acs_ptr[0])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF_SET(__pyx_v_ts, __pyx_t_4);
+ __pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1677
- * for i in range( 1, above_cutoff_startpos.size ):
- * ts = acs_ptr[ 0 ]
- * te = ace_ptr[ 0 ] # <<<<<<<<<<<<<<
- * ti = acia_ptr[ 0 ]
- * acs_ptr += 1
+ /* "MACS2/IO/CallPeakUnit.pyx":1685
+ * # for everything above cutoff
+ * ts = acs_ptr[ 0 ] # get the start
+ * te = ace_ptr[ 0 ] # get the end # <<<<<<<<<<<<<<
+ * ti = acia_ptr[ 0 ]# get the index
+ *
*/
__pyx_v_te = (__pyx_v_ace_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1678
- * ts = acs_ptr[ 0 ]
- * te = ace_ptr[ 0 ]
- * ti = acia_ptr[ 0 ] # <<<<<<<<<<<<<<
- * acs_ptr += 1
- * ace_ptr += 1
+ /* "MACS2/IO/CallPeakUnit.pyx":1686
+ * ts = acs_ptr[ 0 ] # get the start
+ * te = ace_ptr[ 0 ] # get the end
+ * ti = acia_ptr[ 0 ]# get the index # <<<<<<<<<<<<<<
+ *
+ * acs_ptr += 1 # move ptr
*/
__pyx_v_ti = (__pyx_v_acia_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1679
- * te = ace_ptr[ 0 ]
- * ti = acia_ptr[ 0 ]
- * acs_ptr += 1 # <<<<<<<<<<<<<<
+ /* "MACS2/IO/CallPeakUnit.pyx":1688
+ * ti = acia_ptr[ 0 ]# get the index
+ *
+ * acs_ptr += 1 # move ptr # <<<<<<<<<<<<<<
* ace_ptr += 1
* acia_ptr+= 1
*/
__pyx_v_acs_ptr = (__pyx_v_acs_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1680
- * ti = acia_ptr[ 0 ]
- * acs_ptr += 1
+ /* "MACS2/IO/CallPeakUnit.pyx":1689
+ *
+ * acs_ptr += 1 # move ptr
* ace_ptr += 1 # <<<<<<<<<<<<<<
* acia_ptr+= 1
- * tp = treat_array_ptr[ ti ]
+ * tp = treat_array_ptr[ ti ] # get the treatment pileup
*/
__pyx_v_ace_ptr = (__pyx_v_ace_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1681
- * acs_ptr += 1
+ /* "MACS2/IO/CallPeakUnit.pyx":1690
+ * acs_ptr += 1 # move ptr
* ace_ptr += 1
* acia_ptr+= 1 # <<<<<<<<<<<<<<
- * tp = treat_array_ptr[ ti ]
- * cp = ctrl_array_ptr[ ti ]
+ * tp = treat_array_ptr[ ti ] # get the treatment pileup
+ * cp = ctrl_array_ptr[ ti ] # get the control pileup
*/
__pyx_v_acia_ptr = (__pyx_v_acia_ptr + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1682
+ /* "MACS2/IO/CallPeakUnit.pyx":1691
* ace_ptr += 1
* acia_ptr+= 1
- * tp = treat_array_ptr[ ti ] # <<<<<<<<<<<<<<
- * cp = ctrl_array_ptr[ ti ]
- * tl = ts - lastp
+ * tp = treat_array_ptr[ ti ] # get the treatment pileup # <<<<<<<<<<<<<<
+ * cp = ctrl_array_ptr[ ti ] # get the control pileup
+ * tl = ts - lastp # get the distance from the current point to last position of existing peak_content
*/
- __pyx_t_3 = PyFloat_FromDouble((__pyx_v_treat_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF_SET(__pyx_v_tp, __pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_4 = PyFloat_FromDouble((__pyx_v_treat_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF_SET(__pyx_v_tp, __pyx_t_4);
+ __pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1683
+ /* "MACS2/IO/CallPeakUnit.pyx":1692
* acia_ptr+= 1
- * tp = treat_array_ptr[ ti ]
- * cp = ctrl_array_ptr[ ti ] # <<<<<<<<<<<<<<
- * tl = ts - lastp
- * if tl <= lvl2_max_gap:
+ * tp = treat_array_ptr[ ti ] # get the treatment pileup
+ * cp = ctrl_array_ptr[ ti ] # get the control pileup # <<<<<<<<<<<<<<
+ * tl = ts - lastp # get the distance from the current point to last position of existing peak_content
+ *
*/
- __pyx_t_3 = PyFloat_FromDouble((__pyx_v_ctrl_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1683; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF_SET(__pyx_v_cp, __pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_4 = PyFloat_FromDouble((__pyx_v_ctrl_array_ptr[__pyx_v_ti])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF_SET(__pyx_v_cp, __pyx_t_4);
+ __pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1684
- * tp = treat_array_ptr[ ti ]
- * cp = ctrl_array_ptr[ ti ]
- * tl = ts - lastp # <<<<<<<<<<<<<<
+ /* "MACS2/IO/CallPeakUnit.pyx":1693
+ * tp = treat_array_ptr[ ti ] # get the treatment pileup
+ * cp = ctrl_array_ptr[ ti ] # get the control pileup
+ * tl = ts - lastp # get the distance from the current point to last position of existing peak_content # <<<<<<<<<<<<<<
+ *
* if tl <= lvl2_max_gap:
- * # append
*/
- __pyx_t_3 = PyNumber_Subtract(__pyx_v_ts, __pyx_v_lastp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_XDECREF_SET(__pyx_v_tl, __pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_4 = PyNumber_Subtract(__pyx_v_ts, __pyx_v_lastp); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1693; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_XDECREF_SET(__pyx_v_tl, __pyx_t_4);
+ __pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1685
- * cp = ctrl_array_ptr[ ti ]
- * tl = ts - lastp
+ /* "MACS2/IO/CallPeakUnit.pyx":1695
+ * tl = ts - lastp # get the distance from the current point to last position of existing peak_content
+ *
* if tl <= lvl2_max_gap: # <<<<<<<<<<<<<<
* # append
* peak_content.append( ( ts, te, tp, cp, ti ) )
*/
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_lvl2_max_gap); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = PyObject_RichCompare(__pyx_v_tl, __pyx_t_3, Py_LE); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_lvl2_max_gap); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_6 = PyObject_RichCompare(__pyx_v_tl, __pyx_t_4, Py_LE); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (__pyx_t_7) {
- /* "MACS2/IO/CallPeakUnit.pyx":1687
+ /* "MACS2/IO/CallPeakUnit.pyx":1697
* if tl <= lvl2_max_gap:
* # append
* peak_content.append( ( ts, te, tp, cp, ti ) ) # <<<<<<<<<<<<<<
* lastp = te
* else:
*/
- __pyx_t_6 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_3 = __Pyx_PyInt_From_int32_t(__pyx_v_ti); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyTuple_New(5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_From_int32_t(__pyx_v_ti); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_5 = PyTuple_New(5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_v_ts);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_ts);
@@ -20871,21 +20936,21 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__Pyx_INCREF(__pyx_v_cp);
PyTuple_SET_ITEM(__pyx_t_5, 3, __pyx_v_cp);
__Pyx_GIVEREF(__pyx_v_cp);
- PyTuple_SET_ITEM(__pyx_t_5, 4, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_5, 4, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
__pyx_t_6 = 0;
- __pyx_t_3 = 0;
- __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_5); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = 0;
+ __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_peak_content, __pyx_t_5); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1688
+ /* "MACS2/IO/CallPeakUnit.pyx":1698
* # append
* peak_content.append( ( ts, te, tp, cp, ti ) )
* lastp = te # <<<<<<<<<<<<<<
* else:
* # close
*/
- __pyx_t_5 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF_SET(__pyx_v_lastp, __pyx_t_5);
__pyx_t_5 = 0;
@@ -20893,29 +20958,29 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1691
+ /* "MACS2/IO/CallPeakUnit.pyx":1701
* else:
* # close
* self.__close_peak_for_broad_region (peak_content, lvl2peaks, min_length, chrom, lvl2_max_gap/2, score_array_s ) # <<<<<<<<<<<<<<
+ *
* peak_content = [ ( ts, te, tp, cp, ti ), ]
- * lastp = te
*/
- __pyx_t_5 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_for_broad_region(__pyx_v_self, __pyx_v_peak_content, __pyx_v_lvl2peaks, __pyx_v_min_length, __pyx_v_chrom, __Pyx_div_long(__pyx_v_lvl2_max_gap, 2), __pyx_v_score_array_s, NULL)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_for_broad_region(__pyx_v_self, __pyx_v_peak_content, __pyx_v_lvl2peaks, __pyx_v_min_length, __pyx_v_chrom, __Pyx_div_long(__pyx_v_lvl2_max_gap, 2), __pyx_v_score_array_s, NULL)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1692
- * # close
+ /* "MACS2/IO/CallPeakUnit.pyx":1703
* self.__close_peak_for_broad_region (peak_content, lvl2peaks, min_length, chrom, lvl2_max_gap/2, score_array_s )
+ *
* peak_content = [ ( ts, te, tp, cp, ti ), ] # <<<<<<<<<<<<<<
* lastp = te
*
*/
- __pyx_t_5 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = __Pyx_PyInt_From_int32_t(__pyx_v_ti); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = PyTuple_New(5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_From_int32_t(__pyx_v_ti); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_6 = PyTuple_New(5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_INCREF(__pyx_v_ts);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_ts);
@@ -20928,34 +20993,34 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__Pyx_INCREF(__pyx_v_cp);
PyTuple_SET_ITEM(__pyx_t_6, 3, __pyx_v_cp);
__Pyx_GIVEREF(__pyx_v_cp);
- PyTuple_SET_ITEM(__pyx_t_6, 4, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_6, 4, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
__pyx_t_5 = 0;
- __pyx_t_3 = 0;
- __pyx_t_3 = PyList_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyList_SET_ITEM(__pyx_t_3, 0, __pyx_t_6);
+ __pyx_t_4 = 0;
+ __pyx_t_4 = PyList_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ PyList_SET_ITEM(__pyx_t_4, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __Pyx_DECREF_SET(__pyx_v_peak_content, ((PyObject*)__pyx_t_3));
- __pyx_t_3 = 0;
+ __Pyx_DECREF_SET(__pyx_v_peak_content, ((PyObject*)__pyx_t_4));
+ __pyx_t_4 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1693
- * self.__close_peak_for_broad_region (peak_content, lvl2peaks, min_length, chrom, lvl2_max_gap/2, score_array_s )
+ /* "MACS2/IO/CallPeakUnit.pyx":1704
+ *
* peak_content = [ ( ts, te, tp, cp, ti ), ]
* lastp = te # <<<<<<<<<<<<<<
*
* # save the last peak
*/
- __pyx_t_3 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1693; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF_SET(__pyx_v_lastp, __pyx_t_3);
- __pyx_t_3 = 0;
+ __pyx_t_4 = __Pyx_PyInt_From_int32_t(__pyx_v_te); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF_SET(__pyx_v_lastp, __pyx_t_4);
+ __pyx_t_4 = 0;
}
__pyx_L17:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1696
+ /* "MACS2/IO/CallPeakUnit.pyx":1707
*
* # save the last peak
* if peak_content: # <<<<<<<<<<<<<<
@@ -20965,21 +21030,21 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_t_7 = (__pyx_v_peak_content != Py_None) && (PyList_GET_SIZE(__pyx_v_peak_content) != 0);
if (__pyx_t_7) {
- /* "MACS2/IO/CallPeakUnit.pyx":1697
+ /* "MACS2/IO/CallPeakUnit.pyx":1708
* # save the last peak
* if peak_content:
* self.__close_peak_for_broad_region (peak_content, lvl2peaks, min_length, chrom, lvl2_max_gap/2, score_array_s ) # <<<<<<<<<<<<<<
*
* return
*/
- __pyx_t_3 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_for_broad_region(__pyx_v_self, __pyx_v_peak_content, __pyx_v_lvl2peaks, __pyx_v_min_length, __pyx_v_chrom, __Pyx_div_long(__pyx_v_lvl2_max_gap, 2), __pyx_v_score_array_s, NULL)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_4 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak_for_broad_region(__pyx_v_self, __pyx_v_peak_content, __pyx_v_lvl2peaks, __pyx_v_min_length, __pyx_v_chrom, __Pyx_div_long(__pyx_v_lvl2_max_gap, 2), __pyx_v_score_array_s, NULL)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
goto __pyx_L18;
}
__pyx_L18:;
- /* "MACS2/IO/CallPeakUnit.pyx":1699
+ /* "MACS2/IO/CallPeakUnit.pyx":1710
* self.__close_peak_for_broad_region (peak_content, lvl2peaks, min_length, chrom, lvl2_max_gap/2, score_array_s )
*
* return # <<<<<<<<<<<<<<
@@ -20990,7 +21055,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":1535
+ /* "MACS2/IO/CallPeakUnit.pyx":1536
* return broadpeaks
*
* cdef __chrom_call_broadpeak_using_certain_criteria ( self, lvl1peaks, lvl2peaks, str chrom, list scoring_function_s, list lvl1_cutoff_s, list lvl2_cutoff_s, # <<<<<<<<<<<<<<
@@ -21028,7 +21093,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1701
+/* "MACS2/IO/CallPeakUnit.pyx":1712
* return
*
* cdef bool __close_peak_for_broad_region (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<<
@@ -21078,7 +21143,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
if (__pyx_optional_args) {
}
- /* "MACS2/IO/CallPeakUnit.pyx":1718
+ /* "MACS2/IO/CallPeakUnit.pyx":1729
* np.ndarray tarray_pileup, tarray_control, tarray_pscore, tarray_qscore, tarray_fc
*
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ] # <<<<<<<<<<<<<<
@@ -21087,81 +21152,81 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1718; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1729; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_1, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1718; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_1, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1729; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1718; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1729; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_1, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1718; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_1, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1729; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Subtract(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Subtract(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_v_peak_length = __pyx_t_1;
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1719
+ /* "MACS2/IO/CallPeakUnit.pyx":1730
*
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ]
* if peak_length >= min_length: # if the peak is too small, reject it # <<<<<<<<<<<<<<
* tlist_pileup = []
* tlist_control= []
*/
- __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_min_length); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_min_length); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_peak_length, __pyx_t_1, Py_GE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_peak_length, __pyx_t_1, Py_GE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_4) {
- /* "MACS2/IO/CallPeakUnit.pyx":1720
+ /* "MACS2/IO/CallPeakUnit.pyx":1731
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ]
* if peak_length >= min_length: # if the peak is too small, reject it
* tlist_pileup = [] # <<<<<<<<<<<<<<
* tlist_control= []
* tlist_length = []
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_v_tlist_pileup = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1721
+ /* "MACS2/IO/CallPeakUnit.pyx":1732
* if peak_length >= min_length: # if the peak is too small, reject it
* tlist_pileup = []
* tlist_control= [] # <<<<<<<<<<<<<<
* tlist_length = []
* for i in range(len(peak_content)): # each position in broad peak
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_v_tlist_control = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1722
+ /* "MACS2/IO/CallPeakUnit.pyx":1733
* tlist_pileup = []
* tlist_control= []
* tlist_length = [] # <<<<<<<<<<<<<<
* for i in range(len(peak_content)): # each position in broad peak
* (tstart, tend, ttreat_p, tctrl_p, tlist_scores_p) = peak_content[i]
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_v_tlist_length = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1723
+ /* "MACS2/IO/CallPeakUnit.pyx":1734
* tlist_control= []
* tlist_length = []
* for i in range(len(peak_content)): # each position in broad peak # <<<<<<<<<<<<<<
@@ -21170,13 +21235,13 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1734; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_5 = PyList_GET_SIZE(__pyx_v_peak_content); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyList_GET_SIZE(__pyx_v_peak_content); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1734; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
__pyx_v_i = __pyx_t_6;
- /* "MACS2/IO/CallPeakUnit.pyx":1724
+ /* "MACS2/IO/CallPeakUnit.pyx":1735
* tlist_length = []
* for i in range(len(peak_content)): # each position in broad peak
* (tstart, tend, ttreat_p, tctrl_p, tlist_scores_p) = peak_content[i] # <<<<<<<<<<<<<<
@@ -21185,9 +21250,9 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1724; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, __pyx_v_i, int, 1, __Pyx_PyInt_From_int, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) {
PyObject* sequence = __pyx_t_3;
@@ -21199,7 +21264,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
if (unlikely(size != 5)) {
if (size > 5) __Pyx_RaiseTooManyValuesError(5);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
@@ -21225,7 +21290,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
Py_ssize_t i;
PyObject** temps[5] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_7,&__pyx_t_8,&__pyx_t_9};
for (i=0; i < 5; i++) {
- PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(item);
*(temps[i]) = item;
}
@@ -21235,7 +21300,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
} else {
Py_ssize_t index = -1;
PyObject** temps[5] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_7,&__pyx_t_8,&__pyx_t_9};
- __pyx_t_10 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
@@ -21244,7 +21309,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_GOTREF(item);
*(temps[index]) = item;
}
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_11 = NULL;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
goto __pyx_L7_unpacking_done;
@@ -21252,18 +21317,18 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_11 = NULL;
if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L7_unpacking_done:;
}
- __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_13 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyInt_As_int(__pyx_t_2); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_14 = __pyx_PyFloat_AsFloat(__pyx_t_7); if (unlikely((__pyx_t_14 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __pyx_PyFloat_AsFloat(__pyx_t_7); if (unlikely((__pyx_t_14 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_8); if (unlikely((__pyx_t_15 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __pyx_PyFloat_AsFloat(__pyx_t_8); if (unlikely((__pyx_t_15 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_16 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_16 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = __Pyx_PyInt_As_int(__pyx_t_9); if (unlikely((__pyx_t_16 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_v_tstart = __pyx_t_12;
__pyx_v_tend = __pyx_t_13;
@@ -21271,148 +21336,148 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__pyx_v_tctrl_p = __pyx_t_15;
__pyx_v_tlist_scores_p = __pyx_t_16;
- /* "MACS2/IO/CallPeakUnit.pyx":1726
+ /* "MACS2/IO/CallPeakUnit.pyx":1737
* (tstart, tend, ttreat_p, tctrl_p, tlist_scores_p) = peak_content[i]
* #tscore = ttreat_p #self.pqtable[ get_pscore(int(ttreat_p), tctrl_p) ] # use qscore as general score to find summit
* tlist_pileup.append( ttreat_p ) # <<<<<<<<<<<<<<
* tlist_control.append( tctrl_p )
* tlist_length.append( tend - tstart )
*/
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_ttreat_p); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_ttreat_p); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_17 = __Pyx_PyList_Append(__pyx_v_tlist_pileup, __pyx_t_3); if (unlikely(__pyx_t_17 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_17 = __Pyx_PyList_Append(__pyx_v_tlist_pileup, __pyx_t_3); if (unlikely(__pyx_t_17 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1727
+ /* "MACS2/IO/CallPeakUnit.pyx":1738
* #tscore = ttreat_p #self.pqtable[ get_pscore(int(ttreat_p), tctrl_p) ] # use qscore as general score to find summit
* tlist_pileup.append( ttreat_p )
* tlist_control.append( tctrl_p ) # <<<<<<<<<<<<<<
* tlist_length.append( tend - tstart )
*
*/
- __pyx_t_3 = PyFloat_FromDouble(__pyx_v_tctrl_p); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyFloat_FromDouble(__pyx_v_tctrl_p); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_17 = __Pyx_PyList_Append(__pyx_v_tlist_control, __pyx_t_3); if (unlikely(__pyx_t_17 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_17 = __Pyx_PyList_Append(__pyx_v_tlist_control, __pyx_t_3); if (unlikely(__pyx_t_17 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1728
+ /* "MACS2/IO/CallPeakUnit.pyx":1739
* tlist_pileup.append( ttreat_p )
* tlist_control.append( tctrl_p )
* tlist_length.append( tend - tstart ) # <<<<<<<<<<<<<<
*
* tarray_pileup = np.array( tlist_pileup, dtype="float32")
*/
- __pyx_t_3 = __Pyx_PyInt_From_int((__pyx_v_tend - __pyx_v_tstart)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int((__pyx_v_tend - __pyx_v_tstart)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_17 = __Pyx_PyList_Append(__pyx_v_tlist_length, __pyx_t_3); if (unlikely(__pyx_t_17 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_17 = __Pyx_PyList_Append(__pyx_v_tlist_length, __pyx_t_3); if (unlikely(__pyx_t_17 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1730
+ /* "MACS2/IO/CallPeakUnit.pyx":1741
* tlist_length.append( tend - tstart )
*
* tarray_pileup = np.array( tlist_pileup, dtype="float32") # <<<<<<<<<<<<<<
* tarray_control = np.array( tlist_control, dtype="float32")
* tarray_pscore = self.__cal_pscore( tarray_pileup, tarray_control )
*/
- __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_array); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_array); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_tlist_pileup);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_tlist_pileup);
__Pyx_GIVEREF(__pyx_v_tlist_pileup);
- __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_9, __pyx_t_3, __pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_9, __pyx_t_3, __pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (!(likely(((__pyx_t_7) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_7, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_7) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_7, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_tarray_pileup = ((PyArrayObject *)__pyx_t_7);
__pyx_t_7 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1731
+ /* "MACS2/IO/CallPeakUnit.pyx":1742
*
* tarray_pileup = np.array( tlist_pileup, dtype="float32")
* tarray_control = np.array( tlist_control, dtype="float32") # <<<<<<<<<<<<<<
* tarray_pscore = self.__cal_pscore( tarray_pileup, tarray_control )
* tarray_qscore = self.__cal_qscore( tarray_pileup, tarray_control )
*/
- __pyx_t_7 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_array); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_7, __pyx_n_s_array); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_tlist_control);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_tlist_control);
__Pyx_GIVEREF(__pyx_v_tlist_control);
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_t_7, __pyx_t_3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_n_s_float32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_t_7, __pyx_t_3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!(likely(((__pyx_t_9) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_9, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_9) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_9, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_tarray_control = ((PyArrayObject *)__pyx_t_9);
__pyx_t_9 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1732
+ /* "MACS2/IO/CallPeakUnit.pyx":1743
* tarray_pileup = np.array( tlist_pileup, dtype="float32")
* tarray_control = np.array( tlist_control, dtype="float32")
* tarray_pscore = self.__cal_pscore( tarray_pileup, tarray_control ) # <<<<<<<<<<<<<<
* tarray_qscore = self.__cal_qscore( tarray_pileup, tarray_control )
* tarray_fc = self.__cal_FE ( tarray_pileup, tarray_control )
*/
- __pyx_t_9 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_pscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_tarray_pileup), ((PyArrayObject *)__pyx_v_tarray_control))); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_pscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_tarray_pileup), ((PyArrayObject *)__pyx_v_tarray_control))); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_v_tarray_pscore = ((PyArrayObject *)__pyx_t_9);
__pyx_t_9 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1733
+ /* "MACS2/IO/CallPeakUnit.pyx":1744
* tarray_control = np.array( tlist_control, dtype="float32")
* tarray_pscore = self.__cal_pscore( tarray_pileup, tarray_control )
* tarray_qscore = self.__cal_qscore( tarray_pileup, tarray_control ) # <<<<<<<<<<<<<<
* tarray_fc = self.__cal_FE ( tarray_pileup, tarray_control )
*
*/
- __pyx_t_9 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_qscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_tarray_pileup), ((PyArrayObject *)__pyx_v_tarray_control))); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_qscore(__pyx_v_self, ((PyArrayObject *)__pyx_v_tarray_pileup), ((PyArrayObject *)__pyx_v_tarray_control))); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_v_tarray_qscore = ((PyArrayObject *)__pyx_t_9);
__pyx_t_9 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1734
+ /* "MACS2/IO/CallPeakUnit.pyx":1745
* tarray_pscore = self.__cal_pscore( tarray_pileup, tarray_control )
* tarray_qscore = self.__cal_qscore( tarray_pileup, tarray_control )
* tarray_fc = self.__cal_FE ( tarray_pileup, tarray_control ) # <<<<<<<<<<<<<<
*
* peaks.add( chrom, # chromosome
*/
- __pyx_t_9 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_FE(__pyx_v_self, ((PyArrayObject *)__pyx_v_tarray_pileup), ((PyArrayObject *)__pyx_v_tarray_control))); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1734; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments *)__pyx_v_self->__pyx_vtab)->__pyx___cal_FE(__pyx_v_self, ((PyArrayObject *)__pyx_v_tarray_pileup), ((PyArrayObject *)__pyx_v_tarray_control))); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_v_tarray_fc = ((PyArrayObject *)__pyx_t_9);
__pyx_t_9 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1736
+ /* "MACS2/IO/CallPeakUnit.pyx":1747
* tarray_fc = self.__cal_FE ( tarray_pileup, tarray_control )
*
* peaks.add( chrom, # chromosome # <<<<<<<<<<<<<<
* peak_content[0][0], # start
* peak_content[-1][1], # end
*/
- __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_add); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_add); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- /* "MACS2/IO/CallPeakUnit.pyx":1737
+ /* "MACS2/IO/CallPeakUnit.pyx":1748
*
* peaks.add( chrom, # chromosome
* peak_content[0][0], # start # <<<<<<<<<<<<<<
@@ -21421,15 +21486,15 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1748; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1737; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1748; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1737; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1748; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1738
+ /* "MACS2/IO/CallPeakUnit.pyx":1749
* peaks.add( chrom, # chromosome
* peak_content[0][0], # start
* peak_content[-1][1], # end # <<<<<<<<<<<<<<
@@ -21438,22 +21503,22 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1749; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1738; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_GetItemInt_List(__pyx_v_peak_content, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1749; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_t_3, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1738; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_t_3, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1749; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1736
+ /* "MACS2/IO/CallPeakUnit.pyx":1747
* tarray_fc = self.__cal_FE ( tarray_pileup, tarray_control )
*
* peaks.add( chrom, # chromosome # <<<<<<<<<<<<<<
* peak_content[0][0], # start
* peak_content[-1][1], # end
*/
- __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_chrom);
@@ -21464,86 +21529,86 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_GIVEREF(__pyx_t_8);
__pyx_t_7 = 0;
__pyx_t_8 = 0;
- __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_summit, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_summit, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "MACS2/IO/CallPeakUnit.pyx":1740
+ /* "MACS2/IO/CallPeakUnit.pyx":1751
* peak_content[-1][1], # end
* summit = 0,
* peak_score = mean_from_value_length( tarray_qscore, tlist_length ), # <<<<<<<<<<<<<<
* pileup = mean_from_value_length( tarray_pileup, tlist_length ),
* pscore = mean_from_value_length( tarray_pscore, tlist_length ),
*/
- __pyx_t_7 = PyFloat_FromDouble(__pyx_f_5MACS2_2IO_12CallPeakUnit_mean_from_value_length(__pyx_v_tarray_qscore, __pyx_v_tlist_length)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyFloat_FromDouble(__pyx_f_5MACS2_2IO_12CallPeakUnit_mean_from_value_length(__pyx_v_tarray_qscore, __pyx_v_tlist_length)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_peak_score, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_peak_score, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1741
+ /* "MACS2/IO/CallPeakUnit.pyx":1752
* summit = 0,
* peak_score = mean_from_value_length( tarray_qscore, tlist_length ),
* pileup = mean_from_value_length( tarray_pileup, tlist_length ), # <<<<<<<<<<<<<<
* pscore = mean_from_value_length( tarray_pscore, tlist_length ),
* fold_change = mean_from_value_length( tarray_fc, tlist_length ),
*/
- __pyx_t_7 = PyFloat_FromDouble(__pyx_f_5MACS2_2IO_12CallPeakUnit_mean_from_value_length(__pyx_v_tarray_pileup, __pyx_v_tlist_length)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyFloat_FromDouble(__pyx_f_5MACS2_2IO_12CallPeakUnit_mean_from_value_length(__pyx_v_tarray_pileup, __pyx_v_tlist_length)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_pileup, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_pileup, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1742
+ /* "MACS2/IO/CallPeakUnit.pyx":1753
* peak_score = mean_from_value_length( tarray_qscore, tlist_length ),
* pileup = mean_from_value_length( tarray_pileup, tlist_length ),
* pscore = mean_from_value_length( tarray_pscore, tlist_length ), # <<<<<<<<<<<<<<
* fold_change = mean_from_value_length( tarray_fc, tlist_length ),
* qscore = mean_from_value_length( tarray_qscore, tlist_length ),
*/
- __pyx_t_7 = PyFloat_FromDouble(__pyx_f_5MACS2_2IO_12CallPeakUnit_mean_from_value_length(__pyx_v_tarray_pscore, __pyx_v_tlist_length)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyFloat_FromDouble(__pyx_f_5MACS2_2IO_12CallPeakUnit_mean_from_value_length(__pyx_v_tarray_pscore, __pyx_v_tlist_length)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1753; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_pscore, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_pscore, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1743
+ /* "MACS2/IO/CallPeakUnit.pyx":1754
* pileup = mean_from_value_length( tarray_pileup, tlist_length ),
* pscore = mean_from_value_length( tarray_pscore, tlist_length ),
* fold_change = mean_from_value_length( tarray_fc, tlist_length ), # <<<<<<<<<<<<<<
* qscore = mean_from_value_length( tarray_qscore, tlist_length ),
* )
*/
- __pyx_t_7 = PyFloat_FromDouble(__pyx_f_5MACS2_2IO_12CallPeakUnit_mean_from_value_length(__pyx_v_tarray_fc, __pyx_v_tlist_length)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyFloat_FromDouble(__pyx_f_5MACS2_2IO_12CallPeakUnit_mean_from_value_length(__pyx_v_tarray_fc, __pyx_v_tlist_length)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_fold_change, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_fold_change, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1744
+ /* "MACS2/IO/CallPeakUnit.pyx":1755
* pscore = mean_from_value_length( tarray_pscore, tlist_length ),
* fold_change = mean_from_value_length( tarray_fc, tlist_length ),
* qscore = mean_from_value_length( tarray_qscore, tlist_length ), # <<<<<<<<<<<<<<
* )
- * # start a new peak
+ * #if chrom == "chr1" and peak_content[0][0] == 237643 and peak_content[-1][1] == 237935:
*/
- __pyx_t_7 = PyFloat_FromDouble(__pyx_f_5MACS2_2IO_12CallPeakUnit_mean_from_value_length(__pyx_v_tarray_qscore, __pyx_v_tlist_length)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyFloat_FromDouble(__pyx_f_5MACS2_2IO_12CallPeakUnit_mean_from_value_length(__pyx_v_tarray_qscore, __pyx_v_tlist_length)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_qscore, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_qscore, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1736
+ /* "MACS2/IO/CallPeakUnit.pyx":1747
* tarray_fc = self.__cal_FE ( tarray_pileup, tarray_control )
*
* peaks.add( chrom, # chromosome # <<<<<<<<<<<<<<
* peak_content[0][0], # start
* peak_content[-1][1], # end
*/
- __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_9, __pyx_t_3, __pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_9, __pyx_t_3, __pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1747
- * )
+ /* "MACS2/IO/CallPeakUnit.pyx":1760
+ * # print tarray_qscore, tlist_length
* # start a new peak
* return True # <<<<<<<<<<<<<<
*
@@ -21555,7 +21620,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
goto __pyx_L0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1701
+ /* "MACS2/IO/CallPeakUnit.pyx":1712
* return
*
* cdef bool __close_peak_for_broad_region (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<<
@@ -21591,7 +21656,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1749
+/* "MACS2/IO/CallPeakUnit.pyx":1762
* return True
*
* cdef __add_broadpeak (self, bpeaks, str chrom, object lvl2peak, list lvl1peakset): # <<<<<<<<<<<<<<
@@ -21623,33 +21688,33 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__add_broadpeak", 0);
- /* "MACS2/IO/CallPeakUnit.pyx":1760
+ /* "MACS2/IO/CallPeakUnit.pyx":1773
*
* #print lvl2peak["start"], lvl2peak["end"], lvl2peak["score"]
* start = lvl2peak["start"] # <<<<<<<<<<<<<<
* end = lvl2peak["end"]
*
*/
- __pyx_t_1 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_start); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1760; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_start); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1773; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_start = __pyx_t_2;
- /* "MACS2/IO/CallPeakUnit.pyx":1761
+ /* "MACS2/IO/CallPeakUnit.pyx":1774
* #print lvl2peak["start"], lvl2peak["end"], lvl2peak["score"]
* start = lvl2peak["start"]
* end = lvl2peak["end"] # <<<<<<<<<<<<<<
*
* if not lvl1peakset:
*/
- __pyx_t_1 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_end); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1761; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_end); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1774; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1761; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_end = __pyx_t_2;
- /* "MACS2/IO/CallPeakUnit.pyx":1763
+ /* "MACS2/IO/CallPeakUnit.pyx":1776
* end = lvl2peak["end"]
*
* if not lvl1peakset: # <<<<<<<<<<<<<<
@@ -21660,20 +21725,20 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
__pyx_t_4 = ((!__pyx_t_3) != 0);
if (__pyx_t_4) {
- /* "MACS2/IO/CallPeakUnit.pyx":1767
+ /* "MACS2/IO/CallPeakUnit.pyx":1780
* # will complement by adding 1bps start and end to this region
* # may change in the future if gappedPeak format was improved.
* bpeaks.add(chrom, start, end, score=lvl2peak["score"], thickStart=str(start), thickEnd=str(end), # <<<<<<<<<<<<<<
* blockNum = 2, blockSizes = "1,1", blockStarts = "0,"+str(end-start-1), pileup = lvl2peak["pileup"],
* pscore = lvl2peak["pscore"], fold_change = lvl2peak["fc"],
*/
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_bpeaks, __pyx_n_s_add); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_bpeaks, __pyx_n_s_add); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_end); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_end); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_chrom);
@@ -21684,109 +21749,109 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_5 = 0;
__pyx_t_6 = 0;
- __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_score); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_5 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_score); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_5);
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_score, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_score, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_start); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_8, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_8, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_thickStart, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_thickStart, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_end); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_end); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_8, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_8, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_thickEnd, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_thickEnd, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_blockNum, __pyx_int_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_blockSizes, __pyx_kp_s_1_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_blockNum, __pyx_int_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_blockSizes, __pyx_kp_s_1_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "MACS2/IO/CallPeakUnit.pyx":1768
+ /* "MACS2/IO/CallPeakUnit.pyx":1781
* # may change in the future if gappedPeak format was improved.
* bpeaks.add(chrom, start, end, score=lvl2peak["score"], thickStart=str(start), thickEnd=str(end),
* blockNum = 2, blockSizes = "1,1", blockStarts = "0,"+str(end-start-1), pileup = lvl2peak["pileup"], # <<<<<<<<<<<<<<
* pscore = lvl2peak["pscore"], fold_change = lvl2peak["fc"],
* qscore = lvl2peak["qscore"] )
*/
- __pyx_t_5 = __Pyx_PyInt_From_long(((__pyx_v_end - __pyx_v_start) - 1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_long(((__pyx_v_end - __pyx_v_start) - 1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_8, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_8, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyNumber_Add(__pyx_kp_s_0, __pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Add(__pyx_kp_s_0, __pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_blockStarts, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_blockStarts, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_pileup); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1768; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_pileup); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1781; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_pileup, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_pileup, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1769
+ /* "MACS2/IO/CallPeakUnit.pyx":1782
* bpeaks.add(chrom, start, end, score=lvl2peak["score"], thickStart=str(start), thickEnd=str(end),
* blockNum = 2, blockSizes = "1,1", blockStarts = "0,"+str(end-start-1), pileup = lvl2peak["pileup"],
* pscore = lvl2peak["pscore"], fold_change = lvl2peak["fc"], # <<<<<<<<<<<<<<
* qscore = lvl2peak["qscore"] )
* #except:
*/
- __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_pscore); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1769; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_pscore); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_pscore, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_pscore, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_fc); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1769; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_fc); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_fold_change, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_fold_change, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1770
+ /* "MACS2/IO/CallPeakUnit.pyx":1783
* blockNum = 2, blockSizes = "1,1", blockStarts = "0,"+str(end-start-1), pileup = lvl2peak["pileup"],
* pscore = lvl2peak["pscore"], fold_change = lvl2peak["fc"],
* qscore = lvl2peak["qscore"] ) # <<<<<<<<<<<<<<
* #except:
* # print [ chrom, start, end, lvl2peak["score"],".", ".",
*/
- __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_qscore); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1770; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_qscore); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1783; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_qscore, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_qscore, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1767
+ /* "MACS2/IO/CallPeakUnit.pyx":1780
* # will complement by adding 1bps start and end to this region
* # may change in the future if gappedPeak format was improved.
* bpeaks.add(chrom, start, end, score=lvl2peak["score"], thickStart=str(start), thickEnd=str(end), # <<<<<<<<<<<<<<
* blockNum = 2, blockSizes = "1,1", blockStarts = "0,"+str(end-start-1), pileup = lvl2peak["pileup"],
* pscore = lvl2peak["pscore"], fold_change = lvl2peak["fc"],
*/
- __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_7, __pyx_t_6); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_7, __pyx_t_6); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1777
+ /* "MACS2/IO/CallPeakUnit.pyx":1790
* # lvl2peak["qscore"] ]
* # raise Exception("quit")
* return bpeaks # <<<<<<<<<<<<<<
@@ -21799,7 +21864,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
goto __pyx_L0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1779
+ /* "MACS2/IO/CallPeakUnit.pyx":1792
* return bpeaks
*
* thickStart = str(lvl1peakset[0]["start"]) # <<<<<<<<<<<<<<
@@ -21808,26 +21873,26 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
*/
if (unlikely(__pyx_v_lvl1peakset == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_8 = __Pyx_GetItemInt_List(__pyx_v_lvl1peakset, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1779; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = __Pyx_GetItemInt_List(__pyx_v_lvl1peakset, 0, long, 1, __Pyx_PyInt_From_long, 1, 0, 1); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_6 = PyObject_GetItem(__pyx_t_8, __pyx_n_s_start); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1779; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_6 = PyObject_GetItem(__pyx_t_8, __pyx_n_s_start); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_8, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_8, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (!(likely(PyString_CheckExact(__pyx_t_6))||((__pyx_t_6) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_6)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_6))||((__pyx_t_6) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_6)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_thickStart = ((PyObject*)__pyx_t_6);
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1780
+ /* "MACS2/IO/CallPeakUnit.pyx":1793
*
* thickStart = str(lvl1peakset[0]["start"])
* thickEnd = str(lvl1peakset[-1]["end"]) # <<<<<<<<<<<<<<
@@ -21836,26 +21901,26 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
*/
if (unlikely(__pyx_v_lvl1peakset == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_6 = __Pyx_GetItemInt_List(__pyx_v_lvl1peakset, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_6 = __Pyx_GetItemInt_List(__pyx_v_lvl1peakset, -1, long, 1, __Pyx_PyInt_From_long, 1, 1, 1); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1793; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = PyObject_GetItem(__pyx_t_6, __pyx_n_s_end); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = PyObject_GetItem(__pyx_t_6, __pyx_n_s_end); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1793; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
__pyx_t_8 = 0;
- __pyx_t_8 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_6, NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_6, NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (!(likely(PyString_CheckExact(__pyx_t_8))||((__pyx_t_8) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_8)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_8))||((__pyx_t_8) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_8)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_thickEnd = ((PyObject*)__pyx_t_8);
__pyx_t_8 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1781
+ /* "MACS2/IO/CallPeakUnit.pyx":1794
* thickStart = str(lvl1peakset[0]["start"])
* thickEnd = str(lvl1peakset[-1]["end"])
* blockNum = int(len(lvl1peakset)) # <<<<<<<<<<<<<<
@@ -21864,24 +21929,24 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
*/
if (unlikely(__pyx_v_lvl1peakset == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_9 = PyList_GET_SIZE(__pyx_v_lvl1peakset); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyList_GET_SIZE(__pyx_v_lvl1peakset); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_blockNum = ((int)__pyx_t_9);
- /* "MACS2/IO/CallPeakUnit.pyx":1782
+ /* "MACS2/IO/CallPeakUnit.pyx":1795
* thickEnd = str(lvl1peakset[-1]["end"])
* blockNum = int(len(lvl1peakset))
* blockSizes = ",".join(map(str,map(itemgetter("length"),lvl1peakset))) #join( map(lambda x:str(x["length"]),lvl1peakset) ) # <<<<<<<<<<<<<<
* blockStarts = ",".join(getitem_then_subtract(lvl1peakset, start)) #join( map(lambda x:str(x["start"]-start),lvl1peakset) )
*
*/
- __pyx_t_8 = __Pyx_GetModuleGlobalName(__pyx_n_s_itemgetter); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetModuleGlobalName(__pyx_n_s_itemgetter); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_tuple__33, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_tuple__33, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
@@ -21889,10 +21954,10 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_lvl1peakset);
__Pyx_GIVEREF(__pyx_v_lvl1peakset);
__pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_map, __pyx_t_8, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_map, __pyx_t_8, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
@@ -21900,72 +21965,72 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_map, __pyx_t_8, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_map, __pyx_t_8, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = __Pyx_PyString_Join(__pyx_kp_s__32, __pyx_t_6); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyString_Join(__pyx_kp_s__32, __pyx_t_6); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (!(likely(PyString_CheckExact(__pyx_t_8))||((__pyx_t_8) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_8)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_8))||((__pyx_t_8) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_8)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_blockSizes = ((PyObject*)__pyx_t_8);
__pyx_t_8 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1783
+ /* "MACS2/IO/CallPeakUnit.pyx":1796
* blockNum = int(len(lvl1peakset))
* blockSizes = ",".join(map(str,map(itemgetter("length"),lvl1peakset))) #join( map(lambda x:str(x["length"]),lvl1peakset) )
* blockStarts = ",".join(getitem_then_subtract(lvl1peakset, start)) #join( map(lambda x:str(x["start"]-start),lvl1peakset) ) # <<<<<<<<<<<<<<
*
* # add 1bp left and/or right block if necessary
*/
- __pyx_t_8 = __pyx_f_5MACS2_2IO_12CallPeakUnit_getitem_then_subtract(__pyx_v_lvl1peakset, __pyx_v_start); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __pyx_f_5MACS2_2IO_12CallPeakUnit_getitem_then_subtract(__pyx_v_lvl1peakset, __pyx_v_start); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_6 = __Pyx_PyString_Join(__pyx_kp_s__32, __pyx_t_8); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyString_Join(__pyx_kp_s__32, __pyx_t_8); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (!(likely(PyString_CheckExact(__pyx_t_6))||((__pyx_t_6) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_6)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_6))||((__pyx_t_6) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_6)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_blockStarts = ((PyObject*)__pyx_t_6);
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1786
+ /* "MACS2/IO/CallPeakUnit.pyx":1799
*
* # add 1bp left and/or right block if necessary
* if int(thickStart) != start: # <<<<<<<<<<<<<<
* # add 1bp left block
* thickStart = str(start)
*/
- __pyx_t_6 = PyNumber_Int(__pyx_v_thickStart); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Int(__pyx_v_thickStart); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_start); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_start); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_6, __pyx_t_8, Py_NE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_6, __pyx_t_8, Py_NE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_4) {
- /* "MACS2/IO/CallPeakUnit.pyx":1788
+ /* "MACS2/IO/CallPeakUnit.pyx":1801
* if int(thickStart) != start:
* # add 1bp left block
* thickStart = str(start) # <<<<<<<<<<<<<<
* blockNum += 1
* blockSizes = "1,"+blockSizes
*/
- __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_start); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyInt_From_int(__pyx_v_start); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_8, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_8, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (!(likely(PyString_CheckExact(__pyx_t_7))||((__pyx_t_7) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_7)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_7))||((__pyx_t_7) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_7)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF_SET(__pyx_v_thickStart, ((PyObject*)__pyx_t_7));
__pyx_t_7 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1789
+ /* "MACS2/IO/CallPeakUnit.pyx":1802
* # add 1bp left block
* thickStart = str(start)
* blockNum += 1 # <<<<<<<<<<<<<<
@@ -21974,26 +22039,26 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
*/
__pyx_v_blockNum = (__pyx_v_blockNum + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1790
+ /* "MACS2/IO/CallPeakUnit.pyx":1803
* thickStart = str(start)
* blockNum += 1
* blockSizes = "1,"+blockSizes # <<<<<<<<<<<<<<
* blockStarts = "0,"+blockStarts
* if int(thickEnd) != end:
*/
- __pyx_t_7 = PyNumber_Add(__pyx_kp_s_1, __pyx_v_blockSizes); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Add(__pyx_kp_s_1, __pyx_v_blockSizes); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF_SET(__pyx_v_blockSizes, ((PyObject*)__pyx_t_7));
__pyx_t_7 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1791
+ /* "MACS2/IO/CallPeakUnit.pyx":1804
* blockNum += 1
* blockSizes = "1,"+blockSizes
* blockStarts = "0,"+blockStarts # <<<<<<<<<<<<<<
* if int(thickEnd) != end:
* # add 1bp right block
*/
- __pyx_t_7 = PyNumber_Add(__pyx_kp_s_0, __pyx_v_blockStarts); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Add(__pyx_kp_s_0, __pyx_v_blockStarts); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1804; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF_SET(__pyx_v_blockStarts, ((PyObject*)__pyx_t_7));
__pyx_t_7 = 0;
@@ -22001,46 +22066,46 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
}
__pyx_L4:;
- /* "MACS2/IO/CallPeakUnit.pyx":1792
+ /* "MACS2/IO/CallPeakUnit.pyx":1805
* blockSizes = "1,"+blockSizes
* blockStarts = "0,"+blockStarts
* if int(thickEnd) != end: # <<<<<<<<<<<<<<
* # add 1bp right block
* thickEnd = str(end)
*/
- __pyx_t_7 = PyNumber_Int(__pyx_v_thickEnd); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Int(__pyx_v_thickEnd); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_end); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_end); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_6 = PyObject_RichCompare(__pyx_t_7, __pyx_t_8, Py_NE); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_7, __pyx_t_8, Py_NE); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (__pyx_t_4) {
- /* "MACS2/IO/CallPeakUnit.pyx":1794
+ /* "MACS2/IO/CallPeakUnit.pyx":1807
* if int(thickEnd) != end:
* # add 1bp right block
* thickEnd = str(end) # <<<<<<<<<<<<<<
* blockNum += 1
* blockSizes = blockSizes+",1"
*/
- __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_end); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_end); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_8, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_8, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (!(likely(PyString_CheckExact(__pyx_t_6))||((__pyx_t_6) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_6)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_6))||((__pyx_t_6) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_6)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF_SET(__pyx_v_thickEnd, ((PyObject*)__pyx_t_6));
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1795
+ /* "MACS2/IO/CallPeakUnit.pyx":1808
* # add 1bp right block
* thickEnd = str(end)
* blockNum += 1 # <<<<<<<<<<<<<<
@@ -22049,62 +22114,62 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
*/
__pyx_v_blockNum = (__pyx_v_blockNum + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":1796
+ /* "MACS2/IO/CallPeakUnit.pyx":1809
* thickEnd = str(end)
* blockNum += 1
* blockSizes = blockSizes+",1" # <<<<<<<<<<<<<<
* blockStarts = blockStarts+","+str(end-start-1)
*
*/
- __pyx_t_6 = PyNumber_Add(__pyx_v_blockSizes, __pyx_kp_s_1_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Add(__pyx_v_blockSizes, __pyx_kp_s_1_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF_SET(__pyx_v_blockSizes, ((PyObject*)__pyx_t_6));
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1797
+ /* "MACS2/IO/CallPeakUnit.pyx":1810
* blockNum += 1
* blockSizes = blockSizes+",1"
* blockStarts = blockStarts+","+str(end-start-1) # <<<<<<<<<<<<<<
*
* bpeaks.add(chrom, start, end, score=lvl2peak["score"], thickStart=thickStart, thickEnd=thickEnd,
*/
- __pyx_t_6 = PyNumber_Add(__pyx_v_blockStarts, __pyx_kp_s__32); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Add(__pyx_v_blockStarts, __pyx_kp_s__32); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = __Pyx_PyInt_From_long(((__pyx_v_end - __pyx_v_start) - 1)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyInt_From_long(((__pyx_v_end - __pyx_v_start) - 1)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
__pyx_t_8 = 0;
- __pyx_t_8 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_7, NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_7, NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Add(__pyx_t_6, __pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Add(__pyx_t_6, __pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (!(likely(PyString_CheckExact(__pyx_t_7))||((__pyx_t_7) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_7)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_7))||((__pyx_t_7) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_7)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF_SET(__pyx_v_blockStarts, ((PyObject*)__pyx_t_7));
__pyx_t_7 = 0;
goto __pyx_L5;
}
__pyx_L5:;
- /* "MACS2/IO/CallPeakUnit.pyx":1799
+ /* "MACS2/IO/CallPeakUnit.pyx":1812
* blockStarts = blockStarts+","+str(end-start-1)
*
* bpeaks.add(chrom, start, end, score=lvl2peak["score"], thickStart=thickStart, thickEnd=thickEnd, # <<<<<<<<<<<<<<
* blockNum = blockNum, blockSizes = blockSizes, blockStarts = blockStarts, pileup = lvl2peak["pileup"],
* pscore = lvl2peak["pscore"], fold_change = lvl2peak["fc"],
*/
- __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_bpeaks, __pyx_n_s_add); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_GetAttrStr(__pyx_v_bpeaks, __pyx_n_s_add); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_start); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_start); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_end); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_end); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_chrom);
@@ -22115,76 +22180,76 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_8 = 0;
__pyx_t_6 = 0;
- __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_score); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_score); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_score, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_score, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_thickStart, __pyx_v_thickStart) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_thickEnd, __pyx_v_thickEnd) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_thickStart, __pyx_v_thickStart) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_thickEnd, __pyx_v_thickEnd) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "MACS2/IO/CallPeakUnit.pyx":1800
+ /* "MACS2/IO/CallPeakUnit.pyx":1813
*
* bpeaks.add(chrom, start, end, score=lvl2peak["score"], thickStart=thickStart, thickEnd=thickEnd,
* blockNum = blockNum, blockSizes = blockSizes, blockStarts = blockStarts, pileup = lvl2peak["pileup"], # <<<<<<<<<<<<<<
* pscore = lvl2peak["pscore"], fold_change = lvl2peak["fc"],
* qscore = lvl2peak["qscore"] )
*/
- __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_blockNum); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_blockNum); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_blockNum, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_blockNum, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_blockSizes, __pyx_v_blockSizes) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_blockStarts, __pyx_v_blockStarts) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_pileup); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1800; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_blockSizes, __pyx_v_blockSizes) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_blockStarts, __pyx_v_blockStarts) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_pileup); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_pileup, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_pileup, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1801
+ /* "MACS2/IO/CallPeakUnit.pyx":1814
* bpeaks.add(chrom, start, end, score=lvl2peak["score"], thickStart=thickStart, thickEnd=thickEnd,
* blockNum = blockNum, blockSizes = blockSizes, blockStarts = blockStarts, pileup = lvl2peak["pileup"],
* pscore = lvl2peak["pscore"], fold_change = lvl2peak["fc"], # <<<<<<<<<<<<<<
* qscore = lvl2peak["qscore"] )
* return bpeaks
*/
- __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_pscore); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1801; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_pscore); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1814; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_pscore, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_pscore, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_fc); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1801; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_fc); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1814; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_fold_change, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_fold_change, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1802
+ /* "MACS2/IO/CallPeakUnit.pyx":1815
* blockNum = blockNum, blockSizes = blockSizes, blockStarts = blockStarts, pileup = lvl2peak["pileup"],
* pscore = lvl2peak["pscore"], fold_change = lvl2peak["fc"],
* qscore = lvl2peak["qscore"] ) # <<<<<<<<<<<<<<
* return bpeaks
*
*/
- __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_qscore); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1802; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_lvl2peak, __pyx_n_s_qscore); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_qscore, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_qscore, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1799
+ /* "MACS2/IO/CallPeakUnit.pyx":1812
* blockStarts = blockStarts+","+str(end-start-1)
*
* bpeaks.add(chrom, start, end, score=lvl2peak["score"], thickStart=thickStart, thickEnd=thickEnd, # <<<<<<<<<<<<<<
* blockNum = blockNum, blockSizes = blockSizes, blockStarts = blockStarts, pileup = lvl2peak["pileup"],
* pscore = lvl2peak["pscore"], fold_change = lvl2peak["fc"],
*/
- __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_7, __pyx_t_1, __pyx_t_6); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_7, __pyx_t_1, __pyx_t_6); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1803
+ /* "MACS2/IO/CallPeakUnit.pyx":1816
* pscore = lvl2peak["pscore"], fold_change = lvl2peak["fc"],
* qscore = lvl2peak["qscore"] )
* return bpeaks # <<<<<<<<<<<<<<
@@ -22196,7 +22261,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
__pyx_r = __pyx_v_bpeaks;
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":1749
+ /* "MACS2/IO/CallPeakUnit.pyx":1762
* return True
*
* cdef __add_broadpeak (self, bpeaks, str chrom, object lvl2peak, list lvl1peakset): # <<<<<<<<<<<<<<
@@ -22223,7 +22288,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___add_
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1805
+/* "MACS2/IO/CallPeakUnit.pyx":1818
* return bpeaks
*
* cpdef refine_peak_from_tags_distribution ( self, peaks, int window_size = 100, float cutoff = 5 ): # <<<<<<<<<<<<<<
@@ -22299,13 +22364,13 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
if (unlikely(__pyx_skip_dispatch)) ;
/* Check if overridden in Python */
else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) {
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_refine_peak_from_tags_distributi); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_refine_peak_from_tags_distributi); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_13refine_peak_from_tags_distribution)) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_window_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_window_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyFloat_FromDouble(__pyx_v_cutoff); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(__pyx_t_1);
__pyx_t_5 = __pyx_t_1; __pyx_t_6 = NULL;
@@ -22320,7 +22385,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__pyx_t_7 = 1;
}
}
- __pyx_t_8 = PyTuple_New(3+__pyx_t_7); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(3+__pyx_t_7); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
if (__pyx_t_6) {
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_6 = NULL;
@@ -22334,7 +22399,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__Pyx_GIVEREF(__pyx_t_4);
__pyx_t_3 = 0;
__pyx_t_4 = 0;
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_8, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_8, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -22346,17 +22411,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1827
+ /* "MACS2/IO/CallPeakUnit.pyx":1840
* np.ndarray adjusted_summits, passflags
*
* if self.PE_mode: # <<<<<<<<<<<<<<
* return None
*
*/
- __pyx_t_9 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->PE_mode)); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->PE_mode)); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_9) {
- /* "MACS2/IO/CallPeakUnit.pyx":1828
+ /* "MACS2/IO/CallPeakUnit.pyx":1841
*
* if self.PE_mode:
* return None # <<<<<<<<<<<<<<
@@ -22369,14 +22434,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
goto __pyx_L0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1830
+ /* "MACS2/IO/CallPeakUnit.pyx":1843
* return None
*
* pchrnames = sorted(peaks.get_chr_names()) # <<<<<<<<<<<<<<
* retval = []
*
*/
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_get_chr_names); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_get_chr_names); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_8 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_5))) {
@@ -22389,48 +22454,48 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
}
if (__pyx_t_8) {
- __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_8); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_8); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
} else {
- __pyx_t_2 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PySequence_List(__pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PySequence_List(__pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_1 = ((PyObject*)__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_10 = PyList_Sort(__pyx_t_1); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyList_Sort(__pyx_t_1); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_pchrnames = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1831
+ /* "MACS2/IO/CallPeakUnit.pyx":1844
*
* pchrnames = sorted(peaks.get_chr_names())
* retval = [] # <<<<<<<<<<<<<<
*
* # this object should be sorted
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_retval = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1834
+ /* "MACS2/IO/CallPeakUnit.pyx":1847
*
* # this object should be sorted
* if not self.treat.__sorted: self.treat.sort() # <<<<<<<<<<<<<<
* # PeakIO object should be sorted
* peaks.sort()
*/
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->treat, __pyx_n_s_sorted_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->treat, __pyx_n_s_sorted_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_11 = ((!__pyx_t_9) != 0);
if (__pyx_t_11) {
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->treat, __pyx_n_s_sort); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->treat, __pyx_n_s_sort); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_2 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_5))) {
@@ -22443,10 +22508,10 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
}
if (__pyx_t_2) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -22455,14 +22520,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
__pyx_L4:;
- /* "MACS2/IO/CallPeakUnit.pyx":1836
+ /* "MACS2/IO/CallPeakUnit.pyx":1849
* if not self.treat.__sorted: self.treat.sort()
* # PeakIO object should be sorted
* peaks.sort() # <<<<<<<<<<<<<<
*
* chrnames = self.treat.get_chr_names()
*/
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_sort); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_sort); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_2 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_5))) {
@@ -22475,23 +22540,23 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
}
if (__pyx_t_2) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1838
+ /* "MACS2/IO/CallPeakUnit.pyx":1851
* peaks.sort()
*
* chrnames = self.treat.get_chr_names() # <<<<<<<<<<<<<<
*
* ret_peaks = PeakIO()
*/
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->treat, __pyx_n_s_get_chr_names); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->treat, __pyx_n_s_get_chr_names); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_2 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_5))) {
@@ -22504,24 +22569,24 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
}
if (__pyx_t_2) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_v_chrnames = __pyx_t_1;
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1840
+ /* "MACS2/IO/CallPeakUnit.pyx":1853
* chrnames = self.treat.get_chr_names()
*
* ret_peaks = PeakIO() # <<<<<<<<<<<<<<
*
* for c in range(len(pchrnames)):
*/
- __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_PeakIO); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_PeakIO); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_2 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_5))) {
@@ -22534,17 +22599,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
}
if (__pyx_t_2) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
} else {
- __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallNoArg(__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_v_ret_peaks = __pyx_t_1;
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1842
+ /* "MACS2/IO/CallPeakUnit.pyx":1855
* ret_peaks = PeakIO()
*
* for c in range(len(pchrnames)): # <<<<<<<<<<<<<<
@@ -22553,13 +22618,13 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
*/
if (unlikely(__pyx_v_pchrnames == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_7 = PyList_GET_SIZE(__pyx_v_pchrnames); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyList_GET_SIZE(__pyx_v_pchrnames); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
for (__pyx_t_12 = 0; __pyx_t_12 < __pyx_t_7; __pyx_t_12+=1) {
__pyx_v_c = __pyx_t_12;
- /* "MACS2/IO/CallPeakUnit.pyx":1843
+ /* "MACS2/IO/CallPeakUnit.pyx":1856
*
* for c in range(len(pchrnames)):
* chrom = pchrnames[c] # <<<<<<<<<<<<<<
@@ -22568,15 +22633,15 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
*/
if (unlikely(__pyx_v_pchrnames == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1856; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_pchrnames, __pyx_v_c, int32_t, 1, __Pyx_PyInt_From_int32_t, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1843; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_pchrnames, __pyx_v_c, int32_t, 1, __Pyx_PyInt_From_int32_t, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1856; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "str", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1856; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_chrom, ((PyObject*)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1844
+ /* "MACS2/IO/CallPeakUnit.pyx":1857
* for c in range(len(pchrnames)):
* chrom = pchrnames[c]
* assert chrom in chrnames, "chromosome %s can't be found in the FWTrack object. %s" % (chrom, str(chrnames)) # <<<<<<<<<<<<<<
@@ -22585,17 +22650,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
if (unlikely(!Py_OptimizeFlag)) {
- __pyx_t_11 = (__Pyx_PySequence_Contains(__pyx_v_chrom, __pyx_v_chrnames, Py_EQ)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = (__Pyx_PySequence_Contains(__pyx_v_chrom, __pyx_v_chrnames, Py_EQ)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(!(__pyx_t_11 != 0))) {
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_chrnames);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_chrnames);
__Pyx_GIVEREF(__pyx_v_chrnames);
- __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_1, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), __pyx_t_1, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_chrom);
@@ -22603,26 +22668,26 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_PyString_Format(__pyx_kp_s_chromosome_s_can_t_be_found_in_t, __pyx_t_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyString_Format(__pyx_kp_s_chromosome_s_can_t_be_found_in_t, __pyx_t_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
PyErr_SetObject(PyExc_AssertionError, __pyx_t_5);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
}
#endif
- /* "MACS2/IO/CallPeakUnit.pyx":1845
+ /* "MACS2/IO/CallPeakUnit.pyx":1858
* chrom = pchrnames[c]
* assert chrom in chrnames, "chromosome %s can't be found in the FWTrack object. %s" % (chrom, str(chrnames))
* (plus, minus) = self.treat.__locations[chrom] # <<<<<<<<<<<<<<
* cpeaks = peaks.get_data_from_chrom(chrom)
*
*/
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->treat, __pyx_n_s_locations); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->treat, __pyx_n_s_locations); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyObject_GetItem(__pyx_t_5, __pyx_v_chrom); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1845; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = PyObject_GetItem(__pyx_t_5, __pyx_v_chrom); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1858; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
@@ -22635,7 +22700,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
if (unlikely(size != 2)) {
if (size > 2) __Pyx_RaiseTooManyValuesError(2);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
@@ -22648,15 +22713,15 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__Pyx_INCREF(__pyx_t_5);
__Pyx_INCREF(__pyx_t_2);
#else
- __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
#endif
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
} else {
Py_ssize_t index = -1;
- __pyx_t_8 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_13 = Py_TYPE(__pyx_t_8)->tp_iternext;
@@ -22664,7 +22729,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__Pyx_GOTREF(__pyx_t_5);
index = 1; __pyx_t_2 = __pyx_t_13(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_13 = NULL;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
goto __pyx_L8_unpacking_done;
@@ -22672,24 +22737,24 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_13 = NULL;
if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L8_unpacking_done:;
}
- if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_plus, ((PyArrayObject *)__pyx_t_5));
__pyx_t_5 = 0;
__Pyx_XDECREF_SET(__pyx_v_minus, ((PyArrayObject *)__pyx_t_2));
__pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1846
+ /* "MACS2/IO/CallPeakUnit.pyx":1859
* assert chrom in chrnames, "chromosome %s can't be found in the FWTrack object. %s" % (chrom, str(chrnames))
* (plus, minus) = self.treat.__locations[chrom]
* cpeaks = peaks.get_data_from_chrom(chrom) # <<<<<<<<<<<<<<
*
* prev_i = 0
*/
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_get_data_from_chrom); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_peaks, __pyx_n_s_get_data_from_chrom); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_5 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && likely(PyMethod_Check(__pyx_t_2))) {
@@ -22702,25 +22767,25 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
}
if (!__pyx_t_5) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_v_chrom); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_v_chrom); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
} else {
- __pyx_t_8 = PyTuple_New(1+1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(1+1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL;
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_8, 0+1, __pyx_v_chrom);
__Pyx_GIVEREF(__pyx_v_chrom);
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_8, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_8, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (!(likely(PyList_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyList_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_cpeaks, ((PyObject*)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1848
+ /* "MACS2/IO/CallPeakUnit.pyx":1861
* cpeaks = peaks.get_data_from_chrom(chrom)
*
* prev_i = 0 # <<<<<<<<<<<<<<
@@ -22729,7 +22794,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
*/
__pyx_v_prev_i = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1849
+ /* "MACS2/IO/CallPeakUnit.pyx":1862
*
* prev_i = 0
* prev_j = 0 # <<<<<<<<<<<<<<
@@ -22738,7 +22803,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
*/
__pyx_v_prev_j = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1850
+ /* "MACS2/IO/CallPeakUnit.pyx":1863
* prev_i = 0
* prev_j = 0
* for m in range(len(cpeaks)): # <<<<<<<<<<<<<<
@@ -22747,13 +22812,13 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
*/
if (unlikely(__pyx_v_cpeaks == Py_None)) {
PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_14 = PyList_GET_SIZE(__pyx_v_cpeaks); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyList_GET_SIZE(__pyx_v_cpeaks); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
for (__pyx_t_15 = 0; __pyx_t_15 < __pyx_t_14; __pyx_t_15+=1) {
__pyx_v_m = __pyx_t_15;
- /* "MACS2/IO/CallPeakUnit.pyx":1851
+ /* "MACS2/IO/CallPeakUnit.pyx":1864
* prev_j = 0
* for m in range(len(cpeaks)):
* thispeak = cpeaks[m] # <<<<<<<<<<<<<<
@@ -22762,64 +22827,64 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
*/
if (unlikely(__pyx_v_cpeaks == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_cpeaks, __pyx_v_m, int32_t, 1, __Pyx_PyInt_From_int32_t, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1851; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt_List(__pyx_v_cpeaks, __pyx_v_m, int32_t, 1, __Pyx_PyInt_From_int32_t, 1, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1864; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_XDECREF_SET(__pyx_v_thispeak, __pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1852
+ /* "MACS2/IO/CallPeakUnit.pyx":1865
* for m in range(len(cpeaks)):
* thispeak = cpeaks[m]
* startpos = thispeak["start"] - window_size # <<<<<<<<<<<<<<
* endpos = thispeak["end"] + window_size
* temp = []
*/
- __pyx_t_1 = PyObject_GetItem(__pyx_v_thispeak, __pyx_n_s_start); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1852; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = PyObject_GetItem(__pyx_v_thispeak, __pyx_n_s_start); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1865; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_window_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_window_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_8 = PyNumber_Subtract(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Subtract(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_16 = __Pyx_PyInt_As_int32_t(__pyx_t_8); if (unlikely((__pyx_t_16 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = __Pyx_PyInt_As_int32_t(__pyx_t_8); if (unlikely((__pyx_t_16 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_v_startpos = __pyx_t_16;
- /* "MACS2/IO/CallPeakUnit.pyx":1853
+ /* "MACS2/IO/CallPeakUnit.pyx":1866
* thispeak = cpeaks[m]
* startpos = thispeak["start"] - window_size
* endpos = thispeak["end"] + window_size # <<<<<<<<<<<<<<
* temp = []
* for i in range(prev_i,plus.shape[0]):
*/
- __pyx_t_8 = PyObject_GetItem(__pyx_v_thispeak, __pyx_n_s_end); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1853; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_thispeak, __pyx_n_s_end); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1866; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_window_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_window_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyNumber_Add(__pyx_t_8, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Add(__pyx_t_8, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_16 = __Pyx_PyInt_As_int32_t(__pyx_t_1); if (unlikely((__pyx_t_16 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = __Pyx_PyInt_As_int32_t(__pyx_t_1); if (unlikely((__pyx_t_16 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_endpos = __pyx_t_16;
- /* "MACS2/IO/CallPeakUnit.pyx":1854
+ /* "MACS2/IO/CallPeakUnit.pyx":1867
* startpos = thispeak["start"] - window_size
* endpos = thispeak["end"] + window_size
* temp = [] # <<<<<<<<<<<<<<
* for i in range(prev_i,plus.shape[0]):
* pos = plus[i]
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_XDECREF_SET(__pyx_v_temp, ((PyObject*)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1855
+ /* "MACS2/IO/CallPeakUnit.pyx":1868
* endpos = thispeak["end"] + window_size
* temp = []
* for i in range(prev_i,plus.shape[0]): # <<<<<<<<<<<<<<
@@ -22830,20 +22895,20 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
for (__pyx_t_16 = __pyx_v_prev_i; __pyx_t_16 < __pyx_t_17; __pyx_t_16+=1) {
__pyx_v_i = __pyx_t_16;
- /* "MACS2/IO/CallPeakUnit.pyx":1856
+ /* "MACS2/IO/CallPeakUnit.pyx":1869
* temp = []
* for i in range(prev_i,plus.shape[0]):
* pos = plus[i] # <<<<<<<<<<<<<<
* if pos < startpos:
* continue
*/
- __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_plus), __pyx_v_i, int32_t, 1, __Pyx_PyInt_From_int32_t, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1856; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_plus), __pyx_v_i, int32_t, 1, __Pyx_PyInt_From_int32_t, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1869; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_18 = __Pyx_PyInt_As_int32_t(__pyx_t_1); if (unlikely((__pyx_t_18 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1856; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_18 = __Pyx_PyInt_As_int32_t(__pyx_t_1); if (unlikely((__pyx_t_18 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1869; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_pos = __pyx_t_18;
- /* "MACS2/IO/CallPeakUnit.pyx":1857
+ /* "MACS2/IO/CallPeakUnit.pyx":1870
* for i in range(prev_i,plus.shape[0]):
* pos = plus[i]
* if pos < startpos: # <<<<<<<<<<<<<<
@@ -22853,7 +22918,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__pyx_t_11 = ((__pyx_v_pos < __pyx_v_startpos) != 0);
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1858
+ /* "MACS2/IO/CallPeakUnit.pyx":1871
* pos = plus[i]
* if pos < startpos:
* continue # <<<<<<<<<<<<<<
@@ -22863,7 +22928,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
goto __pyx_L11_continue;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1859
+ /* "MACS2/IO/CallPeakUnit.pyx":1872
* if pos < startpos:
* continue
* elif pos > endpos: # <<<<<<<<<<<<<<
@@ -22873,7 +22938,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__pyx_t_11 = ((__pyx_v_pos > __pyx_v_endpos) != 0);
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1860
+ /* "MACS2/IO/CallPeakUnit.pyx":1873
* continue
* elif pos > endpos:
* prev_i = i # <<<<<<<<<<<<<<
@@ -22882,7 +22947,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
*/
__pyx_v_prev_i = __pyx_v_i;
- /* "MACS2/IO/CallPeakUnit.pyx":1861
+ /* "MACS2/IO/CallPeakUnit.pyx":1874
* elif pos > endpos:
* prev_i = i
* break # <<<<<<<<<<<<<<
@@ -22893,32 +22958,32 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1863
+ /* "MACS2/IO/CallPeakUnit.pyx":1876
* break
* else:
* temp.append(pos) # <<<<<<<<<<<<<<
* rt_plus = np.array(temp)
*
*/
- __pyx_t_1 = __Pyx_PyInt_From_int32_t(__pyx_v_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_int32_t(__pyx_v_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_temp, __pyx_t_1); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_temp, __pyx_t_1); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
__pyx_L11_continue:;
}
__pyx_L12_break:;
- /* "MACS2/IO/CallPeakUnit.pyx":1864
+ /* "MACS2/IO/CallPeakUnit.pyx":1877
* else:
* temp.append(pos)
* rt_plus = np.array(temp) # <<<<<<<<<<<<<<
*
* temp = []
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_array); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_array); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = NULL;
@@ -22932,37 +22997,37 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
}
if (!__pyx_t_2) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_8, __pyx_v_temp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_8, __pyx_v_temp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
} else {
- __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = NULL;
__Pyx_INCREF(__pyx_v_temp);
PyTuple_SET_ITEM(__pyx_t_5, 0+1, __pyx_v_temp);
__Pyx_GIVEREF(__pyx_v_temp);
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_rt_plus, ((PyArrayObject *)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1866
+ /* "MACS2/IO/CallPeakUnit.pyx":1879
* rt_plus = np.array(temp)
*
* temp = [] # <<<<<<<<<<<<<<
* for j in range(prev_j,minus.shape[0]):
* pos = minus[j]
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF_SET(__pyx_v_temp, ((PyObject*)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1867
+ /* "MACS2/IO/CallPeakUnit.pyx":1880
*
* temp = []
* for j in range(prev_j,minus.shape[0]): # <<<<<<<<<<<<<<
@@ -22973,20 +23038,20 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
for (__pyx_t_16 = __pyx_v_prev_j; __pyx_t_16 < __pyx_t_17; __pyx_t_16+=1) {
__pyx_v_j = __pyx_t_16;
- /* "MACS2/IO/CallPeakUnit.pyx":1868
+ /* "MACS2/IO/CallPeakUnit.pyx":1881
* temp = []
* for j in range(prev_j,minus.shape[0]):
* pos = minus[j] # <<<<<<<<<<<<<<
* if pos < startpos:
* continue
*/
- __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_minus), __pyx_v_j, int32_t, 1, __Pyx_PyInt_From_int32_t, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1868; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_minus), __pyx_v_j, int32_t, 1, __Pyx_PyInt_From_int32_t, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1881; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_18 = __Pyx_PyInt_As_int32_t(__pyx_t_1); if (unlikely((__pyx_t_18 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_18 = __Pyx_PyInt_As_int32_t(__pyx_t_1); if (unlikely((__pyx_t_18 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_pos = __pyx_t_18;
- /* "MACS2/IO/CallPeakUnit.pyx":1869
+ /* "MACS2/IO/CallPeakUnit.pyx":1882
* for j in range(prev_j,minus.shape[0]):
* pos = minus[j]
* if pos < startpos: # <<<<<<<<<<<<<<
@@ -22996,7 +23061,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__pyx_t_11 = ((__pyx_v_pos < __pyx_v_startpos) != 0);
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1870
+ /* "MACS2/IO/CallPeakUnit.pyx":1883
* pos = minus[j]
* if pos < startpos:
* continue # <<<<<<<<<<<<<<
@@ -23006,7 +23071,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
goto __pyx_L14_continue;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1871
+ /* "MACS2/IO/CallPeakUnit.pyx":1884
* if pos < startpos:
* continue
* elif pos > endpos: # <<<<<<<<<<<<<<
@@ -23016,7 +23081,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__pyx_t_11 = ((__pyx_v_pos > __pyx_v_endpos) != 0);
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1872
+ /* "MACS2/IO/CallPeakUnit.pyx":1885
* continue
* elif pos > endpos:
* prev_j = j # <<<<<<<<<<<<<<
@@ -23025,7 +23090,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
*/
__pyx_v_prev_j = __pyx_v_j;
- /* "MACS2/IO/CallPeakUnit.pyx":1873
+ /* "MACS2/IO/CallPeakUnit.pyx":1886
* elif pos > endpos:
* prev_j = j
* break # <<<<<<<<<<<<<<
@@ -23036,32 +23101,32 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1875
+ /* "MACS2/IO/CallPeakUnit.pyx":1888
* break
* else:
* temp.append(pos) # <<<<<<<<<<<<<<
* rt_minus = np.array(temp)
*
*/
- __pyx_t_1 = __Pyx_PyInt_From_int32_t(__pyx_v_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_int32_t(__pyx_v_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_temp, __pyx_t_1); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyList_Append(__pyx_v_temp, __pyx_t_1); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
__pyx_L14_continue:;
}
__pyx_L15_break:;
- /* "MACS2/IO/CallPeakUnit.pyx":1876
+ /* "MACS2/IO/CallPeakUnit.pyx":1889
* else:
* temp.append(pos)
* rt_minus = np.array(temp) # <<<<<<<<<<<<<<
*
* (adjusted_summits, passflags) = wtd_find_summit(chrom, rt_plus, rt_minus, startpos, endpos, window_size, cutoff)
*/
- __pyx_t_8 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_array); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_8, __pyx_n_s_array); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_8 = NULL;
@@ -23075,32 +23140,32 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
}
if (!__pyx_t_8) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_v_temp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_5, __pyx_v_temp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
} else {
- __pyx_t_2 = PyTuple_New(1+1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1+1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_8); __Pyx_GIVEREF(__pyx_t_8); __pyx_t_8 = NULL;
__Pyx_INCREF(__pyx_v_temp);
PyTuple_SET_ITEM(__pyx_t_2, 0+1, __pyx_v_temp);
__Pyx_GIVEREF(__pyx_v_temp);
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_rt_minus, ((PyArrayObject *)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1878
+ /* "MACS2/IO/CallPeakUnit.pyx":1891
* rt_minus = np.array(temp)
*
* (adjusted_summits, passflags) = wtd_find_summit(chrom, rt_plus, rt_minus, startpos, endpos, window_size, cutoff) # <<<<<<<<<<<<<<
* # those local maxima above cutoff will be defined as good summits
* for i in range(len(adjusted_summits)):
*/
- __pyx_t_1 = __pyx_f_5MACS2_2IO_12CallPeakUnit_wtd_find_summit(__pyx_v_chrom, __pyx_v_rt_plus, __pyx_v_rt_minus, __pyx_v_startpos, __pyx_v_endpos, __pyx_v_window_size, __pyx_v_cutoff); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_5MACS2_2IO_12CallPeakUnit_wtd_find_summit(__pyx_v_chrom, __pyx_v_rt_plus, __pyx_v_rt_minus, __pyx_v_startpos, __pyx_v_endpos, __pyx_v_window_size, __pyx_v_cutoff); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
PyObject* sequence = __pyx_t_1;
@@ -23112,7 +23177,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
if (unlikely(size != 2)) {
if (size > 2) __Pyx_RaiseTooManyValuesError(2);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
@@ -23125,15 +23190,15 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__Pyx_INCREF(__pyx_t_5);
__Pyx_INCREF(__pyx_t_2);
#else
- __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
#endif
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
} else {
Py_ssize_t index = -1;
- __pyx_t_8 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_13 = Py_TYPE(__pyx_t_8)->tp_iternext;
@@ -23141,7 +23206,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__Pyx_GOTREF(__pyx_t_5);
index = 1; __pyx_t_2 = __pyx_t_13(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L17_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_13 = NULL;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
goto __pyx_L18_unpacking_done;
@@ -23149,69 +23214,69 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_13 = NULL;
if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L18_unpacking_done:;
}
- if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_adjusted_summits, ((PyArrayObject *)__pyx_t_5));
__pyx_t_5 = 0;
__Pyx_XDECREF_SET(__pyx_v_passflags, ((PyArrayObject *)__pyx_t_2));
__pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1880
+ /* "MACS2/IO/CallPeakUnit.pyx":1893
* (adjusted_summits, passflags) = wtd_find_summit(chrom, rt_plus, rt_minus, startpos, endpos, window_size, cutoff)
* # those local maxima above cutoff will be defined as good summits
* for i in range(len(adjusted_summits)): # <<<<<<<<<<<<<<
* adjusted_summit = adjusted_summits[i]
* passflag = passflags[i]
*/
- __pyx_t_19 = PyObject_Length(((PyObject *)__pyx_v_adjusted_summits)); if (unlikely(__pyx_t_19 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_19 = PyObject_Length(((PyObject *)__pyx_v_adjusted_summits)); if (unlikely(__pyx_t_19 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
for (__pyx_t_16 = 0; __pyx_t_16 < __pyx_t_19; __pyx_t_16+=1) {
__pyx_v_i = __pyx_t_16;
- /* "MACS2/IO/CallPeakUnit.pyx":1881
+ /* "MACS2/IO/CallPeakUnit.pyx":1894
* # those local maxima above cutoff will be defined as good summits
* for i in range(len(adjusted_summits)):
* adjusted_summit = adjusted_summits[i] # <<<<<<<<<<<<<<
* passflag = passflags[i]
* if passflag:
*/
- __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_adjusted_summits), __pyx_v_i, int32_t, 1, __Pyx_PyInt_From_int32_t, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1881; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_adjusted_summits), __pyx_v_i, int32_t, 1, __Pyx_PyInt_From_int32_t, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_XDECREF_SET(__pyx_v_adjusted_summit, __pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1882
+ /* "MACS2/IO/CallPeakUnit.pyx":1895
* for i in range(len(adjusted_summits)):
* adjusted_summit = adjusted_summits[i]
* passflag = passflags[i] # <<<<<<<<<<<<<<
* if passflag:
* tmppeak = copy(thispeak)
*/
- __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_passflags), __pyx_v_i, int32_t, 1, __Pyx_PyInt_From_int32_t, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1882; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_passflags), __pyx_v_i, int32_t, 1, __Pyx_PyInt_From_int32_t, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1895; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
__Pyx_XDECREF_SET(__pyx_v_passflag, __pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1883
+ /* "MACS2/IO/CallPeakUnit.pyx":1896
* adjusted_summit = adjusted_summits[i]
* passflag = passflags[i]
* if passflag: # <<<<<<<<<<<<<<
* tmppeak = copy(thispeak)
* tmppeak["summit"] = adjusted_summit
*/
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_passflag); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_passflag); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1884
+ /* "MACS2/IO/CallPeakUnit.pyx":1897
* passflag = passflags[i]
* if passflag:
* tmppeak = copy(thispeak) # <<<<<<<<<<<<<<
* tmppeak["summit"] = adjusted_summit
* ret_peaks.add_PeakContent(chrom, tmppeak)
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_copy); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_copy); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_5 = NULL;
if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) {
@@ -23224,16 +23289,16 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
}
if (!__pyx_t_5) {
- __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_v_thispeak); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_v_thispeak); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
} else {
- __pyx_t_8 = PyTuple_New(1+1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(1+1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL;
__Pyx_INCREF(__pyx_v_thispeak);
PyTuple_SET_ITEM(__pyx_t_8, 0+1, __pyx_v_thispeak);
__Pyx_GIVEREF(__pyx_v_thispeak);
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_8, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_8, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
}
@@ -23241,23 +23306,23 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__Pyx_XDECREF_SET(__pyx_v_tmppeak, __pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1885
+ /* "MACS2/IO/CallPeakUnit.pyx":1898
* if passflag:
* tmppeak = copy(thispeak)
* tmppeak["summit"] = adjusted_summit # <<<<<<<<<<<<<<
* ret_peaks.add_PeakContent(chrom, tmppeak)
*
*/
- if (unlikely(PyObject_SetItem(__pyx_v_tmppeak, __pyx_n_s_summit, __pyx_v_adjusted_summit) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyObject_SetItem(__pyx_v_tmppeak, __pyx_n_s_summit, __pyx_v_adjusted_summit) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "MACS2/IO/CallPeakUnit.pyx":1886
+ /* "MACS2/IO/CallPeakUnit.pyx":1899
* tmppeak = copy(thispeak)
* tmppeak["summit"] = adjusted_summit
* ret_peaks.add_PeakContent(chrom, tmppeak) # <<<<<<<<<<<<<<
*
* # rewind window_size
*/
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_ret_peaks, __pyx_n_s_add_PeakContent); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_ret_peaks, __pyx_n_s_add_PeakContent); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_8 = NULL;
__pyx_t_20 = 0;
@@ -23271,7 +23336,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__pyx_t_20 = 1;
}
}
- __pyx_t_5 = PyTuple_New(2+__pyx_t_20); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(2+__pyx_t_20); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
if (__pyx_t_8) {
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_8); __Pyx_GIVEREF(__pyx_t_8); __pyx_t_8 = NULL;
@@ -23282,7 +23347,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__Pyx_INCREF(__pyx_v_tmppeak);
PyTuple_SET_ITEM(__pyx_t_5, 1+__pyx_t_20, __pyx_v_tmppeak);
__Pyx_GIVEREF(__pyx_v_tmppeak);
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -23292,7 +23357,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__pyx_L21:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1889
+ /* "MACS2/IO/CallPeakUnit.pyx":1902
*
* # rewind window_size
* for i in range(prev_i, 0, -1): # <<<<<<<<<<<<<<
@@ -23302,31 +23367,31 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
for (__pyx_t_16 = __pyx_v_prev_i; __pyx_t_16 > 0; __pyx_t_16-=1) {
__pyx_v_i = __pyx_t_16;
- /* "MACS2/IO/CallPeakUnit.pyx":1890
+ /* "MACS2/IO/CallPeakUnit.pyx":1903
* # rewind window_size
* for i in range(prev_i, 0, -1):
* if plus[prev_i] - plus[i] >= window_size: # <<<<<<<<<<<<<<
* break
* prev_i = i
*/
- __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_plus), __pyx_v_prev_i, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1890; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_plus), __pyx_v_prev_i, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1903; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_GetItemInt(((PyObject *)__pyx_v_plus), __pyx_v_i, int32_t, 1, __Pyx_PyInt_From_int32_t, 0, 1, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1890; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_2 = __Pyx_GetItemInt(((PyObject *)__pyx_v_plus), __pyx_v_i, int32_t, 1, __Pyx_PyInt_From_int32_t, 0, 1, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1903; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyNumber_Subtract(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Subtract(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_window_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_window_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_5, __pyx_t_2, Py_GE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_5, __pyx_t_2, Py_GE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1891
+ /* "MACS2/IO/CallPeakUnit.pyx":1904
* for i in range(prev_i, 0, -1):
* if plus[prev_i] - plus[i] >= window_size:
* break # <<<<<<<<<<<<<<
@@ -23338,7 +23403,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
__pyx_L23_break:;
- /* "MACS2/IO/CallPeakUnit.pyx":1892
+ /* "MACS2/IO/CallPeakUnit.pyx":1905
* if plus[prev_i] - plus[i] >= window_size:
* break
* prev_i = i # <<<<<<<<<<<<<<
@@ -23347,7 +23412,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
*/
__pyx_v_prev_i = __pyx_v_i;
- /* "MACS2/IO/CallPeakUnit.pyx":1894
+ /* "MACS2/IO/CallPeakUnit.pyx":1907
* prev_i = i
*
* for j in range(prev_j, 0, -1): # <<<<<<<<<<<<<<
@@ -23357,31 +23422,31 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
for (__pyx_t_16 = __pyx_v_prev_j; __pyx_t_16 > 0; __pyx_t_16-=1) {
__pyx_v_j = __pyx_t_16;
- /* "MACS2/IO/CallPeakUnit.pyx":1895
+ /* "MACS2/IO/CallPeakUnit.pyx":1908
*
* for j in range(prev_j, 0, -1):
* if minus[prev_j] - minus[j] >= window_size: # <<<<<<<<<<<<<<
* break
* prev_j = j
*/
- __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_minus), __pyx_v_prev_j, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1895; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_minus), __pyx_v_prev_j, long, 1, __Pyx_PyInt_From_long, 0, 1, 1); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1908; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_GetItemInt(((PyObject *)__pyx_v_minus), __pyx_v_j, int32_t, 1, __Pyx_PyInt_From_int32_t, 0, 1, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1895; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_2 = __Pyx_GetItemInt(((PyObject *)__pyx_v_minus), __pyx_v_j, int32_t, 1, __Pyx_PyInt_From_int32_t, 0, 1, 1); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1908; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyNumber_Subtract(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Subtract(__pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_window_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_window_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_5, __pyx_t_2, Py_GE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_5, __pyx_t_2, Py_GE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1896
+ /* "MACS2/IO/CallPeakUnit.pyx":1909
* for j in range(prev_j, 0, -1):
* if minus[prev_j] - minus[j] >= window_size:
* break # <<<<<<<<<<<<<<
@@ -23393,7 +23458,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
__pyx_L26_break:;
- /* "MACS2/IO/CallPeakUnit.pyx":1897
+ /* "MACS2/IO/CallPeakUnit.pyx":1910
* if minus[prev_j] - minus[j] >= window_size:
* break
* prev_j = j # <<<<<<<<<<<<<<
@@ -23404,7 +23469,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
}
}
- /* "MACS2/IO/CallPeakUnit.pyx":1899
+ /* "MACS2/IO/CallPeakUnit.pyx":1912
* prev_j = j
* # end of a loop
* return ret_peaks # <<<<<<<<<<<<<<
@@ -23415,7 +23480,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_refine
__pyx_r = __pyx_v_ret_peaks;
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":1805
+ /* "MACS2/IO/CallPeakUnit.pyx":1818
* return bpeaks
*
* cpdef refine_peak_from_tags_distribution ( self, peaks, int window_size = 100, float cutoff = 5 ): # <<<<<<<<<<<<<<
@@ -23500,7 +23565,7 @@ static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_13ref
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "refine_peak_from_tags_distribution") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "refine_peak_from_tags_distribution") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -23513,19 +23578,19 @@ static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_13ref
}
__pyx_v_peaks = values[0];
if (values[1]) {
- __pyx_v_window_size = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_window_size == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_window_size = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_window_size == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_window_size = ((int)100);
}
if (values[2]) {
- __pyx_v_cutoff = __pyx_PyFloat_AsFloat(values[2]); if (unlikely((__pyx_v_cutoff == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_cutoff = __pyx_PyFloat_AsFloat(values[2]); if (unlikely((__pyx_v_cutoff == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_cutoff = ((float)5.0);
}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("refine_peak_from_tags_distribution", 0, 1, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("refine_peak_from_tags_distribution", 0, 1, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("MACS2.IO.CallPeakUnit.CallerFromAlignments.refine_peak_from_tags_distribution", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -23551,7 +23616,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_12ref
__pyx_t_2.__pyx_n = 2;
__pyx_t_2.window_size = __pyx_v_window_size;
__pyx_t_2.cutoff = __pyx_v_cutoff;
- __pyx_t_1 = __pyx_vtabptr_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments->refine_peak_from_tags_distribution(__pyx_v_self, __pyx_v_peaks, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_vtabptr_5MACS2_2IO_12CallPeakUnit_CallerFromAlignments->refine_peak_from_tags_distribution(__pyx_v_self, __pyx_v_peaks, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25862,7 +25927,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_Float64HashTable, __pyx_k_Float64HashTable, sizeof(__pyx_k_Float64HashTable), 0, 0, 1, 1},
{&__pyx_kp_u_Format_string_allocated_too_shor, __pyx_k_Format_string_allocated_too_shor, sizeof(__pyx_k_Format_string_allocated_too_shor), 0, 1, 0, 0},
{&__pyx_kp_u_Format_string_allocated_too_shor_2, __pyx_k_Format_string_allocated_too_shor_2, sizeof(__pyx_k_Format_string_allocated_too_shor_2), 0, 1, 0, 0},
- {&__pyx_n_s_IOError, __pyx_k_IOError, sizeof(__pyx_k_IOError), 0, 0, 1, 1},
{&__pyx_n_s_LOG10_E, __pyx_k_LOG10_E, sizeof(__pyx_k_LOG10_E), 0, 0, 1, 1},
{&__pyx_n_s_LogLR_Asym, __pyx_k_LogLR_Asym, sizeof(__pyx_k_LogLR_Asym), 0, 0, 1, 1},
{&__pyx_n_s_MACS2_IO_CallPeakUnit, __pyx_k_MACS2_IO_CallPeakUnit, sizeof(__pyx_k_MACS2_IO_CallPeakUnit), 0, 0, 1, 1},
@@ -25885,7 +25949,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s_TMP_txt, __pyx_k_TMP_txt, sizeof(__pyx_k_TMP_txt), 0, 0, 1, 0},
{&__pyx_kp_s_TREAT_bdg, __pyx_k_TREAT_bdg, sizeof(__pyx_k_TREAT_bdg), 0, 0, 1, 0},
{&__pyx_kp_s_Tao_Liu_vladimir_liu_gmail_com, __pyx_k_Tao_Liu_vladimir_liu_gmail_com, sizeof(__pyx_k_Tao_Liu_vladimir_liu_gmail_com), 0, 0, 1, 0},
- {&__pyx_kp_s_Users_taoliu_Dropbox_projects_m, __pyx_k_Users_taoliu_Dropbox_projects_m, sizeof(__pyx_k_Users_taoliu_Dropbox_projects_m), 0, 0, 1, 0},
+ {&__pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_k_Users_taoliu_Dropbox_Projects_M, sizeof(__pyx_k_Users_taoliu_Dropbox_Projects_M), 0, 0, 1, 0},
{&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1},
{&__pyx_kp_s__32, __pyx_k__32, sizeof(__pyx_k__32), 0, 0, 1, 0},
{&__pyx_kp_s_access_pq_hash_for_d_times, __pyx_k_access_pq_hash_for_d_times, sizeof(__pyx_k_access_pq_hash_for_d_times), 0, 0, 1, 0},
@@ -25989,6 +26053,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_pileup, __pyx_k_pileup, sizeof(__pyx_k_pileup), 0, 0, 1, 1},
{&__pyx_n_s_pileup_a_chromosome, __pyx_k_pileup_a_chromosome, sizeof(__pyx_k_pileup_a_chromosome), 0, 0, 1, 1},
{&__pyx_n_s_pileup_a_chromosome_c, __pyx_k_pileup_a_chromosome_c, sizeof(__pyx_k_pileup_a_chromosome_c), 0, 0, 1, 1},
+ {&__pyx_n_s_pop, __pyx_k_pop, sizeof(__pyx_k_pop), 0, 0, 1, 1},
{&__pyx_n_s_protocol, __pyx_k_protocol, sizeof(__pyx_k_protocol), 0, 0, 1, 1},
{&__pyx_n_s_pscore, __pyx_k_pscore, sizeof(__pyx_k_pscore), 0, 0, 1, 1},
{&__pyx_kp_s_pscore_qscore_npeaks_lpeaks_avel, __pyx_k_pscore_qscore_npeaks_lpeaks_avel, sizeof(__pyx_k_pscore_qscore_npeaks_lpeaks_avel), 0, 0, 1, 0},
@@ -26055,9 +26120,8 @@ static int __Pyx_InitCachedBuiltins(void) {
__pyx_builtin_zip = __Pyx_GetBuiltinName(__pyx_n_s_zip); if (!__pyx_builtin_zip) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_Exception = __Pyx_GetBuiltinName(__pyx_n_s_Exception); if (!__pyx_builtin_Exception) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_file = __Pyx_GetBuiltinName(__pyx_n_s_file); if (!__pyx_builtin_file) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_IOError = __Pyx_GetBuiltinName(__pyx_n_s_IOError); if (!__pyx_builtin_IOError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_sorted = __Pyx_GetBuiltinName(__pyx_n_s_sorted); if (!__pyx_builtin_sorted) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_StopIteration = __Pyx_GetBuiltinName(__pyx_n_s_StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1522; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_sorted = __Pyx_GetBuiltinName(__pyx_n_s_sorted); if (!__pyx_builtin_sorted) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_StopIteration = __Pyx_GetBuiltinName(__pyx_n_s_StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1523; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
@@ -26190,190 +26254,190 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GOTREF(__pyx_slice__13);
__Pyx_GIVEREF(__pyx_slice__13);
- /* "MACS2/IO/CallPeakUnit.pyx":646
+ /* "MACS2/IO/CallPeakUnit.pyx":647
* float32_t * ctrl_value_ptr
*
* logging.debug ( "Start to calculate pvalue stat..." ) # <<<<<<<<<<<<<<
*
* for i in range( len( self.chromosomes ) ):
*/
- __pyx_tuple__14 = PyTuple_Pack(1, __pyx_kp_s_Start_to_calculate_pvalue_stat); if (unlikely(!__pyx_tuple__14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__14 = PyTuple_Pack(1, __pyx_kp_s_Start_to_calculate_pvalue_stat); if (unlikely(!__pyx_tuple__14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__14);
__Pyx_GIVEREF(__pyx_tuple__14);
- /* "MACS2/IO/CallPeakUnit.pyx":735
+ /* "MACS2/IO/CallPeakUnit.pyx":736
* float32_t * score_array_ptr # score array pointer
*
* logging.debug ( "Start to calculate pvalue stat..." ) # <<<<<<<<<<<<<<
*
* tmplist = sorted( list(np.arange(0.3, 10.0, 0.3)), reverse = True )
*/
- __pyx_tuple__15 = PyTuple_Pack(1, __pyx_kp_s_Start_to_calculate_pvalue_stat); if (unlikely(!__pyx_tuple__15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__15 = PyTuple_Pack(1, __pyx_kp_s_Start_to_calculate_pvalue_stat); if (unlikely(!__pyx_tuple__15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__15);
__Pyx_GIVEREF(__pyx_tuple__15);
- /* "MACS2/IO/CallPeakUnit.pyx":737
+ /* "MACS2/IO/CallPeakUnit.pyx":738
* logging.debug ( "Start to calculate pvalue stat..." )
*
* tmplist = sorted( list(np.arange(0.3, 10.0, 0.3)), reverse = True ) # <<<<<<<<<<<<<<
*
* for i in range( len( self.chromosomes ) ):
*/
- __pyx_tuple__16 = PyTuple_Pack(3, __pyx_float_0_3, __pyx_float_10_0, __pyx_float_0_3); if (unlikely(!__pyx_tuple__16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__16 = PyTuple_Pack(3, __pyx_float_0_3, __pyx_float_10_0, __pyx_float_0_3); if (unlikely(!__pyx_tuple__16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__16);
__Pyx_GIVEREF(__pyx_tuple__16);
- /* "MACS2/IO/CallPeakUnit.pyx":842
+ /* "MACS2/IO/CallPeakUnit.pyx":843
* # write pvalue and total length of predicted peaks
* fhd = file( self.cutoff_analysis_filename, "w" )
* fhd.write( "pscore\tqscore\tnpeaks\tlpeaks\tavelpeak\n" ) # <<<<<<<<<<<<<<
* x = []
* y = []
*/
- __pyx_tuple__17 = PyTuple_Pack(1, __pyx_kp_s_pscore_qscore_npeaks_lpeaks_avel); if (unlikely(!__pyx_tuple__17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__17 = PyTuple_Pack(1, __pyx_kp_s_pscore_qscore_npeaks_lpeaks_avel); if (unlikely(!__pyx_tuple__17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__17);
__Pyx_GIVEREF(__pyx_tuple__17);
- /* "MACS2/IO/CallPeakUnit.pyx":851
+ /* "MACS2/IO/CallPeakUnit.pyx":852
* fhd.close()
* logging.info( "#3 Analysis of cutoff vs num of peaks or total length has been saved in %s" % self.cutoff_analysis_filename )
* logging.info( "#3 Suggest a cutoff..." ) # <<<<<<<<<<<<<<
* optimal_cutoff, optimal_length = find_optimal_cutoff( x, y )
* logging.info( "#3 -10log10pvalue cutoff %.2f will call approximately %d bps regions as significant regions" % ( optimal_cutoff, optimal_length ) )
*/
- __pyx_tuple__18 = PyTuple_Pack(1, __pyx_kp_s_3_Suggest_a_cutoff); if (unlikely(!__pyx_tuple__18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__18 = PyTuple_Pack(1, __pyx_kp_s_3_Suggest_a_cutoff); if (unlikely(!__pyx_tuple__18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__18);
__Pyx_GIVEREF(__pyx_tuple__18);
- /* "MACS2/IO/CallPeakUnit.pyx":877
+ /* "MACS2/IO/CallPeakUnit.pyx":878
* # prepare p-q table
* if not self.pqtable:
* logging.info("#3 Pre-compute pvalue-qvalue table...") # <<<<<<<<<<<<<<
* if auto_cutoff:
* logging.info("#3 Cutoff will be automatically decided!")
*/
- __pyx_tuple__19 = PyTuple_Pack(1, __pyx_kp_s_3_Pre_compute_pvalue_qvalue_tab); if (unlikely(!__pyx_tuple__19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__19 = PyTuple_Pack(1, __pyx_kp_s_3_Pre_compute_pvalue_qvalue_tab); if (unlikely(!__pyx_tuple__19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__19);
__Pyx_GIVEREF(__pyx_tuple__19);
- /* "MACS2/IO/CallPeakUnit.pyx":879
+ /* "MACS2/IO/CallPeakUnit.pyx":880
* logging.info("#3 Pre-compute pvalue-qvalue table...")
* if auto_cutoff:
* logging.info("#3 Cutoff will be automatically decided!") # <<<<<<<<<<<<<<
* self.__pre_computes( max_gap = max_gap, min_length = min_length )
* else:
*/
- __pyx_tuple__20 = PyTuple_Pack(1, __pyx_kp_s_3_Cutoff_will_be_automatically); if (unlikely(!__pyx_tuple__20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__20 = PyTuple_Pack(1, __pyx_kp_s_3_Cutoff_will_be_automatically); if (unlikely(!__pyx_tuple__20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__20);
__Pyx_GIVEREF(__pyx_tuple__20);
- /* "MACS2/IO/CallPeakUnit.pyx":890
+ /* "MACS2/IO/CallPeakUnit.pyx":891
* self.bedGraph_ctrl_f = fopen( self.bedGraph_control_filename, "w" )
*
* logging.info ("#3 In the peak calling step, the following will be performed simultaneously:") # <<<<<<<<<<<<<<
* logging.info ("#3 Write bedGraph files for treatment pileup (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_treat_pileup.bdg")
* logging.info ("#3 Write bedGraph files for control lambda (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_control_lambda.bdg")
*/
- __pyx_tuple__21 = PyTuple_Pack(1, __pyx_kp_s_3_In_the_peak_calling_step_the); if (unlikely(!__pyx_tuple__21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__21 = PyTuple_Pack(1, __pyx_kp_s_3_In_the_peak_calling_step_the); if (unlikely(!__pyx_tuple__21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__21);
__Pyx_GIVEREF(__pyx_tuple__21);
- /* "MACS2/IO/CallPeakUnit.pyx":895
+ /* "MACS2/IO/CallPeakUnit.pyx":896
*
* if self.save_SPMR:
* logging.info ( "#3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads." ) # <<<<<<<<<<<<<<
* elif self.treat_scaling_factor == 1:
* logging.info ( "#3 Pileup will be based on sequencing depth in treatment." )
*/
- __pyx_tuple__22 = PyTuple_Pack(1, __pyx_kp_s_3_SPMR_is_requested_so_pileup_w); if (unlikely(!__pyx_tuple__22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__22 = PyTuple_Pack(1, __pyx_kp_s_3_SPMR_is_requested_so_pileup_w); if (unlikely(!__pyx_tuple__22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__22);
__Pyx_GIVEREF(__pyx_tuple__22);
- /* "MACS2/IO/CallPeakUnit.pyx":897
+ /* "MACS2/IO/CallPeakUnit.pyx":898
* logging.info ( "#3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads." )
* elif self.treat_scaling_factor == 1:
* logging.info ( "#3 Pileup will be based on sequencing depth in treatment." ) # <<<<<<<<<<<<<<
* else:
* logging.info ( "#3 Pileup will be based on sequencing depth in control." )
*/
- __pyx_tuple__23 = PyTuple_Pack(1, __pyx_kp_s_3_Pileup_will_be_based_on_seque); if (unlikely(!__pyx_tuple__23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__23 = PyTuple_Pack(1, __pyx_kp_s_3_Pileup_will_be_based_on_seque); if (unlikely(!__pyx_tuple__23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__23);
__Pyx_GIVEREF(__pyx_tuple__23);
- /* "MACS2/IO/CallPeakUnit.pyx":899
+ /* "MACS2/IO/CallPeakUnit.pyx":900
* logging.info ( "#3 Pileup will be based on sequencing depth in treatment." )
* else:
* logging.info ( "#3 Pileup will be based on sequencing depth in control." ) # <<<<<<<<<<<<<<
*
* if self.trackline:
*/
- __pyx_tuple__24 = PyTuple_Pack(1, __pyx_kp_s_3_Pileup_will_be_based_on_seque_2); if (unlikely(!__pyx_tuple__24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__24 = PyTuple_Pack(1, __pyx_kp_s_3_Pileup_will_be_based_on_seque_2); if (unlikely(!__pyx_tuple__24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 900; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__24);
__Pyx_GIVEREF(__pyx_tuple__24);
- /* "MACS2/IO/CallPeakUnit.pyx":908
+ /* "MACS2/IO/CallPeakUnit.pyx":909
* fprintf( self.bedGraph_ctrl_f, tmp_bytes )
*
* logging.info("#3 Call peaks for each chromosome...") # <<<<<<<<<<<<<<
* for chrom in self.chromosomes:
* # treat/control bedGraph will be saved if requested by user.
*/
- __pyx_tuple__25 = PyTuple_Pack(1, __pyx_kp_s_3_Call_peaks_for_each_chromosom); if (unlikely(!__pyx_tuple__25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__25 = PyTuple_Pack(1, __pyx_kp_s_3_Call_peaks_for_each_chromosom); if (unlikely(!__pyx_tuple__25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__25);
__Pyx_GIVEREF(__pyx_tuple__25);
- /* "MACS2/IO/CallPeakUnit.pyx":1458
+ /* "MACS2/IO/CallPeakUnit.pyx":1459
* # prepare p-q table
* if not self.pqtable:
* logging.info("#3 Pre-compute pvalue-qvalue table...") # <<<<<<<<<<<<<<
* if auto_cutoff:
* logging.info("#3 Cutoff for broad region will be automatically decided!")
*/
- __pyx_tuple__28 = PyTuple_Pack(1, __pyx_kp_s_3_Pre_compute_pvalue_qvalue_tab); if (unlikely(!__pyx_tuple__28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__28 = PyTuple_Pack(1, __pyx_kp_s_3_Pre_compute_pvalue_qvalue_tab); if (unlikely(!__pyx_tuple__28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1459; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__28);
__Pyx_GIVEREF(__pyx_tuple__28);
- /* "MACS2/IO/CallPeakUnit.pyx":1460
+ /* "MACS2/IO/CallPeakUnit.pyx":1461
* logging.info("#3 Pre-compute pvalue-qvalue table...")
* if auto_cutoff:
* logging.info("#3 Cutoff for broad region will be automatically decided!") # <<<<<<<<<<<<<<
* self.__pre_computes( max_gap = lvl2_max_gap, min_length = min_length )
* else:
*/
- __pyx_tuple__29 = PyTuple_Pack(1, __pyx_kp_s_3_Cutoff_for_broad_region_will); if (unlikely(!__pyx_tuple__29)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__29 = PyTuple_Pack(1, __pyx_kp_s_3_Cutoff_for_broad_region_will); if (unlikely(!__pyx_tuple__29)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__29);
__Pyx_GIVEREF(__pyx_tuple__29);
- /* "MACS2/IO/CallPeakUnit.pyx":1470
+ /* "MACS2/IO/CallPeakUnit.pyx":1471
* self.bedGraph_treat_f = fopen( self.bedGraph_treat_filename, "w" )
* self.bedGraph_ctrl_f = fopen( self.bedGraph_control_filename, "w" )
* logging.info ("#3 In the peak calling step, the following will be performed simultaneously:") # <<<<<<<<<<<<<<
* logging.info ("#3 Write bedGraph files for treatment pileup (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_treat_pileup.bdg")
* logging.info ("#3 Write bedGraph files for control lambda (after scaling if necessary)... %s" % self.bedGraph_filename_prefix + "_control_lambda.bdg")
*/
- __pyx_tuple__30 = PyTuple_Pack(1, __pyx_kp_s_3_In_the_peak_calling_step_the); if (unlikely(!__pyx_tuple__30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__30 = PyTuple_Pack(1, __pyx_kp_s_3_In_the_peak_calling_step_the); if (unlikely(!__pyx_tuple__30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__30);
__Pyx_GIVEREF(__pyx_tuple__30);
- /* "MACS2/IO/CallPeakUnit.pyx":1482
+ /* "MACS2/IO/CallPeakUnit.pyx":1483
*
*
* logging.info("#3 Call peaks for each chromosome...") # <<<<<<<<<<<<<<
* for chrom in self.chromosomes:
* self.__chrom_call_broadpeak_using_certain_criteria ( lvl1peaks, lvl2peaks, chrom, scoring_function_symbols, lvl1_cutoff_s, lvl2_cutoff_s, min_length, lvl1_max_gap, lvl2_max_gap, self.save_bedGraph )
*/
- __pyx_tuple__31 = PyTuple_Pack(1, __pyx_kp_s_3_Call_peaks_for_each_chromosom); if (unlikely(!__pyx_tuple__31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__31 = PyTuple_Pack(1, __pyx_kp_s_3_Call_peaks_for_each_chromosom); if (unlikely(!__pyx_tuple__31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__31);
__Pyx_GIVEREF(__pyx_tuple__31);
- /* "MACS2/IO/CallPeakUnit.pyx":1782
+ /* "MACS2/IO/CallPeakUnit.pyx":1795
* thickEnd = str(lvl1peakset[-1]["end"])
* blockNum = int(len(lvl1peakset))
* blockSizes = ",".join(map(str,map(itemgetter("length"),lvl1peakset))) #join( map(lambda x:str(x["length"]),lvl1peakset) ) # <<<<<<<<<<<<<<
* blockStarts = ",".join(getitem_then_subtract(lvl1peakset, start)) #join( map(lambda x:str(x["start"]-start),lvl1peakset) )
*
*/
- __pyx_tuple__33 = PyTuple_Pack(1, __pyx_n_s_length); if (unlikely(!__pyx_tuple__33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__33 = PyTuple_Pack(1, __pyx_n_s_length); if (unlikely(!__pyx_tuple__33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__33);
__Pyx_GIVEREF(__pyx_tuple__33);
@@ -26453,7 +26517,7 @@ static int __Pyx_InitCachedConstants(void) {
__pyx_tuple__40 = PyTuple_Pack(2, __pyx_n_s_args, __pyx_n_s_kwargs); if (unlikely(!__pyx_tuple__40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__40);
__Pyx_GIVEREF(__pyx_tuple__40);
- __pyx_codeobj__41 = (PyObject*)__Pyx_PyCode_New(0, 0, 2, 0, CO_VARARGS|CO_VARKEYWORDS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__40, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_projects_m, __pyx_n_s_do_nothing, 83, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__41)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__41 = (PyObject*)__Pyx_PyCode_New(0, 0, 2, 0, CO_VARARGS|CO_VARKEYWORDS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__40, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_do_nothing, 83, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__41)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -27122,47 +27186,47 @@ PyMODINIT_FUNC PyInit_CallPeakUnit(void)
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1063
+ /* "MACS2/IO/CallPeakUnit.pyx":1064
*
* cdef bool __close_peak_wo_subpeaks (self, list peak_content, peaks, int min_length,
* str chrom, int smoothlen, list score_array_s, list score_cutoff_s=[]): # <<<<<<<<<<<<<<
* """Close the peak region, output peak boundaries, peak summit
* and scores, then add the peak to peakIO object.
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1063; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1064; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_k__26 = ((PyObject*)__pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1123
+ /* "MACS2/IO/CallPeakUnit.pyx":1124
*
* cdef bool __close_peak_with_subpeaks (self, list peak_content, peaks, int min_length,
* str chrom, int smoothlen, list score_array_s, list score_cutoff_s=[], # <<<<<<<<<<<<<<
* float min_valley = 0.9 ):
* """Algorithm implemented by Ben, to profile the pileup signals
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_k__27 = ((PyObject*)__pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1702
+ /* "MACS2/IO/CallPeakUnit.pyx":1713
*
* cdef bool __close_peak_for_broad_region (self, list peak_content, peaks, int min_length,
* str chrom, int smoothlen, list score_array_s, list score_cutoff_s=[]): # <<<<<<<<<<<<<<
* """Close the broad peak region, output peak boundaries, peak summit
* and scores, then add the peak to peakIO object.
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_k__42 = ((PyObject*)__pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
/* "MACS2/IO/CallPeakUnit.pyx":1
- * # Time-stamp: <2015-07-30 15:55:55 Tao Liu> # <<<<<<<<<<<<<<
+ * # Time-stamp: <2015-12-22 16:06:56 Tao Liu> # <<<<<<<<<<<<<<
*
* """Module for Calculate Scores.
*/
diff --git a/MACS2/IO/CallPeakUnit.pyx b/MACS2/IO/CallPeakUnit.pyx
index a790c17..9fa6dd9 100644
--- a/MACS2/IO/CallPeakUnit.pyx
+++ b/MACS2/IO/CallPeakUnit.pyx
@@ -1,4 +1,4 @@
-# Time-stamp: <2015-07-30 15:55:55 Tao Liu>
+# Time-stamp: <2015-12-22 16:06:56 Tao Liu>
"""Module for Calculate Scores.
@@ -461,7 +461,7 @@ cdef class CallerFromAlignments:
self.chr_pos_treat_ctrl = cPickle.load( f )
f.close()
return
- except IOError:
+ except:
temp_fd, temp_filename = mkstemp()
os.close(temp_fd)
self.pileup_data_files[ chrom ] = temp_filename
@@ -507,8 +507,9 @@ cdef class CallerFromAlignments:
f = file(self.pileup_data_files[ chrom ],"wb")
cPickle.dump( self.chr_pos_treat_ctrl, f , protocol=2 )
f.close()
- except IOError:
- pass
+ except:
+ # fail to write then remove the key in pileup_data_files
+ self.pileup_data_files.pop(chrom)
return
cdef list __chrom_pair_treat_ctrl ( self, treat_pv, ctrl_pv ):
@@ -1585,7 +1586,7 @@ cdef class CallerFromAlignments:
# get the regions with scores above cutoffs
above_cutoff = np.nonzero( apply_multiple_cutoffs(score_array_s,lvl1_cutoff_s) )[0] # this is not an optimized method. It would be better to store score array in a 2-D ndarray?
- above_cutoff_index_array = np.arange(pos_array.shape[0])[above_cutoff] # indices
+ above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices
above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff
above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
@@ -1611,6 +1612,9 @@ cdef class CallerFromAlignments:
cp = ctrl_array_ptr[ ti ]
peak_content.append( ( ts, te, tp, cp, ti ) )
+ acs_ptr += 1 # move ptr
+ ace_ptr += 1
+ acia_ptr+= 1
lastp = te
#peak_content.append( (above_cutoff_startpos[0], above_cutoff_endpos[0], treat_array[above_cutoff_index_array[0]], ctrl_array[above_cutoff_index_array[0]], score_array_s, above_cutoff_index_array[0] ) )
@@ -1645,7 +1649,7 @@ cdef class CallerFromAlignments:
# get the regions with scores above cutoffs
above_cutoff = np.nonzero( apply_multiple_cutoffs(score_array_s,lvl2_cutoff_s) )[0] # this is not an optimized method. It would be better to store score array in a 2-D ndarray?
- above_cutoff_index_array = np.arange(pos_array.shape[0])[above_cutoff] # indices
+ above_cutoff_index_array = np.arange(pos_array.shape[0],dtype="int32")[above_cutoff] # indices
above_cutoff_endpos = pos_array[above_cutoff] # end positions of regions where score is above cutoff
above_cutoff_startpos = pos_array[above_cutoff-1] # start positions of regions where score is above cutoff
@@ -1669,19 +1673,25 @@ cdef class CallerFromAlignments:
ti = acia_ptr[ 0 ]
tp = treat_array_ptr[ ti ]
cp = ctrl_array_ptr[ ti ]
-
peak_content.append( ( ts, te, tp, cp, ti ) )
+ acs_ptr += 1 # move ptr
+ ace_ptr += 1
+ acia_ptr+= 1
+
lastp = te
for i in range( 1, above_cutoff_startpos.size ):
- ts = acs_ptr[ 0 ]
- te = ace_ptr[ 0 ]
- ti = acia_ptr[ 0 ]
- acs_ptr += 1
+ # for everything above cutoff
+ ts = acs_ptr[ 0 ] # get the start
+ te = ace_ptr[ 0 ] # get the end
+ ti = acia_ptr[ 0 ]# get the index
+
+ acs_ptr += 1 # move ptr
ace_ptr += 1
acia_ptr+= 1
- tp = treat_array_ptr[ ti ]
- cp = ctrl_array_ptr[ ti ]
- tl = ts - lastp
+ tp = treat_array_ptr[ ti ] # get the treatment pileup
+ cp = ctrl_array_ptr[ ti ] # get the control pileup
+ tl = ts - lastp # get the distance from the current point to last position of existing peak_content
+
if tl <= lvl2_max_gap:
# append
peak_content.append( ( ts, te, tp, cp, ti ) )
@@ -1689,6 +1699,7 @@ cdef class CallerFromAlignments:
else:
# close
self.__close_peak_for_broad_region (peak_content, lvl2peaks, min_length, chrom, lvl2_max_gap/2, score_array_s )
+
peak_content = [ ( ts, te, tp, cp, ti ), ]
lastp = te
@@ -1743,6 +1754,8 @@ cdef class CallerFromAlignments:
fold_change = mean_from_value_length( tarray_fc, tlist_length ),
qscore = mean_from_value_length( tarray_qscore, tlist_length ),
)
+ #if chrom == "chr1" and peak_content[0][0] == 237643 and peak_content[-1][1] == 237935:
+ # print tarray_qscore, tlist_length
# start a new peak
return True
diff --git a/MACS2/IO/FixWidthTrack.c b/MACS2/IO/FixWidthTrack.c
index d1923a6..d86a8e6 100644
--- a/MACS2/IO/FixWidthTrack.c
+++ b/MACS2/IO/FixWidthTrack.c
@@ -455,7 +455,7 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
"MACS2/IO/FixWidthTrack.pyx",
- "__init__.pxd",
+ "numpy.pxd",
"type.pxd",
"bool.pxd",
"complex.pxd",
@@ -496,7 +496,7 @@ typedef struct {
} __Pyx_BufFmt_Context;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726
+/* "numpy.pxd":723
* # in Cython to enable them only on the right systems.
*
* ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
@@ -505,7 +505,7 @@ typedef struct {
*/
typedef npy_int8 __pyx_t_5numpy_int8_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":727
+/* "numpy.pxd":724
*
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
@@ -514,7 +514,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t;
*/
typedef npy_int16 __pyx_t_5numpy_int16_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":728
+/* "numpy.pxd":725
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
@@ -523,7 +523,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t;
*/
typedef npy_int32 __pyx_t_5numpy_int32_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":729
+/* "numpy.pxd":726
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
@@ -532,7 +532,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t;
*/
typedef npy_int64 __pyx_t_5numpy_int64_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733
+/* "numpy.pxd":730
* #ctypedef npy_int128 int128_t
*
* ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
@@ -541,7 +541,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t;
*/
typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":734
+/* "numpy.pxd":731
*
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
@@ -550,7 +550,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t;
*/
typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":735
+/* "numpy.pxd":732
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
@@ -559,7 +559,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t;
*/
typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":736
+/* "numpy.pxd":733
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
@@ -568,7 +568,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t;
*/
typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":740
+/* "numpy.pxd":737
* #ctypedef npy_uint128 uint128_t
*
* ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
@@ -577,7 +577,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t;
*/
typedef npy_float32 __pyx_t_5numpy_float32_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":741
+/* "numpy.pxd":738
*
* ctypedef npy_float32 float32_t
* ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
@@ -586,7 +586,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t;
*/
typedef npy_float64 __pyx_t_5numpy_float64_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":750
+/* "numpy.pxd":747
* # The int types are mapped a bit surprising --
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t # <<<<<<<<<<<<<<
@@ -595,7 +595,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t;
*/
typedef npy_long __pyx_t_5numpy_int_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751
+/* "numpy.pxd":748
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
@@ -604,7 +604,7 @@ typedef npy_long __pyx_t_5numpy_int_t;
*/
typedef npy_longlong __pyx_t_5numpy_long_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752
+/* "numpy.pxd":749
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
@@ -613,7 +613,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t;
*/
typedef npy_longlong __pyx_t_5numpy_longlong_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":754
+/* "numpy.pxd":751
* ctypedef npy_longlong longlong_t
*
* ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
@@ -622,7 +622,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t;
*/
typedef npy_ulong __pyx_t_5numpy_uint_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755
+/* "numpy.pxd":752
*
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
@@ -631,7 +631,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756
+/* "numpy.pxd":753
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
@@ -640,7 +640,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758
+/* "numpy.pxd":755
* ctypedef npy_ulonglong ulonglong_t
*
* ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
@@ -649,7 +649,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
*/
typedef npy_intp __pyx_t_5numpy_intp_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759
+/* "numpy.pxd":756
*
* ctypedef npy_intp intp_t
* ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
@@ -658,7 +658,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t;
*/
typedef npy_uintp __pyx_t_5numpy_uintp_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":761
+/* "numpy.pxd":758
* ctypedef npy_uintp uintp_t
*
* ctypedef npy_double float_t # <<<<<<<<<<<<<<
@@ -667,7 +667,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t;
*/
typedef npy_double __pyx_t_5numpy_float_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762
+/* "numpy.pxd":759
*
* ctypedef npy_double float_t
* ctypedef npy_double double_t # <<<<<<<<<<<<<<
@@ -676,7 +676,7 @@ typedef npy_double __pyx_t_5numpy_float_t;
*/
typedef npy_double __pyx_t_5numpy_double_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763
+/* "numpy.pxd":760
* ctypedef npy_double float_t
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
@@ -708,7 +708,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
/*--- Type declarations ---*/
struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":765
+/* "numpy.pxd":762
* ctypedef npy_longdouble longdouble_t
*
* ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
@@ -717,7 +717,7 @@ struct __pyx_obj_5MACS2_2IO_13FixWidthTrack_FWTrack;
*/
typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766
+/* "numpy.pxd":763
*
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
@@ -726,7 +726,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
*/
typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":767
+/* "numpy.pxd":764
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
@@ -735,7 +735,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
*/
typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":769
+/* "numpy.pxd":766
* ctypedef npy_clongdouble clongdouble_t
*
* ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
@@ -1341,6 +1341,8 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
#endif
#endif
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ptrdiff_t(ptrdiff_t value);
+
static CYTHON_INLINE int __Pyx_StrEq(const char *, const char *); /*proto*/
static int __Pyx_check_binary_version(void);
@@ -1810,6 +1812,7 @@ static PyObject *__pyx_n_s_zeros;
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_5;
+static PyObject *__pyx_int_15;
static PyObject *__pyx_tuple__2;
static PyObject *__pyx_tuple__3;
static PyObject *__pyx_tuple__4;
@@ -5429,7 +5432,7 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* i_dup = 0
* plus = self.__locations[k][0] # <<<<<<<<<<<<<<
* size = plus.shape[0]
- * dup_plus = np.zeros( self.__pointer[k][0],dtype='int32' )
+ * dup_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' )
*/
if (unlikely(__pyx_v_self->__pyx___locations == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
@@ -5466,16 +5469,16 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* i_dup = 0
* plus = self.__locations[k][0]
* size = plus.shape[0] # <<<<<<<<<<<<<<
- * dup_plus = np.zeros( self.__pointer[k][0],dtype='int32' )
- * if len(plus) < 1:
+ * dup_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' )
+ * if len(plus) <= 1:
*/
__pyx_v_size = (__pyx_v_plus->dimensions[0]);
/* "MACS2/IO/FixWidthTrack.pyx":292
* plus = self.__locations[k][0]
* size = plus.shape[0]
- * dup_plus = np.zeros( self.__pointer[k][0],dtype='int32' ) # <<<<<<<<<<<<<<
- * if len(plus) < 1:
+ * dup_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' ) # <<<<<<<<<<<<<<
+ * if len(plus) <= 1:
* new_plus = plus # do nothing
*/
__pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -5492,19 +5495,22 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
__pyx_t_5 = __Pyx_GetItemInt(__pyx_t_2, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Add(__pyx_t_5, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_5 = 0;
- __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_5, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_10 = ((PyArrayObject *)__pyx_t_3);
{
@@ -5529,21 +5535,21 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
/* "MACS2/IO/FixWidthTrack.pyx":293
* size = plus.shape[0]
- * dup_plus = np.zeros( self.__pointer[k][0],dtype='int32' )
- * if len(plus) < 1: # <<<<<<<<<<<<<<
+ * dup_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' )
+ * if len(plus) <= 1: # <<<<<<<<<<<<<<
* new_plus = plus # do nothing
* else:
*/
__pyx_t_15 = PyObject_Length(((PyObject *)__pyx_v_plus)); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = ((__pyx_t_15 < 1) != 0);
+ __pyx_t_7 = ((__pyx_t_15 <= 1) != 0);
if (__pyx_t_7) {
/* "MACS2/IO/FixWidthTrack.pyx":294
- * dup_plus = np.zeros( self.__pointer[k][0],dtype='int32' )
- * if len(plus) < 1:
+ * dup_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' )
+ * if len(plus) <= 1:
* new_plus = plus # do nothing # <<<<<<<<<<<<<<
* else:
- * new_plus = np.zeros( self.__pointer[k][0],dtype='int32' )
+ * new_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' )
*/
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -5570,14 +5576,14 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
/* "MACS2/IO/FixWidthTrack.pyx":296
* new_plus = plus # do nothing
* else:
- * new_plus = np.zeros( self.__pointer[k][0],dtype='int32' ) # <<<<<<<<<<<<<<
+ * new_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' ) # <<<<<<<<<<<<<<
* new_plus[ i_new ] = plus[ i_new ] # first item
* i_new += 1
*/
__pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (unlikely(__pyx_v_self->__pyx___pointer == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
@@ -5585,22 +5591,25 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
}
__pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___pointer, __pyx_v_k); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_3, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_Add(__pyx_t_5, __pyx_int_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ __pyx_t_3 = 0;
+ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_10 = ((PyArrayObject *)__pyx_t_1);
{
@@ -5625,7 +5634,7 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
/* "MACS2/IO/FixWidthTrack.pyx":297
* else:
- * new_plus = np.zeros( self.__pointer[k][0],dtype='int32' )
+ * new_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' )
* new_plus[ i_new ] = plus[ i_new ] # first item # <<<<<<<<<<<<<<
* i_new += 1
* current_loc = plus[0]
@@ -5635,7 +5644,7 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_new_plus.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_new_plus.diminfo[0].strides) = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_plus.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_plus.diminfo[0].strides));
/* "MACS2/IO/FixWidthTrack.pyx":298
- * new_plus = np.zeros( self.__pointer[k][0],dtype='int32' )
+ * new_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' )
* new_plus[ i_new ] = plus[ i_new ] # first item
* i_new += 1 # <<<<<<<<<<<<<<
* current_loc = plus[0]
@@ -5735,10 +5744,10 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
*/
__pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_n); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_v_maxint, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_v_maxint, Py_GT); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_7) {
/* "MACS2/IO/FixWidthTrack.pyx":309
@@ -5792,24 +5801,24 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* dup_plus.resize( i_dup, refcheck=False )
* self.total += i_new
*/
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_new_plus), __pyx_n_s_resize); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_new_plus), __pyx_n_s_resize); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__pyx_t_1 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_5, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":315
* i_new += 1
@@ -5818,24 +5827,24 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* self.total += i_new
* self.dup_total += i_dup
*/
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_dup_plus), __pyx_n_s_resize); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_dup_plus), __pyx_n_s_resize); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_dup); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":316
* new_plus.resize( i_new, refcheck=False )
@@ -5862,17 +5871,17 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* self.__dup_pointer[k][0] = i_dup
* # unnecessary shape calls
*/
- __pyx_t_2 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
if (unlikely(__pyx_v_self->__pyx___pointer == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_1 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___pointer, __pyx_v_k); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_1, 0, __pyx_t_2, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_1, 0, __pyx_t_3, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":319
* self.dup_total += i_dup
@@ -5881,17 +5890,17 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* # unnecessary shape calls
* # self.total += new_plus.shape[0]
*/
- __pyx_t_2 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_dup); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_dup); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
if (unlikely(__pyx_v_self->__pyx___dup_pointer == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_1 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___dup_pointer, __pyx_v_k); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_1, 0, __pyx_t_2, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_1, 0, __pyx_t_3, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":329
* # however, on Mac OSX, it seems directly assigning 0
@@ -5900,24 +5909,24 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* plus.resize( 0, refcheck=False )
* # hope there would be no mem leak...
*/
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_plus), __pyx_n_s_resize); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_plus), __pyx_n_s_resize); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v_self->buffer_size); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_5, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":330
* # doesn't do a thing.
@@ -5926,16 +5935,16 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* # hope there would be no mem leak...
*
*/
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_plus), __pyx_n_s_resize); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_plus), __pyx_n_s_resize); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_tuple__8, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__8, __pyx_t_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
}
__pyx_L6:;
@@ -5962,17 +5971,17 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* i_dup = 0
* minus = self.__locations[k][1] # <<<<<<<<<<<<<<
* size = minus.shape[0]
- * dup_minus = np.zeros( self.__pointer[k][1],dtype='int32' )
+ * dup_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' )
*/
if (unlikely(__pyx_v_self->__pyx___locations == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___locations, __pyx_v_k); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_3, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_5 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___locations, __pyx_v_k); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_5, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_10 = ((PyArrayObject *)__pyx_t_1);
{
@@ -5999,22 +6008,22 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* i_dup = 0
* minus = self.__locations[k][1]
* size = minus.shape[0] # <<<<<<<<<<<<<<
- * dup_minus = np.zeros( self.__pointer[k][1],dtype='int32' )
- * if len(minus) < 1:
+ * dup_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' )
+ * if len(minus) <= 1:
*/
__pyx_v_size = (__pyx_v_minus->dimensions[0]);
/* "MACS2/IO/FixWidthTrack.pyx":338
* minus = self.__locations[k][1]
* size = minus.shape[0]
- * dup_minus = np.zeros( self.__pointer[k][1],dtype='int32' ) # <<<<<<<<<<<<<<
- * if len(minus) < 1:
+ * dup_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' ) # <<<<<<<<<<<<<<
+ * if len(minus) <= 1:
* new_minus = minus # do nothing
*/
__pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (unlikely(__pyx_v_self->__pyx___pointer == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
@@ -6022,24 +6031,27 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
}
__pyx_t_1 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___pointer, __pyx_v_k); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_1, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_1, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Add(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_5 = 0;
- __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_1, __pyx_t_5); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_2, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = ((PyArrayObject *)__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = ((PyArrayObject *)__pyx_t_3);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_dup_minus.rcbuffer->pybuffer);
@@ -6057,26 +6069,26 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_10 = 0;
- __Pyx_XDECREF_SET(__pyx_v_dup_minus, ((PyArrayObject *)__pyx_t_2));
- __pyx_t_2 = 0;
+ __Pyx_XDECREF_SET(__pyx_v_dup_minus, ((PyArrayObject *)__pyx_t_3));
+ __pyx_t_3 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":339
* size = minus.shape[0]
- * dup_minus = np.zeros( self.__pointer[k][1],dtype='int32' )
- * if len(minus) < 1: # <<<<<<<<<<<<<<
+ * dup_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' )
+ * if len(minus) <= 1: # <<<<<<<<<<<<<<
* new_minus = minus # do nothing
* else:
*/
__pyx_t_15 = PyObject_Length(((PyObject *)__pyx_v_minus)); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = ((__pyx_t_15 < 1) != 0);
+ __pyx_t_7 = ((__pyx_t_15 <= 1) != 0);
if (__pyx_t_7) {
/* "MACS2/IO/FixWidthTrack.pyx":340
- * dup_minus = np.zeros( self.__pointer[k][1],dtype='int32' )
- * if len(minus) < 1:
+ * dup_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' )
+ * if len(minus) <= 1:
* new_minus = minus # do nothing # <<<<<<<<<<<<<<
* else:
- * new_minus = np.zeros( self.__pointer[k][1],dtype='int32' )
+ * new_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' )
*/
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -6103,39 +6115,42 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
/* "MACS2/IO/FixWidthTrack.pyx":342
* new_minus = minus # do nothing
* else:
- * new_minus = np.zeros( self.__pointer[k][1],dtype='int32' ) # <<<<<<<<<<<<<<
+ * new_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' ) # <<<<<<<<<<<<<<
* new_minus[ i_new ] = minus[ i_new ] # first item
* i_new += 1
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_zeros); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_zeros); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (unlikely(__pyx_v_self->__pyx___pointer == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_2 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___pointer, __pyx_v_k); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___pointer, __pyx_v_k); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_3, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_2, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyNumber_Add(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_2, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ __pyx_t_3 = 0;
+ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = ((PyArrayObject *)__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = ((PyArrayObject *)__pyx_t_5);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_new_minus.rcbuffer->pybuffer);
@@ -6153,12 +6168,12 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_10 = 0;
- __Pyx_XDECREF_SET(__pyx_v_new_minus, ((PyArrayObject *)__pyx_t_3));
- __pyx_t_3 = 0;
+ __Pyx_XDECREF_SET(__pyx_v_new_minus, ((PyArrayObject *)__pyx_t_5));
+ __pyx_t_5 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":343
* else:
- * new_minus = np.zeros( self.__pointer[k][1],dtype='int32' )
+ * new_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' )
* new_minus[ i_new ] = minus[ i_new ] # first item # <<<<<<<<<<<<<<
* i_new += 1
* current_loc = minus[0]
@@ -6168,7 +6183,7 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_new_minus.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_new_minus.diminfo[0].strides) = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_minus.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_minus.diminfo[0].strides));
/* "MACS2/IO/FixWidthTrack.pyx":344
- * new_minus = np.zeros( self.__pointer[k][1],dtype='int32' )
+ * new_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' )
* new_minus[ i_new ] = minus[ i_new ] # first item
* i_new += 1 # <<<<<<<<<<<<<<
* current_loc = minus[0]
@@ -6266,12 +6281,12 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* dup_minus [ i_dup ] = p
* i_dup += 1
*/
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_n); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_v_maxint, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_n); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_5, __pyx_v_maxint, Py_GT); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_7) {
/* "MACS2/IO/FixWidthTrack.pyx":355
@@ -6325,24 +6340,24 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* dup_minus.resize( i_dup , refcheck = False)
* # shape calls unnecessary
*/
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_new_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_new_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":361
* i_new += 1
@@ -6351,24 +6366,24 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* # shape calls unnecessary
* self.total += i_new
*/
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_dup_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_dup_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_5 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_dup); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_dup); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":363
* dup_minus.resize( i_dup , refcheck = False)
@@ -6395,17 +6410,17 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* self.__dup_pointer[k][1] = i_dup
* # self.total += new_minus.shape[0]
*/
- __pyx_t_1 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
if (unlikely(__pyx_v_self->__pyx___pointer == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___pointer, __pyx_v_k); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_3);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_3, 1, __pyx_t_1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___pointer, __pyx_v_k); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_5);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_5, 1, __pyx_t_3, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":366
* self.dup_total += i_dup
@@ -6414,17 +6429,17 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* # self.total += new_minus.shape[0]
* # dups.total += dup_minus.shape[0]
*/
- __pyx_t_1 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_dup); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_dup); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
if (unlikely(__pyx_v_self->__pyx___dup_pointer == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___dup_pointer, __pyx_v_k); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_3);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_3, 1, __pyx_t_1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___dup_pointer, __pyx_v_k); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_5);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_5, 1, __pyx_t_3, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":375
* # however, on Mac OSX, it seems directly assigning 0
@@ -6433,24 +6448,24 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* minus.resize( 0, refcheck=False )
* # hope there would be no mem leak...
*/
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v_self->buffer_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = __Pyx_PyInt_From_long(__pyx_v_self->buffer_size); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_2, __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":376
* # doesn't do a thing.
@@ -6459,15 +6474,15 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_separate_dups(struc
* # hope there would be no mem leak...
*
*/
- __pyx_t_5 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_tuple__9, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_tuple__9, __pyx_t_5); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
__pyx_L11:;
@@ -7947,7 +7962,7 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
* i_new = 0
* plus = self.__locations[k][0] # <<<<<<<<<<<<<<
* size = plus.shape[0]
- * if len(plus) < 1:
+ * if len(plus) <= 1:
*/
if (unlikely(__pyx_v_self->__pyx___locations == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
@@ -7984,7 +7999,7 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
* i_new = 0
* plus = self.__locations[k][0]
* size = plus.shape[0] # <<<<<<<<<<<<<<
- * if len(plus) < 1:
+ * if len(plus) <= 1:
* new_plus = plus # do nothing
*/
__pyx_v_size = (__pyx_v_plus->dimensions[0]);
@@ -7992,20 +8007,20 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
/* "MACS2/IO/FixWidthTrack.pyx":484
* plus = self.__locations[k][0]
* size = plus.shape[0]
- * if len(plus) < 1: # <<<<<<<<<<<<<<
+ * if len(plus) <= 1: # <<<<<<<<<<<<<<
* new_plus = plus # do nothing
* else:
*/
__pyx_t_16 = PyObject_Length(((PyObject *)__pyx_v_plus)); if (unlikely(__pyx_t_16 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = ((__pyx_t_16 < 1) != 0);
+ __pyx_t_8 = ((__pyx_t_16 <= 1) != 0);
if (__pyx_t_8) {
/* "MACS2/IO/FixWidthTrack.pyx":485
* size = plus.shape[0]
- * if len(plus) < 1:
+ * if len(plus) <= 1:
* new_plus = plus # do nothing # <<<<<<<<<<<<<<
* else:
- * new_plus = np.zeros( self.__pointer[k][0],dtype='int32' )
+ * new_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' )
*/
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -8032,7 +8047,7 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
/* "MACS2/IO/FixWidthTrack.pyx":487
* new_plus = plus # do nothing
* else:
- * new_plus = np.zeros( self.__pointer[k][0],dtype='int32' ) # <<<<<<<<<<<<<<
+ * new_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' ) # <<<<<<<<<<<<<<
* new_plus[ i_new ] = plus[ i_new ] # first item
* i_new += 1
*/
@@ -8050,19 +8065,22 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
__pyx_t_4 = __Pyx_GetItemInt(__pyx_t_2, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Add(__pyx_t_4, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_4 = 0;
- __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_2, __pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_4, __pyx_t_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!(likely(((__pyx_t_6) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_6, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_11 = ((PyArrayObject *)__pyx_t_6);
{
@@ -8087,7 +8105,7 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
/* "MACS2/IO/FixWidthTrack.pyx":488
* else:
- * new_plus = np.zeros( self.__pointer[k][0],dtype='int32' )
+ * new_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' )
* new_plus[ i_new ] = plus[ i_new ] # first item # <<<<<<<<<<<<<<
* i_new += 1
* n = 1 # the number of tags in the current location
@@ -8097,7 +8115,7 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_new_plus.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_new_plus.diminfo[0].strides) = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_plus.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_plus.diminfo[0].strides));
/* "MACS2/IO/FixWidthTrack.pyx":489
- * new_plus = np.zeros( self.__pointer[k][0],dtype='int32' )
+ * new_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' )
* new_plus[ i_new ] = plus[ i_new ] # first item
* i_new += 1 # <<<<<<<<<<<<<<
* n = 1 # the number of tags in the current location
@@ -8204,50 +8222,50 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
* else:
* current_loc = p
*/
- __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_debug); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_p); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_debug); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_p); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_k);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_k);
__Pyx_GIVEREF(__pyx_v_k);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Duplicate_reads_found_at_s_d_at, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = __Pyx_PyString_Format(__pyx_kp_s_Duplicate_reads_found_at_s_d_at, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = NULL;
- if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) {
- __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_2);
+ if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_4))) {
+ __pyx_t_1 = PyMethod_GET_SELF(__pyx_t_4);
if (likely(__pyx_t_1)) {
- PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
+ PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_4);
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(function);
- __Pyx_DECREF_SET(__pyx_t_2, function);
+ __Pyx_DECREF_SET(__pyx_t_4, function);
}
}
if (!__pyx_t_1) {
- __pyx_t_6 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_6 = __Pyx_PyObject_CallOneArg(__pyx_t_4, __pyx_t_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_GOTREF(__pyx_t_6);
} else {
__pyx_t_3 = PyTuple_New(1+1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); __pyx_t_1 = NULL;
- PyTuple_SET_ITEM(__pyx_t_3, 0+1, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_3, 0+1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
}
__pyx_L11:;
@@ -8304,22 +8322,22 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
*/
__pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_new_plus), __pyx_n_s_resize); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_4 = 0;
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
+ if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":507
* n = 1
@@ -8337,17 +8355,17 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
* # self.total += new_plus.shape[0]
* # self.__pointer[k][0] = new_plus.shape[0]
*/
- __pyx_t_4 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_2 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
if (unlikely(__pyx_v_self->__pyx___pointer == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_2 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___pointer, __pyx_v_k); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_2);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_2, 0, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___pointer, __pyx_v_k); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_4);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_4, 0, __pyx_t_2, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":515
* # however, on Mac OSX, it seems directly assigning 0
@@ -8356,23 +8374,23 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
* plus.resize( 0, refcheck=False )
* # hope there would be no mem leak...
*/
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_plus), __pyx_n_s_resize); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = __Pyx_PyInt_From_long(__pyx_v_self->buffer_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_plus), __pyx_n_s_resize); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = __Pyx_PyInt_From_long(__pyx_v_self->buffer_size); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_4 = 0;
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":516
@@ -8384,13 +8402,13 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
*/
__pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_plus), __pyx_n_s_resize); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_tuple__14, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_tuple__14, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
}
__pyx_L7:;
@@ -8409,7 +8427,7 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
* i_new = 0
* minus = self.__locations[k][1] # <<<<<<<<<<<<<<
* size = minus.shape[0]
- * if len(minus) < 1:
+ * if len(minus) <= 1:
*/
if (unlikely(__pyx_v_self->__pyx___locations == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
@@ -8417,11 +8435,11 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
}
__pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___locations, __pyx_v_k); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_3, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_3, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = ((PyArrayObject *)__pyx_t_2);
+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = ((PyArrayObject *)__pyx_t_4);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_minus.rcbuffer->pybuffer);
@@ -8439,14 +8457,14 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_11 = 0;
- __Pyx_XDECREF_SET(__pyx_v_minus, ((PyArrayObject *)__pyx_t_2));
- __pyx_t_2 = 0;
+ __Pyx_XDECREF_SET(__pyx_v_minus, ((PyArrayObject *)__pyx_t_4));
+ __pyx_t_4 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":522
* i_new = 0
* minus = self.__locations[k][1]
* size = minus.shape[0] # <<<<<<<<<<<<<<
- * if len(minus) < 1:
+ * if len(minus) <= 1:
* new_minus = minus # do nothing
*/
__pyx_v_size = (__pyx_v_minus->dimensions[0]);
@@ -8454,20 +8472,20 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
/* "MACS2/IO/FixWidthTrack.pyx":523
* minus = self.__locations[k][1]
* size = minus.shape[0]
- * if len(minus) < 1: # <<<<<<<<<<<<<<
+ * if len(minus) <= 1: # <<<<<<<<<<<<<<
* new_minus = minus # do nothing
* else:
*/
__pyx_t_16 = PyObject_Length(((PyObject *)__pyx_v_minus)); if (unlikely(__pyx_t_16 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = ((__pyx_t_16 < 1) != 0);
+ __pyx_t_8 = ((__pyx_t_16 <= 1) != 0);
if (__pyx_t_8) {
/* "MACS2/IO/FixWidthTrack.pyx":524
* size = minus.shape[0]
- * if len(minus) < 1:
+ * if len(minus) <= 1:
* new_minus = minus # do nothing # <<<<<<<<<<<<<<
* else:
- * new_minus = np.zeros( self.__pointer[k][1],dtype='int32' )
+ * new_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' )
*/
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -8494,39 +8512,42 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
/* "MACS2/IO/FixWidthTrack.pyx":526
* new_minus = minus # do nothing
* else:
- * new_minus = np.zeros( self.__pointer[k][1],dtype='int32' ) # <<<<<<<<<<<<<<
+ * new_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' ) # <<<<<<<<<<<<<<
* new_minus[ i_new ] = minus[ i_new ] # first item
* i_new += 1
*/
- __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_2, __pyx_n_s_zeros); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_zeros); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (unlikely(__pyx_v_self->__pyx___pointer == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_2 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___pointer, __pyx_v_k); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_2, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_4 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___pointer, __pyx_v_k); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_4, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_6 = 0;
- __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_4 = PyNumber_Add(__pyx_t_6, __pyx_int_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_4 = 0;
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
+ if (PyDict_SetItem(__pyx_t_4, __pyx_n_s_dtype, __pyx_n_s_int32) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_6, __pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = ((PyArrayObject *)__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = ((PyArrayObject *)__pyx_t_2);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_new_minus.rcbuffer->pybuffer);
@@ -8544,12 +8565,12 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_11 = 0;
- __Pyx_XDECREF_SET(__pyx_v_new_minus, ((PyArrayObject *)__pyx_t_4));
- __pyx_t_4 = 0;
+ __Pyx_XDECREF_SET(__pyx_v_new_minus, ((PyArrayObject *)__pyx_t_2));
+ __pyx_t_2 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":527
* else:
- * new_minus = np.zeros( self.__pointer[k][1],dtype='int32' )
+ * new_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' )
* new_minus[ i_new ] = minus[ i_new ] # first item # <<<<<<<<<<<<<<
* i_new += 1
* n = 1 # the number of tags in the current location
@@ -8559,7 +8580,7 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_new_minus.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_new_minus.diminfo[0].strides) = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int32_t *, __pyx_pybuffernd_minus.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_minus.diminfo[0].strides));
/* "MACS2/IO/FixWidthTrack.pyx":528
- * new_minus = np.zeros( self.__pointer[k][1],dtype='int32' )
+ * new_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' )
* new_minus[ i_new ] = minus[ i_new ] # first item
* i_new += 1 # <<<<<<<<<<<<<<
* n = 1 # the number of tags in the current location
@@ -8666,51 +8687,51 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
* else:
* current_loc = p
*/
- __pyx_t_6 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_6, __pyx_n_s_debug); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyInt_From_int(__pyx_v_p); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_debug); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_p); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_k);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_k);
__Pyx_GIVEREF(__pyx_v_k);
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyString_Format(__pyx_kp_s_Duplicate_reads_found_at_s_d_at, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_4 = 0;
+ __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_Duplicate_reads_found_at_s_d_at, __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_3 = NULL;
- if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) {
- __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_2);
+ if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_6))) {
+ __pyx_t_3 = PyMethod_GET_SELF(__pyx_t_6);
if (likely(__pyx_t_3)) {
- PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_2);
+ PyObject* function = PyMethod_GET_FUNCTION(__pyx_t_6);
__Pyx_INCREF(__pyx_t_3);
__Pyx_INCREF(function);
- __Pyx_DECREF_SET(__pyx_t_2, function);
+ __Pyx_DECREF_SET(__pyx_t_6, function);
}
}
if (!__pyx_t_3) {
- __pyx_t_4 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_2 = __Pyx_PyObject_CallOneArg(__pyx_t_6, __pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_GOTREF(__pyx_t_2);
} else {
__pyx_t_1 = PyTuple_New(1+1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = NULL;
- PyTuple_SET_ITEM(__pyx_t_1, 0+1, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_6 = 0;
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_1, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_1, 0+1, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_4 = 0;
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_1, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
}
__pyx_L16:;
goto __pyx_L15;
@@ -8764,24 +8785,24 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
* self.total += i_new
* self.__pointer[k][1] = i_new
*/
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_new_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_new_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_6 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_6 = 0;
+ __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_1, __pyx_t_6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":546
* n = 1
@@ -8799,17 +8820,17 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
* # self.total += new_minus.shape[0]
* # self.__pointer[k][1] = new_minus.shape[0]
*/
- __pyx_t_6 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_4 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
if (unlikely(__pyx_v_self->__pyx___pointer == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_2 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___pointer, __pyx_v_k); if (unlikely(__pyx_t_2 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_2);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_2, 1, __pyx_t_6, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_6 = __Pyx_PyDict_GetItem(__pyx_v_self->__pyx___pointer, __pyx_v_k); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_6);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_6, 1, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":554
* # however, on Mac OSX, it seems directly assigning 0
@@ -8818,24 +8839,24 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
* minus.resize( 0, refcheck=False )
* # hope there would be no mem leak...
*/
- __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_6 = __Pyx_PyInt_From_long(__pyx_v_self->buffer_size); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = __Pyx_PyInt_From_long(__pyx_v_self->buffer_size); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_6 = 0;
+ __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_1, __pyx_t_6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_1, __pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
/* "MACS2/IO/FixWidthTrack.pyx":555
* # doesn't do a thing.
@@ -8844,15 +8865,15 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_7FWTrack_filter_dup(struct _
* # hope there would be no mem leak...
*
*/
- __pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_minus), __pyx_n_s_resize); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_t_2, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_tuple__15, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__15, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
__pyx_L12:;
@@ -17113,7 +17134,7 @@ static PyObject *__pyx_f_5MACS2_2IO_13FixWidthTrack_wtd_find_summit(CYTHON_UNUSE
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197
+/* "numpy.pxd":194
* # experimental exception made for __getbuffer__ and __releasebuffer__
* # -- the details of this may change.
* def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
@@ -17163,7 +17184,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__Pyx_GIVEREF(__pyx_v_info->obj);
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":203
+ /* "numpy.pxd":200
* # of flags
*
* if info == NULL: return # <<<<<<<<<<<<<<
@@ -17176,7 +17197,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
goto __pyx_L0;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":206
+ /* "numpy.pxd":203
*
* cdef int copy_shape, i, ndim
* cdef int endian_detector = 1 # <<<<<<<<<<<<<<
@@ -17185,7 +17206,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_endian_detector = 1;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":207
+ /* "numpy.pxd":204
* cdef int copy_shape, i, ndim
* cdef int endian_detector = 1
* cdef bint little_endian = ((<char*>&endian_detector)[0] != 0) # <<<<<<<<<<<<<<
@@ -17194,7 +17215,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":209
+ /* "numpy.pxd":206
* cdef bint little_endian = ((<char*>&endian_detector)[0] != 0)
*
* ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<<
@@ -17203,7 +17224,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_ndim = PyArray_NDIM(__pyx_v_self);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211
+ /* "numpy.pxd":208
* ndim = PyArray_NDIM(self)
*
* if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<<
@@ -17213,7 +17234,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0);
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":212
+ /* "numpy.pxd":209
*
* if sizeof(npy_intp) != sizeof(Py_ssize_t):
* copy_shape = 1 # <<<<<<<<<<<<<<
@@ -17225,7 +17246,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":214
+ /* "numpy.pxd":211
* copy_shape = 1
* else:
* copy_shape = 0 # <<<<<<<<<<<<<<
@@ -17236,7 +17257,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
__pyx_L4:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216
+ /* "numpy.pxd":213
* copy_shape = 0
*
* if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<<
@@ -17250,7 +17271,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
goto __pyx_L6_bool_binop_done;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":217
+ /* "numpy.pxd":214
*
* if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<<
@@ -17262,21 +17283,21 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218
+ /* "numpy.pxd":215
* if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)):
* raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<<
*
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
*/
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__18, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__18, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220
+ /* "numpy.pxd":217
* raise ValueError(u"ndarray is not C contiguous")
*
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<<
@@ -17290,7 +17311,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
goto __pyx_L9_bool_binop_done;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":221
+ /* "numpy.pxd":218
*
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<<
@@ -17302,21 +17323,21 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_L9_bool_binop_done:;
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222
+ /* "numpy.pxd":219
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)):
* raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<<
*
* info.buf = PyArray_DATA(self)
*/
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__19, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__19, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":224
+ /* "numpy.pxd":221
* raise ValueError(u"ndarray is not Fortran contiguous")
*
* info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<<
@@ -17325,7 +17346,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->buf = PyArray_DATA(__pyx_v_self);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":225
+ /* "numpy.pxd":222
*
* info.buf = PyArray_DATA(self)
* info.ndim = ndim # <<<<<<<<<<<<<<
@@ -17334,7 +17355,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->ndim = __pyx_v_ndim;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226
+ /* "numpy.pxd":223
* info.buf = PyArray_DATA(self)
* info.ndim = ndim
* if copy_shape: # <<<<<<<<<<<<<<
@@ -17344,7 +17365,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_t_1 = (__pyx_v_copy_shape != 0);
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":229
+ /* "numpy.pxd":226
* # Allocate new buffer for strides and shape info.
* # This is allocated as one block, strides first.
* info.strides = <Py_ssize_t*>stdlib.malloc(sizeof(Py_ssize_t) * <size_t>ndim * 2) # <<<<<<<<<<<<<<
@@ -17353,7 +17374,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2)));
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":230
+ /* "numpy.pxd":227
* # This is allocated as one block, strides first.
* info.strides = <Py_ssize_t*>stdlib.malloc(sizeof(Py_ssize_t) * <size_t>ndim * 2)
* info.shape = info.strides + ndim # <<<<<<<<<<<<<<
@@ -17362,7 +17383,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":231
+ /* "numpy.pxd":228
* info.strides = <Py_ssize_t*>stdlib.malloc(sizeof(Py_ssize_t) * <size_t>ndim * 2)
* info.shape = info.strides + ndim
* for i in range(ndim): # <<<<<<<<<<<<<<
@@ -17373,7 +17394,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
__pyx_v_i = __pyx_t_5;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":232
+ /* "numpy.pxd":229
* info.shape = info.strides + ndim
* for i in range(ndim):
* info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<<
@@ -17382,7 +17403,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
(__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":233
+ /* "numpy.pxd":230
* for i in range(ndim):
* info.strides[i] = PyArray_STRIDES(self)[i]
* info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<<
@@ -17395,7 +17416,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":235
+ /* "numpy.pxd":232
* info.shape[i] = PyArray_DIMS(self)[i]
* else:
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self) # <<<<<<<<<<<<<<
@@ -17404,7 +17425,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self));
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":236
+ /* "numpy.pxd":233
* else:
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self)
* info.shape = <Py_ssize_t*>PyArray_DIMS(self) # <<<<<<<<<<<<<<
@@ -17415,7 +17436,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
__pyx_L11:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":237
+ /* "numpy.pxd":234
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self)
* info.shape = <Py_ssize_t*>PyArray_DIMS(self)
* info.suboffsets = NULL # <<<<<<<<<<<<<<
@@ -17424,7 +17445,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->suboffsets = NULL;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":238
+ /* "numpy.pxd":235
* info.shape = <Py_ssize_t*>PyArray_DIMS(self)
* info.suboffsets = NULL
* info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<<
@@ -17433,7 +17454,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":239
+ /* "numpy.pxd":236
* info.suboffsets = NULL
* info.itemsize = PyArray_ITEMSIZE(self)
* info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<<
@@ -17442,7 +17463,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0));
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":242
+ /* "numpy.pxd":239
*
* cdef int t
* cdef char* f = NULL # <<<<<<<<<<<<<<
@@ -17451,7 +17472,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_f = NULL;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":243
+ /* "numpy.pxd":240
* cdef int t
* cdef char* f = NULL
* cdef dtype descr = self.descr # <<<<<<<<<<<<<<
@@ -17463,7 +17484,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_descr = ((PyArray_Descr *)__pyx_t_3);
__pyx_t_3 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":247
+ /* "numpy.pxd":244
* cdef int offset
*
* cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<<
@@ -17472,7 +17493,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":249
+ /* "numpy.pxd":246
* cdef bint hasfields = PyDataType_HASFIELDS(descr)
*
* if not hasfields and not copy_shape: # <<<<<<<<<<<<<<
@@ -17490,7 +17511,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_L15_bool_binop_done:;
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":251
+ /* "numpy.pxd":248
* if not hasfields and not copy_shape:
* # do not call releasebuffer
* info.obj = None # <<<<<<<<<<<<<<
@@ -17506,7 +17527,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":254
+ /* "numpy.pxd":251
* else:
* # need to call releasebuffer
* info.obj = self # <<<<<<<<<<<<<<
@@ -17521,7 +17542,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
__pyx_L14:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":256
+ /* "numpy.pxd":253
* info.obj = self
*
* if not hasfields: # <<<<<<<<<<<<<<
@@ -17531,7 +17552,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0);
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257
+ /* "numpy.pxd":254
*
* if not hasfields:
* t = descr.type_num # <<<<<<<<<<<<<<
@@ -17541,7 +17562,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_t_4 = __pyx_v_descr->type_num;
__pyx_v_t = __pyx_t_4;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258
+ /* "numpy.pxd":255
* if not hasfields:
* t = descr.type_num
* if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<<
@@ -17561,7 +17582,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
__pyx_L20_next_or:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259
+ /* "numpy.pxd":256
* t = descr.type_num
* if ((descr.byteorder == c'>' and little_endian) or
* (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<<
@@ -17579,21 +17600,21 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_L19_bool_binop_done:;
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260
+ /* "numpy.pxd":257
* if ((descr.byteorder == c'>' and little_endian) or
* (descr.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<<
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B"
*/
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__20, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__20, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":277
+ /* "numpy.pxd":274
* elif t == NPY_CDOUBLE: f = "Zd"
* elif t == NPY_CLONGDOUBLE: f = "Zg"
* elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<<
@@ -17602,7 +17623,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
switch (__pyx_v_t) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":261
+ /* "numpy.pxd":258
* (descr.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported")
* if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<<
@@ -17613,7 +17634,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_b;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":262
+ /* "numpy.pxd":259
* raise ValueError(u"Non-native byte order not supported")
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<<
@@ -17624,7 +17645,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_B;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":263
+ /* "numpy.pxd":260
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B"
* elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<<
@@ -17635,7 +17656,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_h;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":264
+ /* "numpy.pxd":261
* elif t == NPY_UBYTE: f = "B"
* elif t == NPY_SHORT: f = "h"
* elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<<
@@ -17646,7 +17667,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_H;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265
+ /* "numpy.pxd":262
* elif t == NPY_SHORT: f = "h"
* elif t == NPY_USHORT: f = "H"
* elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<<
@@ -17657,7 +17678,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_i_2;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266
+ /* "numpy.pxd":263
* elif t == NPY_USHORT: f = "H"
* elif t == NPY_INT: f = "i"
* elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<<
@@ -17668,7 +17689,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_I;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":267
+ /* "numpy.pxd":264
* elif t == NPY_INT: f = "i"
* elif t == NPY_UINT: f = "I"
* elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<<
@@ -17679,7 +17700,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_l;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268
+ /* "numpy.pxd":265
* elif t == NPY_UINT: f = "I"
* elif t == NPY_LONG: f = "l"
* elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<<
@@ -17690,7 +17711,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_L;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":269
+ /* "numpy.pxd":266
* elif t == NPY_LONG: f = "l"
* elif t == NPY_ULONG: f = "L"
* elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<<
@@ -17701,7 +17722,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_q;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270
+ /* "numpy.pxd":267
* elif t == NPY_ULONG: f = "L"
* elif t == NPY_LONGLONG: f = "q"
* elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<<
@@ -17712,7 +17733,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_Q;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271
+ /* "numpy.pxd":268
* elif t == NPY_LONGLONG: f = "q"
* elif t == NPY_ULONGLONG: f = "Q"
* elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<<
@@ -17723,7 +17744,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_f;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272
+ /* "numpy.pxd":269
* elif t == NPY_ULONGLONG: f = "Q"
* elif t == NPY_FLOAT: f = "f"
* elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<<
@@ -17734,7 +17755,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_d;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":273
+ /* "numpy.pxd":270
* elif t == NPY_FLOAT: f = "f"
* elif t == NPY_DOUBLE: f = "d"
* elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<<
@@ -17745,7 +17766,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_g;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274
+ /* "numpy.pxd":271
* elif t == NPY_DOUBLE: f = "d"
* elif t == NPY_LONGDOUBLE: f = "g"
* elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<<
@@ -17756,7 +17777,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_Zf;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":275
+ /* "numpy.pxd":272
* elif t == NPY_LONGDOUBLE: f = "g"
* elif t == NPY_CFLOAT: f = "Zf"
* elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<<
@@ -17767,7 +17788,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_Zd;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276
+ /* "numpy.pxd":273
* elif t == NPY_CFLOAT: f = "Zf"
* elif t == NPY_CDOUBLE: f = "Zd"
* elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<<
@@ -17778,7 +17799,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_Zg;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":277
+ /* "numpy.pxd":274
* elif t == NPY_CDOUBLE: f = "Zd"
* elif t == NPY_CLONGDOUBLE: f = "Zg"
* elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<<
@@ -17790,33 +17811,33 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
break;
default:
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":279
+ /* "numpy.pxd":276
* elif t == NPY_OBJECT: f = "O"
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<<
* info.format = f
* return
*/
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_t); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_t); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
break;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280
+ /* "numpy.pxd":277
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
* info.format = f # <<<<<<<<<<<<<<
@@ -17825,7 +17846,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->format = __pyx_v_f;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":281
+ /* "numpy.pxd":278
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
* info.format = f
* return # <<<<<<<<<<<<<<
@@ -17837,7 +17858,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283
+ /* "numpy.pxd":280
* return
* else:
* info.format = <char*>stdlib.malloc(_buffer_format_string_len) # <<<<<<<<<<<<<<
@@ -17846,7 +17867,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->format = ((char *)malloc(255));
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":284
+ /* "numpy.pxd":281
* else:
* info.format = <char*>stdlib.malloc(_buffer_format_string_len)
* info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<<
@@ -17855,7 +17876,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
(__pyx_v_info->format[0]) = '^';
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":285
+ /* "numpy.pxd":282
* info.format = <char*>stdlib.malloc(_buffer_format_string_len)
* info.format[0] = c'^' # Native data types, manual alignment
* offset = 0 # <<<<<<<<<<<<<<
@@ -17864,17 +17885,17 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_offset = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":286
+ /* "numpy.pxd":283
* info.format[0] = c'^' # Native data types, manual alignment
* offset = 0
* f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<<
* info.format + _buffer_format_string_len,
* &offset)
*/
- __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 255), (&__pyx_v_offset)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 255), (&__pyx_v_offset)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_f = __pyx_t_7;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":289
+ /* "numpy.pxd":286
* info.format + _buffer_format_string_len,
* &offset)
* f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<<
@@ -17884,7 +17905,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
(__pyx_v_f[0]) = '\x00';
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197
+ /* "numpy.pxd":194
* # experimental exception made for __getbuffer__ and __releasebuffer__
* # -- the details of this may change.
* def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
@@ -17916,7 +17937,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291
+/* "numpy.pxd":288
* f[0] = c'\0' # Terminate format string
*
* def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<<
@@ -17940,7 +17961,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
int __pyx_t_1;
__Pyx_RefNannySetupContext("__releasebuffer__", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292
+ /* "numpy.pxd":289
*
* def __releasebuffer__(ndarray self, Py_buffer* info):
* if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<<
@@ -17950,7 +17971,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
__pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0);
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293
+ /* "numpy.pxd":290
* def __releasebuffer__(ndarray self, Py_buffer* info):
* if PyArray_HASFIELDS(self):
* stdlib.free(info.format) # <<<<<<<<<<<<<<
@@ -17962,7 +17983,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
}
__pyx_L3:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":294
+ /* "numpy.pxd":291
* if PyArray_HASFIELDS(self):
* stdlib.free(info.format)
* if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<<
@@ -17972,7 +17993,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
__pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0);
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":295
+ /* "numpy.pxd":292
* stdlib.free(info.format)
* if sizeof(npy_intp) != sizeof(Py_ssize_t):
* stdlib.free(info.strides) # <<<<<<<<<<<<<<
@@ -17984,7 +18005,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
}
__pyx_L4:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291
+ /* "numpy.pxd":288
* f[0] = c'\0' # Terminate format string
*
* def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<<
@@ -17996,7 +18017,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
__Pyx_RefNannyFinishContext();
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":771
+/* "numpy.pxd":768
* ctypedef npy_cdouble complex_t
*
* cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<<
@@ -18013,7 +18034,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":772
+ /* "numpy.pxd":769
*
* cdef inline object PyArray_MultiIterNew1(a):
* return PyArray_MultiIterNew(1, <void*>a) # <<<<<<<<<<<<<<
@@ -18021,13 +18042,13 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__
* cdef inline object PyArray_MultiIterNew2(a, b):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":771
+ /* "numpy.pxd":768
* ctypedef npy_cdouble complex_t
*
* cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<<
@@ -18046,7 +18067,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":774
+/* "numpy.pxd":771
* return PyArray_MultiIterNew(1, <void*>a)
*
* cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<<
@@ -18063,7 +18084,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":775
+ /* "numpy.pxd":772
*
* cdef inline object PyArray_MultiIterNew2(a, b):
* return PyArray_MultiIterNew(2, <void*>a, <void*>b) # <<<<<<<<<<<<<<
@@ -18071,13 +18092,13 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__
* cdef inline object PyArray_MultiIterNew3(a, b, c):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(2, ((void *)__pyx_v_a), ((void *)__pyx_v_b)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(2, ((void *)__pyx_v_a), ((void *)__pyx_v_b)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":774
+ /* "numpy.pxd":771
* return PyArray_MultiIterNew(1, <void*>a)
*
* cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<<
@@ -18096,7 +18117,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777
+/* "numpy.pxd":774
* return PyArray_MultiIterNew(2, <void*>a, <void*>b)
*
* cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<<
@@ -18113,7 +18134,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":778
+ /* "numpy.pxd":775
*
* cdef inline object PyArray_MultiIterNew3(a, b, c):
* return PyArray_MultiIterNew(3, <void*>a, <void*>b, <void*> c) # <<<<<<<<<<<<<<
@@ -18121,13 +18142,13 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__
* cdef inline object PyArray_MultiIterNew4(a, b, c, d):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(3, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(3, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777
+ /* "numpy.pxd":774
* return PyArray_MultiIterNew(2, <void*>a, <void*>b)
*
* cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<<
@@ -18146,7 +18167,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":780
+/* "numpy.pxd":777
* return PyArray_MultiIterNew(3, <void*>a, <void*>b, <void*> c)
*
* cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<<
@@ -18163,7 +18184,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("PyArray_MultiIterNew4", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":781
+ /* "numpy.pxd":778
*
* cdef inline object PyArray_MultiIterNew4(a, b, c, d):
* return PyArray_MultiIterNew(4, <void*>a, <void*>b, <void*>c, <void*> d) # <<<<<<<<<<<<<<
@@ -18171,13 +18192,13 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__
* cdef inline object PyArray_MultiIterNew5(a, b, c, d, e):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(4, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(4, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":780
+ /* "numpy.pxd":777
* return PyArray_MultiIterNew(3, <void*>a, <void*>b, <void*> c)
*
* cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<<
@@ -18196,7 +18217,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783
+/* "numpy.pxd":780
* return PyArray_MultiIterNew(4, <void*>a, <void*>b, <void*>c, <void*> d)
*
* cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<<
@@ -18213,7 +18234,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("PyArray_MultiIterNew5", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":784
+ /* "numpy.pxd":781
*
* cdef inline object PyArray_MultiIterNew5(a, b, c, d, e):
* return PyArray_MultiIterNew(5, <void*>a, <void*>b, <void*>c, <void*> d, <void*> e) # <<<<<<<<<<<<<<
@@ -18221,13 +18242,13 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__
* cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(5, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d), ((void *)__pyx_v_e)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(5, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d), ((void *)__pyx_v_e)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783
+ /* "numpy.pxd":780
* return PyArray_MultiIterNew(4, <void*>a, <void*>b, <void*>c, <void*> d)
*
* cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<<
@@ -18246,7 +18267,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":786
+/* "numpy.pxd":783
* return PyArray_MultiIterNew(5, <void*>a, <void*>b, <void*>c, <void*> d, <void*> e)
*
* cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<<
@@ -18268,7 +18289,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
Py_ssize_t __pyx_t_2;
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
- int __pyx_t_5;
+ PyObject *__pyx_t_5 = NULL;
int __pyx_t_6;
int __pyx_t_7;
long __pyx_t_8;
@@ -18278,7 +18299,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("_util_dtypestring", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":793
+ /* "numpy.pxd":790
* cdef int delta_offset
* cdef tuple i
* cdef int endian_detector = 1 # <<<<<<<<<<<<<<
@@ -18287,7 +18308,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
__pyx_v_endian_detector = 1;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":794
+ /* "numpy.pxd":791
* cdef tuple i
* cdef int endian_detector = 1
* cdef bint little_endian = ((<char*>&endian_detector)[0] != 0) # <<<<<<<<<<<<<<
@@ -18296,7 +18317,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
__pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":797
+ /* "numpy.pxd":794
* cdef tuple fields
*
* for childname in descr.names: # <<<<<<<<<<<<<<
@@ -18305,42 +18326,38 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
if (unlikely(__pyx_v_descr->names == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
for (;;) {
if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
#if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
__Pyx_XDECREF_SET(__pyx_v_childname, __pyx_t_3);
__pyx_t_3 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":798
+ /* "numpy.pxd":795
*
* for childname in descr.names:
* fields = descr.fields[childname] # <<<<<<<<<<<<<<
* child, new_offset = fields
*
*/
- if (unlikely(__pyx_v_descr->fields == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = PyObject_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- if (!(likely(PyTuple_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "tuple", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyTuple_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "tuple", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_fields, ((PyObject*)__pyx_t_3));
__pyx_t_3 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":799
+ /* "numpy.pxd":796
* for childname in descr.names:
* fields = descr.fields[childname]
* child, new_offset = fields # <<<<<<<<<<<<<<
*
- * if (end - f) - <int>(new_offset - offset[0]) < 15:
+ * if (end - f) - (new_offset - offset[0]) < 15:
*/
if (likely(__pyx_v_fields != Py_None)) {
PyObject* sequence = __pyx_v_fields;
@@ -18352,7 +18369,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
if (unlikely(size != 2)) {
if (size > 2) __Pyx_RaiseTooManyValuesError(2);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
@@ -18360,52 +18377,59 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__Pyx_INCREF(__pyx_t_3);
__Pyx_INCREF(__pyx_t_4);
#else
- __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
#endif
} else {
- __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_dtype))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_dtype))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_child, ((PyArray_Descr *)__pyx_t_3));
__pyx_t_3 = 0;
__Pyx_XDECREF_SET(__pyx_v_new_offset, __pyx_t_4);
__pyx_t_4 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801
+ /* "numpy.pxd":798
* child, new_offset = fields
*
- * if (end - f) - <int>(new_offset - offset[0]) < 15: # <<<<<<<<<<<<<<
+ * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<<
* raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd")
*
*/
- __pyx_t_4 = __Pyx_PyInt_From_int((__pyx_v_offset[0])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_From_ptrdiff_t((__pyx_v_end - __pyx_v_f)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyNumber_Subtract(__pyx_v_new_offset, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int((__pyx_v_offset[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyNumber_Subtract(__pyx_v_new_offset, __pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyNumber_Subtract(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_3, __pyx_int_15, Py_LT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0);
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802
+ /* "numpy.pxd":799
*
- * if (end - f) - <int>(new_offset - offset[0]) < 15:
+ * if (end - f) - (new_offset - offset[0]) < 15:
* raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<<
*
* if ((child.byteorder == c'>' and little_endian) or
*/
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__21, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_Raise(__pyx_t_3, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__21, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":804
+ /* "numpy.pxd":801
* raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd")
*
* if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<<
@@ -18425,7 +18449,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
}
__pyx_L8_next_or:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":805
+ /* "numpy.pxd":802
*
* if ((child.byteorder == c'>' and little_endian) or
* (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<<
@@ -18443,21 +18467,21 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__pyx_L7_bool_binop_done:;
if (__pyx_t_6) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":806
+ /* "numpy.pxd":803
* if ((child.byteorder == c'>' and little_endian) or
* (child.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<<
* # One could encode it in the format string and have Cython
* # complain instead, BUT: < and > in format strings also imply
*/
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__22, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_Raise(__pyx_t_3, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__22, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816
+ /* "numpy.pxd":813
*
* # Output padding bytes
* while offset[0] < new_offset: # <<<<<<<<<<<<<<
@@ -18465,15 +18489,15 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* f += 1
*/
while (1) {
- __pyx_t_3 = __Pyx_PyInt_From_int((__pyx_v_offset[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_t_3, __pyx_v_new_offset, Py_LT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_int((__pyx_v_offset[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_5, __pyx_v_new_offset, Py_LT); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (!__pyx_t_6) break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":817
+ /* "numpy.pxd":814
* # Output padding bytes
* while offset[0] < new_offset:
* f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<<
@@ -18482,7 +18506,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
(__pyx_v_f[0]) = 120;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":818
+ /* "numpy.pxd":815
* while offset[0] < new_offset:
* f[0] = 120 # "x"; pad byte
* f += 1 # <<<<<<<<<<<<<<
@@ -18491,7 +18515,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
__pyx_v_f = (__pyx_v_f + 1);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":819
+ /* "numpy.pxd":816
* f[0] = 120 # "x"; pad byte
* f += 1
* offset[0] += 1 # <<<<<<<<<<<<<<
@@ -18502,7 +18526,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
(__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1);
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":821
+ /* "numpy.pxd":818
* offset[0] += 1
*
* offset[0] += child.itemsize # <<<<<<<<<<<<<<
@@ -18512,7 +18536,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__pyx_t_8 = 0;
(__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823
+ /* "numpy.pxd":820
* offset[0] += child.itemsize
*
* if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<<
@@ -18522,19 +18546,19 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0);
if (__pyx_t_6) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":824
+ /* "numpy.pxd":821
*
* if not PyDataType_HASFIELDS(child):
* t = child.type_num # <<<<<<<<<<<<<<
* if end - f < 5:
* raise RuntimeError(u"Format string allocated too short.")
*/
- __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_child->type_num); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_child->type_num); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_3);
+ __pyx_t_3 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":825
+ /* "numpy.pxd":822
* if not PyDataType_HASFIELDS(child):
* t = child.type_num
* if end - f < 5: # <<<<<<<<<<<<<<
@@ -18544,267 +18568,267 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0);
if (__pyx_t_6) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826
+ /* "numpy.pxd":823
* t = child.type_num
* if end - f < 5:
* raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<<
*
* # Until ticket #99 is fixed, use integers to avoid warnings
*/
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__23, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_Raise(__pyx_t_4, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__23, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_Raise(__pyx_t_3, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":829
+ /* "numpy.pxd":826
*
* # Until ticket #99 is fixed, use integers to avoid warnings
* if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<<
* elif t == NPY_UBYTE: f[0] = 66 #"B"
* elif t == NPY_SHORT: f[0] = 104 #"h"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_BYTE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_BYTE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 98;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":830
+ /* "numpy.pxd":827
* # Until ticket #99 is fixed, use integers to avoid warnings
* if t == NPY_BYTE: f[0] = 98 #"b"
* elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<<
* elif t == NPY_SHORT: f[0] = 104 #"h"
* elif t == NPY_USHORT: f[0] = 72 #"H"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_UBYTE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_UBYTE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 66;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":831
+ /* "numpy.pxd":828
* if t == NPY_BYTE: f[0] = 98 #"b"
* elif t == NPY_UBYTE: f[0] = 66 #"B"
* elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<<
* elif t == NPY_USHORT: f[0] = 72 #"H"
* elif t == NPY_INT: f[0] = 105 #"i"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_SHORT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_SHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 104;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":832
+ /* "numpy.pxd":829
* elif t == NPY_UBYTE: f[0] = 66 #"B"
* elif t == NPY_SHORT: f[0] = 104 #"h"
* elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<<
* elif t == NPY_INT: f[0] = 105 #"i"
* elif t == NPY_UINT: f[0] = 73 #"I"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_USHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_USHORT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 72;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833
+ /* "numpy.pxd":830
* elif t == NPY_SHORT: f[0] = 104 #"h"
* elif t == NPY_USHORT: f[0] = 72 #"H"
* elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<<
* elif t == NPY_UINT: f[0] = 73 #"I"
* elif t == NPY_LONG: f[0] = 108 #"l"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_INT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_INT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 105;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":834
+ /* "numpy.pxd":831
* elif t == NPY_USHORT: f[0] = 72 #"H"
* elif t == NPY_INT: f[0] = 105 #"i"
* elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<<
* elif t == NPY_LONG: f[0] = 108 #"l"
* elif t == NPY_ULONG: f[0] = 76 #"L"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_UINT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_UINT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 73;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":835
+ /* "numpy.pxd":832
* elif t == NPY_INT: f[0] = 105 #"i"
* elif t == NPY_UINT: f[0] = 73 #"I"
* elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<<
* elif t == NPY_ULONG: f[0] = 76 #"L"
* elif t == NPY_LONGLONG: f[0] = 113 #"q"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_LONG); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_LONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 108;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836
+ /* "numpy.pxd":833
* elif t == NPY_UINT: f[0] = 73 #"I"
* elif t == NPY_LONG: f[0] = 108 #"l"
* elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<<
* elif t == NPY_LONGLONG: f[0] = 113 #"q"
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_ULONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_ULONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 76;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":837
+ /* "numpy.pxd":834
* elif t == NPY_LONG: f[0] = 108 #"l"
* elif t == NPY_ULONG: f[0] = 76 #"L"
* elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<<
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q"
* elif t == NPY_FLOAT: f[0] = 102 #"f"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_LONGLONG); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_LONGLONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 113;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":838
+ /* "numpy.pxd":835
* elif t == NPY_ULONG: f[0] = 76 #"L"
* elif t == NPY_LONGLONG: f[0] = 113 #"q"
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<<
* elif t == NPY_FLOAT: f[0] = 102 #"f"
* elif t == NPY_DOUBLE: f[0] = 100 #"d"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_ULONGLONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_ULONGLONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 81;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":839
+ /* "numpy.pxd":836
* elif t == NPY_LONGLONG: f[0] = 113 #"q"
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q"
* elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<<
* elif t == NPY_DOUBLE: f[0] = 100 #"d"
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_FLOAT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_FLOAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 102;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":840
+ /* "numpy.pxd":837
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q"
* elif t == NPY_FLOAT: f[0] = 102 #"f"
* elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<<
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g"
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf
*/
- __pyx_t_3 = PyInt_FromLong(NPY_DOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_DOUBLE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 100;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":841
+ /* "numpy.pxd":838
* elif t == NPY_FLOAT: f[0] = 102 #"f"
* elif t == NPY_DOUBLE: f[0] = 100 #"d"
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<<
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd
*/
- __pyx_t_4 = PyInt_FromLong(NPY_LONGDOUBLE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_LONGDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 103;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842
+ /* "numpy.pxd":839
* elif t == NPY_DOUBLE: f[0] = 100 #"d"
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g"
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<<
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg
*/
- __pyx_t_3 = PyInt_FromLong(NPY_CFLOAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_CFLOAT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 90;
(__pyx_v_f[1]) = 102;
@@ -18812,19 +18836,19 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":843
+ /* "numpy.pxd":840
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g"
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<<
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg
* elif t == NPY_OBJECT: f[0] = 79 #"O"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_CDOUBLE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_CDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 90;
(__pyx_v_f[1]) = 100;
@@ -18832,19 +18856,19 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":844
+ /* "numpy.pxd":841
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<<
* elif t == NPY_OBJECT: f[0] = 79 #"O"
* else:
*/
- __pyx_t_3 = PyInt_FromLong(NPY_CLONGDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_CLONGDOUBLE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 90;
(__pyx_v_f[1]) = 103;
@@ -18852,49 +18876,49 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":845
+ /* "numpy.pxd":842
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg
* elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<<
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
*/
- __pyx_t_4 = PyInt_FromLong(NPY_OBJECT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_OBJECT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 79;
goto __pyx_L15;
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":847
+ /* "numpy.pxd":844
* elif t == NPY_OBJECT: f[0] = 79 #"O"
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<<
* f += 1
* else:
*/
- __pyx_t_3 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_v_t); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_v_t); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0, 0);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_5 = 0;
+ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_L15:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":848
+ /* "numpy.pxd":845
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
* f += 1 # <<<<<<<<<<<<<<
@@ -18906,19 +18930,19 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":852
+ /* "numpy.pxd":849
* # Cython ignores struct boundary information ("T{...}"),
* # so don't output it
* f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<<
* return f
*
*/
- __pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_child, __pyx_v_f, __pyx_v_end, __pyx_v_offset); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_child, __pyx_v_f, __pyx_v_end, __pyx_v_offset); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_f = __pyx_t_9;
}
__pyx_L13:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":797
+ /* "numpy.pxd":794
* cdef tuple fields
*
* for childname in descr.names: # <<<<<<<<<<<<<<
@@ -18928,7 +18952,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":853
+ /* "numpy.pxd":850
* # so don't output it
* f = _util_dtypestring(child, f, end, offset)
* return f # <<<<<<<<<<<<<<
@@ -18938,7 +18962,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__pyx_r = __pyx_v_f;
goto __pyx_L0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":786
+ /* "numpy.pxd":783
* return PyArray_MultiIterNew(5, <void*>a, <void*>b, <void*>c, <void*> d, <void*> e)
*
* cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<<
@@ -18951,6 +18975,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_t_5);
__Pyx_AddTraceback("numpy._util_dtypestring", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
@@ -18963,7 +18988,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":969
+/* "numpy.pxd":965
*
*
* cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<<
@@ -18978,7 +19003,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
int __pyx_t_2;
__Pyx_RefNannySetupContext("set_array_base", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":971
+ /* "numpy.pxd":967
* cdef inline void set_array_base(ndarray arr, object base):
* cdef PyObject* baseptr
* if base is None: # <<<<<<<<<<<<<<
@@ -18989,7 +19014,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
__pyx_t_2 = (__pyx_t_1 != 0);
if (__pyx_t_2) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":972
+ /* "numpy.pxd":968
* cdef PyObject* baseptr
* if base is None:
* baseptr = NULL # <<<<<<<<<<<<<<
@@ -19001,7 +19026,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":974
+ /* "numpy.pxd":970
* baseptr = NULL
* else:
* Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<<
@@ -19010,7 +19035,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
*/
Py_INCREF(__pyx_v_base);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":975
+ /* "numpy.pxd":971
* else:
* Py_INCREF(base) # important to do this before decref below!
* baseptr = <PyObject*>base # <<<<<<<<<<<<<<
@@ -19021,7 +19046,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
}
__pyx_L3:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976
+ /* "numpy.pxd":972
* Py_INCREF(base) # important to do this before decref below!
* baseptr = <PyObject*>base
* Py_XDECREF(arr.base) # <<<<<<<<<<<<<<
@@ -19030,7 +19055,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
*/
Py_XDECREF(__pyx_v_arr->base);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":977
+ /* "numpy.pxd":973
* baseptr = <PyObject*>base
* Py_XDECREF(arr.base)
* arr.base = baseptr # <<<<<<<<<<<<<<
@@ -19039,7 +19064,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
*/
__pyx_v_arr->base = __pyx_v_baseptr;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":969
+ /* "numpy.pxd":965
*
*
* cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<<
@@ -19051,7 +19076,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
__Pyx_RefNannyFinishContext();
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979
+/* "numpy.pxd":975
* arr.base = baseptr
*
* cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<<
@@ -19065,7 +19090,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
int __pyx_t_1;
__Pyx_RefNannySetupContext("get_array_base", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":980
+ /* "numpy.pxd":976
*
* cdef inline object get_array_base(ndarray arr):
* if arr.base is NULL: # <<<<<<<<<<<<<<
@@ -19075,7 +19100,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
__pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0);
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":981
+ /* "numpy.pxd":977
* cdef inline object get_array_base(ndarray arr):
* if arr.base is NULL:
* return None # <<<<<<<<<<<<<<
@@ -19089,7 +19114,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":983
+ /* "numpy.pxd":979
* return None
* else:
* return <object>arr.base # <<<<<<<<<<<<<<
@@ -19100,7 +19125,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
goto __pyx_L0;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979
+ /* "numpy.pxd":975
* arr.base = baseptr
*
* cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<<
@@ -19767,8 +19792,8 @@ static int __Pyx_InitCachedBuiltins(void) {
__pyx_builtin_round = __Pyx_GetBuiltinName(__pyx_n_s_round); if (!__pyx_builtin_round) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_file = __Pyx_GetBuiltinName(__pyx_n_s_file); if (!__pyx_builtin_file) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_sum = __Pyx_GetBuiltinName(__pyx_n_s_sum); if (!__pyx_builtin_sum) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1004; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
return -1;
@@ -19921,69 +19946,69 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GOTREF(__pyx_tuple__15);
__Pyx_GIVEREF(__pyx_tuple__15);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218
+ /* "numpy.pxd":215
* if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)):
* raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<<
*
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
*/
- __pyx_tuple__18 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple__18)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__18 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple__18)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__18);
__Pyx_GIVEREF(__pyx_tuple__18);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222
+ /* "numpy.pxd":219
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)):
* raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<<
*
* info.buf = PyArray_DATA(self)
*/
- __pyx_tuple__19 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__19)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__19 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__19)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__19);
__Pyx_GIVEREF(__pyx_tuple__19);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260
+ /* "numpy.pxd":257
* if ((descr.byteorder == c'>' and little_endian) or
* (descr.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<<
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B"
*/
- __pyx_tuple__20 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__20)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__20 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__20)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__20);
__Pyx_GIVEREF(__pyx_tuple__20);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802
+ /* "numpy.pxd":799
*
- * if (end - f) - <int>(new_offset - offset[0]) < 15:
+ * if (end - f) - (new_offset - offset[0]) < 15:
* raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<<
*
* if ((child.byteorder == c'>' and little_endian) or
*/
- __pyx_tuple__21 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__21)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__21 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__21)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__21);
__Pyx_GIVEREF(__pyx_tuple__21);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":806
+ /* "numpy.pxd":803
* if ((child.byteorder == c'>' and little_endian) or
* (child.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<<
* # One could encode it in the format string and have Cython
* # complain instead, BUT: < and > in format strings also imply
*/
- __pyx_tuple__22 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__22)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__22 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__22)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__22);
__Pyx_GIVEREF(__pyx_tuple__22);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826
+ /* "numpy.pxd":823
* t = child.type_num
* if end - f < 5:
* raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<<
*
* # Until ticket #99 is fixed, use integers to avoid warnings
*/
- __pyx_tuple__23 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__23)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__23 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__23)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__23);
__Pyx_GIVEREF(__pyx_tuple__23);
__Pyx_RefNannyFinishContext();
@@ -19998,6 +20023,7 @@ static int __Pyx_InitGlobals(void) {
__pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_int_5 = PyInt_FromLong(5); if (unlikely(!__pyx_int_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_int_15 = PyInt_FromLong(15); if (unlikely(!__pyx_int_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
return -1;
@@ -20132,10 +20158,10 @@ PyMODINIT_FUNC PyInit_FixWidthTrack(void)
__pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
@@ -20354,7 +20380,7 @@ PyMODINIT_FUNC PyInit_FixWidthTrack(void)
if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979
+ /* "numpy.pxd":975
* arr.base = baseptr
*
* cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<<
@@ -23097,6 +23123,32 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_npy_int32(npy_int32 value) {
#endif
#endif
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ptrdiff_t(ptrdiff_t value) {
+ const ptrdiff_t neg_one = (ptrdiff_t) -1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (is_unsigned) {
+ if (sizeof(ptrdiff_t) < sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(ptrdiff_t) <= sizeof(unsigned long)) {
+ return PyLong_FromUnsignedLong((unsigned long) value);
+ } else if (sizeof(ptrdiff_t) <= sizeof(unsigned long long)) {
+ return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ }
+ } else {
+ if (sizeof(ptrdiff_t) <= sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(ptrdiff_t) <= sizeof(long long)) {
+ return PyLong_FromLongLong((long long) value);
+ }
+ }
+ {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&value;
+ return _PyLong_FromByteArray(bytes, sizeof(ptrdiff_t),
+ little, !is_unsigned);
+ }
+}
+
static CYTHON_INLINE int __Pyx_StrEq(const char *s1, const char *s2) {
while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
return *s1 == *s2;
diff --git a/MACS2/IO/FixWidthTrack.pyx b/MACS2/IO/FixWidthTrack.pyx
index ec80e04..a294a09 100644
--- a/MACS2/IO/FixWidthTrack.pyx
+++ b/MACS2/IO/FixWidthTrack.pyx
@@ -289,11 +289,11 @@ cdef class FWTrack:
i_dup = 0
plus = self.__locations[k][0]
size = plus.shape[0]
- dup_plus = np.zeros( self.__pointer[k][0],dtype='int32' )
- if len(plus) < 1:
+ dup_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' )
+ if len(plus) <= 1:
new_plus = plus # do nothing
else:
- new_plus = np.zeros( self.__pointer[k][0],dtype='int32' )
+ new_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' )
new_plus[ i_new ] = plus[ i_new ] # first item
i_new += 1
current_loc = plus[0]
@@ -335,11 +335,11 @@ cdef class FWTrack:
i_dup = 0
minus = self.__locations[k][1]
size = minus.shape[0]
- dup_minus = np.zeros( self.__pointer[k][1],dtype='int32' )
- if len(minus) < 1:
+ dup_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' )
+ if len(minus) <= 1:
new_minus = minus # do nothing
else:
- new_minus = np.zeros( self.__pointer[k][1],dtype='int32' )
+ new_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' )
new_minus[ i_new ] = minus[ i_new ] # first item
i_new += 1
current_loc = minus[0]
@@ -481,10 +481,10 @@ cdef class FWTrack:
i_new = 0
plus = self.__locations[k][0]
size = plus.shape[0]
- if len(plus) < 1:
+ if len(plus) <= 1:
new_plus = plus # do nothing
else:
- new_plus = np.zeros( self.__pointer[k][0],dtype='int32' )
+ new_plus = np.zeros( self.__pointer[k][0] + 1,dtype='int32' )
new_plus[ i_new ] = plus[ i_new ] # first item
i_new += 1
n = 1 # the number of tags in the current location
@@ -520,10 +520,10 @@ cdef class FWTrack:
i_new = 0
minus = self.__locations[k][1]
size = minus.shape[0]
- if len(minus) < 1:
+ if len(minus) <= 1:
new_minus = minus # do nothing
else:
- new_minus = np.zeros( self.__pointer[k][1],dtype='int32' )
+ new_minus = np.zeros( self.__pointer[k][1] + 1,dtype='int32' )
new_minus[ i_new ] = minus[ i_new ] # first item
i_new += 1
n = 1 # the number of tags in the current location
diff --git a/MACS2/IO/PairedEndTrack.c b/MACS2/IO/PairedEndTrack.c
index 195ff4b..7ce73ed 100644
--- a/MACS2/IO/PairedEndTrack.c
+++ b/MACS2/IO/PairedEndTrack.c
@@ -5148,7 +5148,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
* i_dup = 0
* locs = self.__locations[k] # <<<<<<<<<<<<<<
* size = locs.shape[0]
- * if size < 1:
+ * if size <= 1:
*/
if (unlikely(__pyx_v_self->__locations == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
@@ -5164,7 +5164,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
* i_dup = 0
* locs = self.__locations[k]
* size = locs.shape[0] # <<<<<<<<<<<<<<
- * if size < 1:
+ * if size <= 1:
* new_locs = locs
*/
__pyx_v_size = (__pyx_v_locs->dimensions[0]);
@@ -5172,19 +5172,19 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
/* "MACS2/IO/PairedEndTrack.pyx":301
* locs = self.__locations[k]
* size = locs.shape[0]
- * if size < 1: # <<<<<<<<<<<<<<
+ * if size <= 1: # <<<<<<<<<<<<<<
* new_locs = locs
* else:
*/
- __pyx_t_3 = ((__pyx_v_size < 1) != 0);
+ __pyx_t_3 = ((__pyx_v_size <= 1) != 0);
if (__pyx_t_3) {
/* "MACS2/IO/PairedEndTrack.pyx":302
* size = locs.shape[0]
- * if size < 1:
+ * if size <= 1:
* new_locs = locs # <<<<<<<<<<<<<<
* else:
- * new_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ * new_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
*/
__Pyx_INCREF(((PyObject *)__pyx_v_locs));
__Pyx_XDECREF_SET(__pyx_v_new_locs, __pyx_v_locs);
@@ -5195,8 +5195,8 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
/* "MACS2/IO/PairedEndTrack.pyx":304
* new_locs = locs
* else:
- * new_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment. # <<<<<<<<<<<<<<
- * dup_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ * new_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment. # <<<<<<<<<<<<<<
+ * dup_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
* i_new += 1
*/
__pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -5210,13 +5210,16 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
}
__pyx_t_1 = __Pyx_PyDict_GetItem(__pyx_v_self->__pointer, __pyx_v_k); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Add(__pyx_t_1, __pyx_int_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_6 = 0;
+ __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__pyx_t_5 = PyList_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_tuple__9);
@@ -5225,28 +5228,28 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
__Pyx_INCREF(__pyx_tuple__10);
PyList_SET_ITEM(__pyx_t_5, 1, __pyx_tuple__10);
__Pyx_GIVEREF(__pyx_tuple__10);
- if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, __pyx_n_s_dtype, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_6, __pyx_t_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_1, __pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_new_locs, ((PyArrayObject *)__pyx_t_5));
__pyx_t_5 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":305
* else:
- * new_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
- * dup_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment. # <<<<<<<<<<<<<<
+ * new_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ * dup_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment. # <<<<<<<<<<<<<<
* i_new += 1
* n = 1
*/
__pyx_t_5 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_zeros); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_6 = __Pyx_PyObject_GetAttrStr(__pyx_t_5, __pyx_n_s_zeros); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (unlikely(__pyx_v_self->__pointer == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
@@ -5254,13 +5257,16 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
}
__pyx_t_5 = __Pyx_PyDict_GetItem(__pyx_v_self->__pointer, __pyx_v_k); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_5 = 0;
- __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Add(__pyx_t_5, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(__pyx_tuple__11);
@@ -5269,20 +5275,20 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
__Pyx_INCREF(__pyx_tuple__12);
PyList_SET_ITEM(__pyx_t_4, 1, __pyx_tuple__12);
__Pyx_GIVEREF(__pyx_tuple__12);
- if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_dtype, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_6, __pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_dup_locs, ((PyArrayObject *)__pyx_t_4));
__pyx_t_4 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":306
- * new_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
- * dup_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ * new_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ * dup_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
* i_new += 1 # <<<<<<<<<<<<<<
* n = 1
*
@@ -5290,7 +5296,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
__pyx_v_i_new = (__pyx_v_i_new + 1);
/* "MACS2/IO/PairedEndTrack.pyx":307
- * dup_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ * dup_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
* i_new += 1
* n = 1 # <<<<<<<<<<<<<<
*
@@ -5307,11 +5313,11 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
*/
__pyx_t_4 = __Pyx_GetItemInt(((PyObject *)__pyx_v_locs), 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_4, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_4, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_9 = __Pyx_PyInt_As_int(__pyx_t_5); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_9 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_current_loc_start = __pyx_t_9;
/* "MACS2/IO/PairedEndTrack.pyx":310
@@ -5321,11 +5327,11 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
* new_locs[i_new][0] = current_loc_start
* new_locs[i_new][1] = current_loc_end
*/
- __pyx_t_5 = __Pyx_GetItemInt(((PyObject *)__pyx_v_locs), 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 310; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_5, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 310; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_locs), 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 310; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_1, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 310; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_9 = __Pyx_PyInt_As_int(__pyx_t_4); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_v_current_loc_end = __pyx_t_9;
@@ -5339,10 +5345,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
*/
__pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_current_loc_start); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_5);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_5, 0, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_1);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_1, 0, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":312
@@ -5354,10 +5360,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
*/
__pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_current_loc_end); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_5);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_5, 1, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_1);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_1, 1, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":313
@@ -5389,11 +5395,11 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
*/
__pyx_t_4 = __Pyx_GetItemInt(((PyObject *)__pyx_v_locs), __pyx_v_i_old, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_4, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_4, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_11 = __Pyx_PyInt_As_int(__pyx_t_5); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_11 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_loc_start = __pyx_t_11;
/* "MACS2/IO/PairedEndTrack.pyx":316
@@ -5403,11 +5409,11 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
* all_same = ((loc_start == current_loc_start) and
* (loc_end == current_loc_end))
*/
- __pyx_t_5 = __Pyx_GetItemInt(((PyObject *)__pyx_v_locs), __pyx_v_i_old, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_5, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_locs), __pyx_v_i_old, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_1, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_4 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_11 = __Pyx_PyInt_As_int(__pyx_t_4); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_v_loc_end = __pyx_t_11;
@@ -5422,10 +5428,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
__pyx_t_3 = (__pyx_v_loc_start == __pyx_v_current_loc_start);
if (__pyx_t_3) {
} else {
- __pyx_t_5 = __Pyx_PyBool_FromLong(__pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_4 = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = __pyx_t_1;
+ __pyx_t_1 = 0;
goto __pyx_L9_bool_binop_done;
}
@@ -5437,10 +5443,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
* n += 1
*/
__pyx_t_3 = (__pyx_v_loc_end == __pyx_v_current_loc_end);
- __pyx_t_5 = __Pyx_PyBool_FromLong(__pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_4 = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = __pyx_t_1;
+ __pyx_t_1 = 0;
__pyx_L9_bool_binop_done:;
__Pyx_XDECREF_SET(__pyx_v_all_same, __pyx_t_4);
__pyx_t_4 = 0;
@@ -5515,10 +5521,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
*/
__pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_loc_start); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = __Pyx_GetItemInt(((PyObject *)__pyx_v_dup_locs), __pyx_v_i_dup, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_5);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_5, 0, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_dup_locs), __pyx_v_i_dup, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_1);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_1, 0, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":327
@@ -5530,10 +5536,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
*/
__pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_loc_end); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = __Pyx_GetItemInt(((PyObject *)__pyx_v_dup_locs), __pyx_v_i_dup, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_5);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_5, 1, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_dup_locs), __pyx_v_i_dup, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_1);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_1, 1, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":328
@@ -5557,10 +5563,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
*/
__pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_loc_start); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_5);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_5, 0, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_1);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_1, 0, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":331
@@ -5572,10 +5578,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
*/
__pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_loc_end); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_5);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_5, 1, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_1 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_1 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_1);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_1, 1, __pyx_t_4, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":332
@@ -5608,22 +5614,22 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
*/
__pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_new_locs), __pyx_n_s_resize); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_5 = 0;
- __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_6, __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":335
* i_new += 1
@@ -5632,23 +5638,23 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
* self.total += i_new
* self.dup_total += i_dup
*/
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_dup_locs), __pyx_n_s_resize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_dup); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_dup_locs), __pyx_n_s_resize); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_5 = 0;
- __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_dup); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_6, __pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_5, __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":336
@@ -5712,22 +5718,22 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
*/
__pyx_t_4 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_locs), __pyx_n_s_resize); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = __Pyx_PyInt_From_long(__pyx_v_self->buffer_size); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_5 = 0;
- __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v_self->buffer_size); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_6, __pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_5, __pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":350
* # doesn't do a thing.
@@ -5736,16 +5742,16 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
* # hope there would be no mem leak...
*
*/
- __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_locs), __pyx_n_s_resize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_locs), __pyx_n_s_resize); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_tuple__13, __pyx_t_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_tuple__13, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":353
* # hope there would be no mem leak...
@@ -6052,7 +6058,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
* i_new = 0
* locs = self.__locations[k] # <<<<<<<<<<<<<<
* size = locs.shape[0]
- * if size < 1:
+ * if size <= 1:
*/
if (unlikely(__pyx_v_self->__locations == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
@@ -6068,7 +6074,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
* i_new = 0
* locs = self.__locations[k]
* size = locs.shape[0] # <<<<<<<<<<<<<<
- * if size < 1:
+ * if size <= 1:
* new_locs = locs
*/
__pyx_v_size = (__pyx_v_locs->dimensions[0]);
@@ -6076,19 +6082,19 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
/* "MACS2/IO/PairedEndTrack.pyx":388
* locs = self.__locations[k]
* size = locs.shape[0]
- * if size < 1: # <<<<<<<<<<<<<<
+ * if size <= 1: # <<<<<<<<<<<<<<
* new_locs = locs
* else:
*/
- __pyx_t_2 = ((__pyx_v_size < 1) != 0);
+ __pyx_t_2 = ((__pyx_v_size <= 1) != 0);
if (__pyx_t_2) {
/* "MACS2/IO/PairedEndTrack.pyx":389
* size = locs.shape[0]
- * if size < 1:
+ * if size <= 1:
* new_locs = locs # <<<<<<<<<<<<<<
* else:
- * new_locs = np.zeros( self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ * new_locs = np.zeros( self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
*/
__Pyx_INCREF(((PyObject *)__pyx_v_locs));
__Pyx_XDECREF_SET(__pyx_v_new_locs, __pyx_v_locs);
@@ -6099,7 +6105,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
/* "MACS2/IO/PairedEndTrack.pyx":391
* new_locs = locs
* else:
- * new_locs = np.zeros( self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment. # <<<<<<<<<<<<<<
+ * new_locs = np.zeros( self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment. # <<<<<<<<<<<<<<
* i_new += 1
* n = 1 # the number of tags in the current location
*/
@@ -6114,13 +6120,16 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
}
__pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_self->__pointer, __pyx_v_k); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Add(__pyx_t_3, __pyx_int_1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__pyx_t_8 = PyList_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(__pyx_tuple__14);
@@ -6129,20 +6138,20 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
__Pyx_INCREF(__pyx_tuple__15);
PyList_SET_ITEM(__pyx_t_8, 1, __pyx_tuple__15);
__Pyx_GIVEREF(__pyx_tuple__15);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_dtype, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_7, __pyx_n_s_dtype, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_7, __pyx_t_3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_3, __pyx_t_7); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (!(likely(((__pyx_t_8) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_8, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_new_locs, ((PyArrayObject *)__pyx_t_8));
__pyx_t_8 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":392
* else:
- * new_locs = np.zeros( self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ * new_locs = np.zeros( self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
* i_new += 1 # <<<<<<<<<<<<<<
* n = 1 # the number of tags in the current location
*
@@ -6150,7 +6159,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
__pyx_v_i_new = (__pyx_v_i_new + 1);
/* "MACS2/IO/PairedEndTrack.pyx":393
- * new_locs = np.zeros( self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ * new_locs = np.zeros( self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
* i_new += 1
* n = 1 # the number of tags in the current location # <<<<<<<<<<<<<<
*
@@ -6167,11 +6176,11 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
*/
__pyx_t_8 = __Pyx_GetItemInt(((PyObject *)__pyx_v_locs), 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_8, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_8, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_9 = __Pyx_PyInt_As_int(__pyx_t_3); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_9 = __Pyx_PyInt_As_int(__pyx_t_7); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_v_current_loc_start = __pyx_t_9;
/* "MACS2/IO/PairedEndTrack.pyx":396
@@ -6181,11 +6190,11 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
* new_locs[i_new][0] = current_loc_start
* new_locs[i_new][1] = current_loc_end
*/
- __pyx_t_3 = __Pyx_GetItemInt(((PyObject *)__pyx_v_locs), 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_t_3, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_7 = __Pyx_GetItemInt(((PyObject *)__pyx_v_locs), 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_t_7, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_9 = __Pyx_PyInt_As_int(__pyx_t_8); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_v_current_loc_end = __pyx_t_9;
@@ -6199,10 +6208,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
*/
__pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_current_loc_start); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_3);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_3, 0, __pyx_t_8, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_7 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_7);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_7, 0, __pyx_t_8, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":398
@@ -6214,10 +6223,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
*/
__pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_current_loc_end); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_3);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_3, 1, __pyx_t_8, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_7 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_7);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_7, 1, __pyx_t_8, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":399
@@ -6249,11 +6258,11 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
*/
__pyx_t_8 = __Pyx_GetItemInt(((PyObject *)__pyx_v_locs), __pyx_v_i_old, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_8, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_8, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_9 = __Pyx_PyInt_As_int(__pyx_t_3); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_9 = __Pyx_PyInt_As_int(__pyx_t_7); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_v_loc_start = __pyx_t_9;
/* "MACS2/IO/PairedEndTrack.pyx":402
@@ -6263,11 +6272,11 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
* all_same = ((loc_start == current_loc_start) and
* (loc_end == current_loc_end))
*/
- __pyx_t_3 = __Pyx_GetItemInt(((PyObject *)__pyx_v_locs), __pyx_v_i_old, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_t_3, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_7 = __Pyx_GetItemInt(((PyObject *)__pyx_v_locs), __pyx_v_i_old, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_t_7, 1, long, 1, __Pyx_PyInt_From_long, 0, 0, 0); if (unlikely(__pyx_t_8 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_9 = __Pyx_PyInt_As_int(__pyx_t_8); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_v_loc_end = __pyx_t_9;
@@ -6282,10 +6291,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
__pyx_t_2 = (__pyx_v_loc_start == __pyx_v_current_loc_start);
if (__pyx_t_2) {
} else {
- __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_8 = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_8 = __pyx_t_7;
+ __pyx_t_7 = 0;
goto __pyx_L10_bool_binop_done;
}
@@ -6297,10 +6306,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
* n += 1
*/
__pyx_t_2 = (__pyx_v_loc_end == __pyx_v_current_loc_end);
- __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_8 = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_8 = __pyx_t_7;
+ __pyx_t_7 = 0;
__pyx_L10_bool_binop_done:;
__Pyx_XDECREF_SET(__pyx_v_all_same, __pyx_t_8);
__pyx_t_8 = 0;
@@ -6343,10 +6352,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
*/
__pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_loc_start); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_3);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_3, 0, __pyx_t_8, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_7 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_7);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_7, 0, __pyx_t_8, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":409
@@ -6358,10 +6367,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
*/
__pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_loc_end); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_3);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_3, 1, __pyx_t_8, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_7 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_7);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_7, 1, __pyx_t_8, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":410
@@ -6415,10 +6424,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
*/
__pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_loc_start); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_3);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_3, 0, __pyx_t_8, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_7 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_7);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_7, 0, __pyx_t_8, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":416
@@ -6430,10 +6439,10 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
*/
__pyx_t_8 = __Pyx_PyInt_From_int(__pyx_v_loc_end); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- __Pyx_GOTREF(__pyx_t_3);
- if (unlikely(__Pyx_SetItemInt(__pyx_t_3, 1, __pyx_t_8, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_7 = __Pyx_GetItemInt(((PyObject *)__pyx_v_new_locs), __pyx_v_i_new, unsigned long, 0, __Pyx_PyInt_From_unsigned_long, 0, 0, 0); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __Pyx_GOTREF(__pyx_t_7);
+ if (unlikely(__Pyx_SetItemInt(__pyx_t_7, 1, __pyx_t_8, long, 1, __Pyx_PyInt_From_long, 0, 0, 0) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":417
@@ -6475,21 +6484,21 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
*/
__pyx_t_8 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_new_locs), __pyx_n_s_resize); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyInt_From_unsigned_long(__pyx_v_i_new); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_t_7, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ if (PyDict_SetItem(__pyx_t_7, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_t_3, __pyx_t_7); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":421
@@ -6537,21 +6546,21 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
*/
__pyx_t_6 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_locs), __pyx_n_s_resize); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v_self->buffer_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyInt_From_long(__pyx_v_self->buffer_size); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_7, __pyx_t_3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ if (PyDict_SetItem(__pyx_t_7, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_Call(__pyx_t_6, __pyx_t_3, __pyx_t_7); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":429
@@ -6563,14 +6572,14 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_24filter_dup(str
*/
__pyx_t_8 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_locs), __pyx_n_s_resize); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_tuple__16, __pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
+ if (PyDict_SetItem(__pyx_t_7, __pyx_n_s_refcheck, Py_False) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_8, __pyx_tuple__16, __pyx_t_7); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":432
* # hope there would be no mem leak...
@@ -12934,8 +12943,8 @@ static int __Pyx_InitCachedConstants(void) {
/* "MACS2/IO/PairedEndTrack.pyx":304
* new_locs = locs
* else:
- * new_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment. # <<<<<<<<<<<<<<
- * dup_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ * new_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment. # <<<<<<<<<<<<<<
+ * dup_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
* i_new += 1
*/
__pyx_tuple__9 = PyTuple_Pack(2, __pyx_n_s_l, __pyx_n_s_int32); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -12947,8 +12956,8 @@ static int __Pyx_InitCachedConstants(void) {
/* "MACS2/IO/PairedEndTrack.pyx":305
* else:
- * new_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
- * dup_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment. # <<<<<<<<<<<<<<
+ * new_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ * dup_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment. # <<<<<<<<<<<<<<
* i_new += 1
* n = 1
*/
@@ -12973,7 +12982,7 @@ static int __Pyx_InitCachedConstants(void) {
/* "MACS2/IO/PairedEndTrack.pyx":391
* new_locs = locs
* else:
- * new_locs = np.zeros( self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment. # <<<<<<<<<<<<<<
+ * new_locs = np.zeros( self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment. # <<<<<<<<<<<<<<
* i_new += 1
* n = 1 # the number of tags in the current location
*/
diff --git a/MACS2/IO/PairedEndTrack.pyx b/MACS2/IO/PairedEndTrack.pyx
index af616c5..27c3023 100644
--- a/MACS2/IO/PairedEndTrack.pyx
+++ b/MACS2/IO/PairedEndTrack.pyx
@@ -298,11 +298,11 @@ cdef class PETrackI:
i_dup = 0
locs = self.__locations[k]
size = locs.shape[0]
- if size < 1:
+ if size <= 1:
new_locs = locs
else:
- new_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
- dup_locs = np.zeros(self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ new_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ dup_locs = np.zeros(self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
i_new += 1
n = 1
@@ -385,10 +385,10 @@ cdef class PETrackI:
i_new = 0
locs = self.__locations[k]
size = locs.shape[0]
- if size < 1:
+ if size <= 1:
new_locs = locs
else:
- new_locs = np.zeros( self.__pointer[k], dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
+ new_locs = np.zeros( self.__pointer[k] + 1, dtype=[('l','int32'),('r','int32')]) # note: ['l'] is the leftmost end, ['r'] is the rightmost end of fragment.
i_new += 1
n = 1 # the number of tags in the current location
diff --git a/MACS2/IO/Parser.c b/MACS2/IO/Parser.c
index c44441c..e8ba81e 100644
--- a/MACS2/IO/Parser.c
+++ b/MACS2/IO/Parser.c
@@ -454,13 +454,13 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
"MACS2/IO/Parser.pyx",
- "__init__.pxd",
+ "numpy.pxd",
"type.pxd",
"bool.pxd",
"complex.pxd",
};
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726
+/* "numpy.pxd":723
* # in Cython to enable them only on the right systems.
*
* ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
@@ -469,7 +469,7 @@ static const char *__pyx_f[] = {
*/
typedef npy_int8 __pyx_t_5numpy_int8_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":727
+/* "numpy.pxd":724
*
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
@@ -478,7 +478,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t;
*/
typedef npy_int16 __pyx_t_5numpy_int16_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":728
+/* "numpy.pxd":725
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
@@ -487,7 +487,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t;
*/
typedef npy_int32 __pyx_t_5numpy_int32_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":729
+/* "numpy.pxd":726
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
@@ -496,7 +496,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t;
*/
typedef npy_int64 __pyx_t_5numpy_int64_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733
+/* "numpy.pxd":730
* #ctypedef npy_int128 int128_t
*
* ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
@@ -505,7 +505,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t;
*/
typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":734
+/* "numpy.pxd":731
*
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
@@ -514,7 +514,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t;
*/
typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":735
+/* "numpy.pxd":732
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
@@ -523,7 +523,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t;
*/
typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":736
+/* "numpy.pxd":733
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
@@ -532,7 +532,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t;
*/
typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":740
+/* "numpy.pxd":737
* #ctypedef npy_uint128 uint128_t
*
* ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
@@ -541,7 +541,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t;
*/
typedef npy_float32 __pyx_t_5numpy_float32_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":741
+/* "numpy.pxd":738
*
* ctypedef npy_float32 float32_t
* ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
@@ -550,7 +550,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t;
*/
typedef npy_float64 __pyx_t_5numpy_float64_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":750
+/* "numpy.pxd":747
* # The int types are mapped a bit surprising --
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t # <<<<<<<<<<<<<<
@@ -559,7 +559,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t;
*/
typedef npy_long __pyx_t_5numpy_int_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751
+/* "numpy.pxd":748
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
@@ -568,7 +568,7 @@ typedef npy_long __pyx_t_5numpy_int_t;
*/
typedef npy_longlong __pyx_t_5numpy_long_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752
+/* "numpy.pxd":749
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
@@ -577,7 +577,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t;
*/
typedef npy_longlong __pyx_t_5numpy_longlong_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":754
+/* "numpy.pxd":751
* ctypedef npy_longlong longlong_t
*
* ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
@@ -586,7 +586,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t;
*/
typedef npy_ulong __pyx_t_5numpy_uint_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755
+/* "numpy.pxd":752
*
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
@@ -595,7 +595,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756
+/* "numpy.pxd":753
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
@@ -604,7 +604,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758
+/* "numpy.pxd":755
* ctypedef npy_ulonglong ulonglong_t
*
* ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
@@ -613,7 +613,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
*/
typedef npy_intp __pyx_t_5numpy_intp_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759
+/* "numpy.pxd":756
*
* ctypedef npy_intp intp_t
* ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
@@ -622,7 +622,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t;
*/
typedef npy_uintp __pyx_t_5numpy_uintp_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":761
+/* "numpy.pxd":758
* ctypedef npy_uintp uintp_t
*
* ctypedef npy_double float_t # <<<<<<<<<<<<<<
@@ -631,7 +631,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t;
*/
typedef npy_double __pyx_t_5numpy_float_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762
+/* "numpy.pxd":759
*
* ctypedef npy_double float_t
* ctypedef npy_double double_t # <<<<<<<<<<<<<<
@@ -640,7 +640,7 @@ typedef npy_double __pyx_t_5numpy_float_t;
*/
typedef npy_double __pyx_t_5numpy_double_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763
+/* "numpy.pxd":760
* ctypedef npy_double float_t
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
@@ -681,7 +681,7 @@ struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser;
struct __pyx_obj_5MACS2_2IO_6Parser_BowtieParser;
struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":765
+/* "numpy.pxd":762
* ctypedef npy_longdouble longdouble_t
*
* ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
@@ -690,7 +690,7 @@ struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser;
*/
typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766
+/* "numpy.pxd":763
*
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
@@ -699,7 +699,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
*/
typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":767
+/* "numpy.pxd":764
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
@@ -708,7 +708,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
*/
typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":769
+/* "numpy.pxd":766
* ctypedef npy_clongdouble clongdouble_t
*
* ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
@@ -1286,26 +1286,6 @@ static CYTHON_INLINE unsigned int __Pyx_abs_int(int x) {
return (unsigned int) abs(x);
}
-#if PY_MAJOR_VERSION >= 3
-static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
- PyObject *value;
- value = PyDict_GetItemWithError(d, key);
- if (unlikely(!value)) {
- if (!PyErr_Occurred()) {
- PyObject* args = PyTuple_Pack(1, key);
- if (likely(args))
- PyErr_SetObject(PyExc_KeyError, args);
- Py_XDECREF(args);
- }
- return NULL;
- }
- Py_INCREF(value);
- return value;
-}
-#else
- #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
-#endif
-
static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type);
static int __Pyx_SetVtable(PyObject *dict, void *vtable);
@@ -1503,6 +1483,8 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
#endif
#endif
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ptrdiff_t(ptrdiff_t value);
+
static CYTHON_INLINE int __Pyx_StrEq(const char *, const char *); /*proto*/
static int __Pyx_check_binary_version(void);
@@ -2029,6 +2011,7 @@ static PyObject *__pyx_int_8;
static PyObject *__pyx_int_9;
static PyObject *__pyx_int_10;
static PyObject *__pyx_int_12;
+static PyObject *__pyx_int_15;
static PyObject *__pyx_int_16;
static PyObject *__pyx_int_20;
static PyObject *__pyx_int_32;
@@ -16615,7 +16598,7 @@ static struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed __pyx_f_5MACS2_2IO_6Parser
* (n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] )
* if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048: # <<<<<<<<<<<<<<
* return ret #unmapped sequence or bad sequence or 2nd or sup alignment
- * if bwflag & 256 or bwflag & 2048:
+ * #if bwflag & 256 or bwflag & 2048:
*/
__pyx_t_1 = ((__pyx_v_bwflag & 4) != 0);
if (!__pyx_t_1) {
@@ -16650,45 +16633,16 @@ static struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed __pyx_f_5MACS2_2IO_6Parser
* (n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] )
* if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
* return ret #unmapped sequence or bad sequence or 2nd or sup alignment # <<<<<<<<<<<<<<
- * if bwflag & 256 or bwflag & 2048:
- * return ret # secondary or supplementary alignment
- */
- __pyx_r = __pyx_v_ret;
- goto __pyx_L0;
- }
-
- /* "MACS2/IO/Parser.pyx":1245
- * if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
- * return ret #unmapped sequence or bad sequence or 2nd or sup alignment
- * if bwflag & 256 or bwflag & 2048: # <<<<<<<<<<<<<<
- * return ret # secondary or supplementary alignment
- * if bwflag & 1:
- */
- __pyx_t_1 = ((__pyx_v_bwflag & 256) != 0);
- if (!__pyx_t_1) {
- } else {
- __pyx_t_2 = __pyx_t_1;
- goto __pyx_L13_bool_binop_done;
- }
- __pyx_t_1 = ((__pyx_v_bwflag & 2048) != 0);
- __pyx_t_2 = __pyx_t_1;
- __pyx_L13_bool_binop_done:;
- if (__pyx_t_2) {
-
- /* "MACS2/IO/Parser.pyx":1246
- * return ret #unmapped sequence or bad sequence or 2nd or sup alignment
- * if bwflag & 256 or bwflag & 2048:
- * return ret # secondary or supplementary alignment # <<<<<<<<<<<<<<
- * if bwflag & 1:
- * # paired read. We should only keep sequence if the mate is mapped
+ * #if bwflag & 256 or bwflag & 2048:
+ * # return ret # secondary or supplementary alignment
*/
__pyx_r = __pyx_v_ret;
goto __pyx_L0;
}
/* "MACS2/IO/Parser.pyx":1247
- * if bwflag & 256 or bwflag & 2048:
- * return ret # secondary or supplementary alignment
+ * #if bwflag & 256 or bwflag & 2048:
+ * # return ret # secondary or supplementary alignment
* if bwflag & 1: # <<<<<<<<<<<<<<
* # paired read. We should only keep sequence if the mate is mapped
* # and if this is the left mate, all is within the flag!
@@ -16758,9 +16712,9 @@ static struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed __pyx_f_5MACS2_2IO_6Parser
__pyx_r = __pyx_v_ret;
goto __pyx_L0;
}
- goto __pyx_L15;
+ goto __pyx_L12;
}
- __pyx_L15:;
+ __pyx_L12:;
/* "MACS2/IO/Parser.pyx":1258
* return ret
@@ -19903,7 +19857,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11PySAMParser_10close(struct __pyx_
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197
+/* "numpy.pxd":194
* # experimental exception made for __getbuffer__ and __releasebuffer__
* # -- the details of this may change.
* def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
@@ -19953,7 +19907,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__Pyx_GIVEREF(__pyx_v_info->obj);
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":203
+ /* "numpy.pxd":200
* # of flags
*
* if info == NULL: return # <<<<<<<<<<<<<<
@@ -19966,7 +19920,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
goto __pyx_L0;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":206
+ /* "numpy.pxd":203
*
* cdef int copy_shape, i, ndim
* cdef int endian_detector = 1 # <<<<<<<<<<<<<<
@@ -19975,7 +19929,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_endian_detector = 1;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":207
+ /* "numpy.pxd":204
* cdef int copy_shape, i, ndim
* cdef int endian_detector = 1
* cdef bint little_endian = ((<char*>&endian_detector)[0] != 0) # <<<<<<<<<<<<<<
@@ -19984,7 +19938,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":209
+ /* "numpy.pxd":206
* cdef bint little_endian = ((<char*>&endian_detector)[0] != 0)
*
* ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<<
@@ -19993,7 +19947,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_ndim = PyArray_NDIM(__pyx_v_self);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211
+ /* "numpy.pxd":208
* ndim = PyArray_NDIM(self)
*
* if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<<
@@ -20003,7 +19957,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0);
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":212
+ /* "numpy.pxd":209
*
* if sizeof(npy_intp) != sizeof(Py_ssize_t):
* copy_shape = 1 # <<<<<<<<<<<<<<
@@ -20015,7 +19969,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":214
+ /* "numpy.pxd":211
* copy_shape = 1
* else:
* copy_shape = 0 # <<<<<<<<<<<<<<
@@ -20026,7 +19980,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
__pyx_L4:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216
+ /* "numpy.pxd":213
* copy_shape = 0
*
* if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<<
@@ -20040,7 +19994,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
goto __pyx_L6_bool_binop_done;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":217
+ /* "numpy.pxd":214
*
* if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<<
@@ -20052,21 +20006,21 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_L6_bool_binop_done:;
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218
+ /* "numpy.pxd":215
* if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)):
* raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<<
*
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
*/
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__93, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__93, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220
+ /* "numpy.pxd":217
* raise ValueError(u"ndarray is not C contiguous")
*
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<<
@@ -20080,7 +20034,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
goto __pyx_L9_bool_binop_done;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":221
+ /* "numpy.pxd":218
*
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<<
@@ -20092,21 +20046,21 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_L9_bool_binop_done:;
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222
+ /* "numpy.pxd":219
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)):
* raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<<
*
* info.buf = PyArray_DATA(self)
*/
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__94, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__94, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":224
+ /* "numpy.pxd":221
* raise ValueError(u"ndarray is not Fortran contiguous")
*
* info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<<
@@ -20115,7 +20069,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->buf = PyArray_DATA(__pyx_v_self);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":225
+ /* "numpy.pxd":222
*
* info.buf = PyArray_DATA(self)
* info.ndim = ndim # <<<<<<<<<<<<<<
@@ -20124,7 +20078,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->ndim = __pyx_v_ndim;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226
+ /* "numpy.pxd":223
* info.buf = PyArray_DATA(self)
* info.ndim = ndim
* if copy_shape: # <<<<<<<<<<<<<<
@@ -20134,7 +20088,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_t_1 = (__pyx_v_copy_shape != 0);
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":229
+ /* "numpy.pxd":226
* # Allocate new buffer for strides and shape info.
* # This is allocated as one block, strides first.
* info.strides = <Py_ssize_t*>stdlib.malloc(sizeof(Py_ssize_t) * <size_t>ndim * 2) # <<<<<<<<<<<<<<
@@ -20143,7 +20097,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2)));
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":230
+ /* "numpy.pxd":227
* # This is allocated as one block, strides first.
* info.strides = <Py_ssize_t*>stdlib.malloc(sizeof(Py_ssize_t) * <size_t>ndim * 2)
* info.shape = info.strides + ndim # <<<<<<<<<<<<<<
@@ -20152,7 +20106,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":231
+ /* "numpy.pxd":228
* info.strides = <Py_ssize_t*>stdlib.malloc(sizeof(Py_ssize_t) * <size_t>ndim * 2)
* info.shape = info.strides + ndim
* for i in range(ndim): # <<<<<<<<<<<<<<
@@ -20163,7 +20117,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
__pyx_v_i = __pyx_t_5;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":232
+ /* "numpy.pxd":229
* info.shape = info.strides + ndim
* for i in range(ndim):
* info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<<
@@ -20172,7 +20126,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
(__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":233
+ /* "numpy.pxd":230
* for i in range(ndim):
* info.strides[i] = PyArray_STRIDES(self)[i]
* info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<<
@@ -20185,7 +20139,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":235
+ /* "numpy.pxd":232
* info.shape[i] = PyArray_DIMS(self)[i]
* else:
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self) # <<<<<<<<<<<<<<
@@ -20194,7 +20148,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self));
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":236
+ /* "numpy.pxd":233
* else:
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self)
* info.shape = <Py_ssize_t*>PyArray_DIMS(self) # <<<<<<<<<<<<<<
@@ -20205,7 +20159,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
__pyx_L11:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":237
+ /* "numpy.pxd":234
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self)
* info.shape = <Py_ssize_t*>PyArray_DIMS(self)
* info.suboffsets = NULL # <<<<<<<<<<<<<<
@@ -20214,7 +20168,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->suboffsets = NULL;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":238
+ /* "numpy.pxd":235
* info.shape = <Py_ssize_t*>PyArray_DIMS(self)
* info.suboffsets = NULL
* info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<<
@@ -20223,7 +20177,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":239
+ /* "numpy.pxd":236
* info.suboffsets = NULL
* info.itemsize = PyArray_ITEMSIZE(self)
* info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<<
@@ -20232,7 +20186,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0));
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":242
+ /* "numpy.pxd":239
*
* cdef int t
* cdef char* f = NULL # <<<<<<<<<<<<<<
@@ -20241,7 +20195,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_f = NULL;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":243
+ /* "numpy.pxd":240
* cdef int t
* cdef char* f = NULL
* cdef dtype descr = self.descr # <<<<<<<<<<<<<<
@@ -20253,7 +20207,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_descr = ((PyArray_Descr *)__pyx_t_3);
__pyx_t_3 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":247
+ /* "numpy.pxd":244
* cdef int offset
*
* cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<<
@@ -20262,7 +20216,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":249
+ /* "numpy.pxd":246
* cdef bint hasfields = PyDataType_HASFIELDS(descr)
*
* if not hasfields and not copy_shape: # <<<<<<<<<<<<<<
@@ -20280,7 +20234,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_L15_bool_binop_done:;
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":251
+ /* "numpy.pxd":248
* if not hasfields and not copy_shape:
* # do not call releasebuffer
* info.obj = None # <<<<<<<<<<<<<<
@@ -20296,7 +20250,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":254
+ /* "numpy.pxd":251
* else:
* # need to call releasebuffer
* info.obj = self # <<<<<<<<<<<<<<
@@ -20311,7 +20265,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
__pyx_L14:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":256
+ /* "numpy.pxd":253
* info.obj = self
*
* if not hasfields: # <<<<<<<<<<<<<<
@@ -20321,7 +20275,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0);
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257
+ /* "numpy.pxd":254
*
* if not hasfields:
* t = descr.type_num # <<<<<<<<<<<<<<
@@ -20331,7 +20285,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_t_4 = __pyx_v_descr->type_num;
__pyx_v_t = __pyx_t_4;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258
+ /* "numpy.pxd":255
* if not hasfields:
* t = descr.type_num
* if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<<
@@ -20351,7 +20305,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
__pyx_L20_next_or:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259
+ /* "numpy.pxd":256
* t = descr.type_num
* if ((descr.byteorder == c'>' and little_endian) or
* (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<<
@@ -20369,21 +20323,21 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_L19_bool_binop_done:;
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260
+ /* "numpy.pxd":257
* if ((descr.byteorder == c'>' and little_endian) or
* (descr.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<<
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B"
*/
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__95, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__95, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":277
+ /* "numpy.pxd":274
* elif t == NPY_CDOUBLE: f = "Zd"
* elif t == NPY_CLONGDOUBLE: f = "Zg"
* elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<<
@@ -20392,7 +20346,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
switch (__pyx_v_t) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":261
+ /* "numpy.pxd":258
* (descr.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported")
* if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<<
@@ -20403,7 +20357,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_b;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":262
+ /* "numpy.pxd":259
* raise ValueError(u"Non-native byte order not supported")
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<<
@@ -20414,7 +20368,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_B_2;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":263
+ /* "numpy.pxd":260
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B"
* elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<<
@@ -20425,7 +20379,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_h;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":264
+ /* "numpy.pxd":261
* elif t == NPY_UBYTE: f = "B"
* elif t == NPY_SHORT: f = "h"
* elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<<
@@ -20436,7 +20390,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_H;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265
+ /* "numpy.pxd":262
* elif t == NPY_SHORT: f = "h"
* elif t == NPY_USHORT: f = "H"
* elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<<
@@ -20447,7 +20401,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_i_2;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266
+ /* "numpy.pxd":263
* elif t == NPY_USHORT: f = "H"
* elif t == NPY_INT: f = "i"
* elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<<
@@ -20458,7 +20412,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_I;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":267
+ /* "numpy.pxd":264
* elif t == NPY_INT: f = "i"
* elif t == NPY_UINT: f = "I"
* elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<<
@@ -20469,7 +20423,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_l;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268
+ /* "numpy.pxd":265
* elif t == NPY_UINT: f = "I"
* elif t == NPY_LONG: f = "l"
* elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<<
@@ -20480,7 +20434,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_L;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":269
+ /* "numpy.pxd":266
* elif t == NPY_LONG: f = "l"
* elif t == NPY_ULONG: f = "L"
* elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<<
@@ -20491,7 +20445,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_q;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270
+ /* "numpy.pxd":267
* elif t == NPY_ULONG: f = "L"
* elif t == NPY_LONGLONG: f = "q"
* elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<<
@@ -20502,7 +20456,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_Q;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271
+ /* "numpy.pxd":268
* elif t == NPY_LONGLONG: f = "q"
* elif t == NPY_ULONGLONG: f = "Q"
* elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<<
@@ -20513,7 +20467,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_f;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272
+ /* "numpy.pxd":269
* elif t == NPY_ULONGLONG: f = "Q"
* elif t == NPY_FLOAT: f = "f"
* elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<<
@@ -20524,7 +20478,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_d_2;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":273
+ /* "numpy.pxd":270
* elif t == NPY_FLOAT: f = "f"
* elif t == NPY_DOUBLE: f = "d"
* elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<<
@@ -20535,7 +20489,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_g;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274
+ /* "numpy.pxd":271
* elif t == NPY_DOUBLE: f = "d"
* elif t == NPY_LONGDOUBLE: f = "g"
* elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<<
@@ -20546,7 +20500,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_Zf;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":275
+ /* "numpy.pxd":272
* elif t == NPY_LONGDOUBLE: f = "g"
* elif t == NPY_CFLOAT: f = "Zf"
* elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<<
@@ -20557,7 +20511,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_Zd;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276
+ /* "numpy.pxd":273
* elif t == NPY_CFLOAT: f = "Zf"
* elif t == NPY_CDOUBLE: f = "Zd"
* elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<<
@@ -20568,7 +20522,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_Zg;
break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":277
+ /* "numpy.pxd":274
* elif t == NPY_CDOUBLE: f = "Zd"
* elif t == NPY_CLONGDOUBLE: f = "Zg"
* elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<<
@@ -20580,33 +20534,33 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
break;
default:
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":279
+ /* "numpy.pxd":276
* elif t == NPY_OBJECT: f = "O"
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<<
* info.format = f
* return
*/
- __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_t); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_t); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
break;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280
+ /* "numpy.pxd":277
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
* info.format = f # <<<<<<<<<<<<<<
@@ -20615,7 +20569,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->format = __pyx_v_f;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":281
+ /* "numpy.pxd":278
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
* info.format = f
* return # <<<<<<<<<<<<<<
@@ -20627,7 +20581,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283
+ /* "numpy.pxd":280
* return
* else:
* info.format = <char*>stdlib.malloc(_buffer_format_string_len) # <<<<<<<<<<<<<<
@@ -20636,7 +20590,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->format = ((char *)malloc(255));
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":284
+ /* "numpy.pxd":281
* else:
* info.format = <char*>stdlib.malloc(_buffer_format_string_len)
* info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<<
@@ -20645,7 +20599,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
(__pyx_v_info->format[0]) = '^';
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":285
+ /* "numpy.pxd":282
* info.format = <char*>stdlib.malloc(_buffer_format_string_len)
* info.format[0] = c'^' # Native data types, manual alignment
* offset = 0 # <<<<<<<<<<<<<<
@@ -20654,17 +20608,17 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_offset = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":286
+ /* "numpy.pxd":283
* info.format[0] = c'^' # Native data types, manual alignment
* offset = 0
* f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<<
* info.format + _buffer_format_string_len,
* &offset)
*/
- __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 255), (&__pyx_v_offset)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 255), (&__pyx_v_offset)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_f = __pyx_t_7;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":289
+ /* "numpy.pxd":286
* info.format + _buffer_format_string_len,
* &offset)
* f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<<
@@ -20674,7 +20628,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
(__pyx_v_f[0]) = '\x00';
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197
+ /* "numpy.pxd":194
* # experimental exception made for __getbuffer__ and __releasebuffer__
* # -- the details of this may change.
* def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
@@ -20706,7 +20660,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291
+/* "numpy.pxd":288
* f[0] = c'\0' # Terminate format string
*
* def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<<
@@ -20730,7 +20684,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
int __pyx_t_1;
__Pyx_RefNannySetupContext("__releasebuffer__", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292
+ /* "numpy.pxd":289
*
* def __releasebuffer__(ndarray self, Py_buffer* info):
* if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<<
@@ -20740,7 +20694,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
__pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0);
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293
+ /* "numpy.pxd":290
* def __releasebuffer__(ndarray self, Py_buffer* info):
* if PyArray_HASFIELDS(self):
* stdlib.free(info.format) # <<<<<<<<<<<<<<
@@ -20752,7 +20706,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
}
__pyx_L3:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":294
+ /* "numpy.pxd":291
* if PyArray_HASFIELDS(self):
* stdlib.free(info.format)
* if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<<
@@ -20762,7 +20716,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
__pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0);
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":295
+ /* "numpy.pxd":292
* stdlib.free(info.format)
* if sizeof(npy_intp) != sizeof(Py_ssize_t):
* stdlib.free(info.strides) # <<<<<<<<<<<<<<
@@ -20774,7 +20728,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
}
__pyx_L4:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291
+ /* "numpy.pxd":288
* f[0] = c'\0' # Terminate format string
*
* def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<<
@@ -20786,7 +20740,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s
__Pyx_RefNannyFinishContext();
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":771
+/* "numpy.pxd":768
* ctypedef npy_cdouble complex_t
*
* cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<<
@@ -20803,7 +20757,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":772
+ /* "numpy.pxd":769
*
* cdef inline object PyArray_MultiIterNew1(a):
* return PyArray_MultiIterNew(1, <void*>a) # <<<<<<<<<<<<<<
@@ -20811,13 +20765,13 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__
* cdef inline object PyArray_MultiIterNew2(a, b):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":771
+ /* "numpy.pxd":768
* ctypedef npy_cdouble complex_t
*
* cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<<
@@ -20836,7 +20790,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":774
+/* "numpy.pxd":771
* return PyArray_MultiIterNew(1, <void*>a)
*
* cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<<
@@ -20853,7 +20807,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":775
+ /* "numpy.pxd":772
*
* cdef inline object PyArray_MultiIterNew2(a, b):
* return PyArray_MultiIterNew(2, <void*>a, <void*>b) # <<<<<<<<<<<<<<
@@ -20861,13 +20815,13 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__
* cdef inline object PyArray_MultiIterNew3(a, b, c):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(2, ((void *)__pyx_v_a), ((void *)__pyx_v_b)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(2, ((void *)__pyx_v_a), ((void *)__pyx_v_b)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":774
+ /* "numpy.pxd":771
* return PyArray_MultiIterNew(1, <void*>a)
*
* cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<<
@@ -20886,7 +20840,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777
+/* "numpy.pxd":774
* return PyArray_MultiIterNew(2, <void*>a, <void*>b)
*
* cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<<
@@ -20903,7 +20857,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":778
+ /* "numpy.pxd":775
*
* cdef inline object PyArray_MultiIterNew3(a, b, c):
* return PyArray_MultiIterNew(3, <void*>a, <void*>b, <void*> c) # <<<<<<<<<<<<<<
@@ -20911,13 +20865,13 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__
* cdef inline object PyArray_MultiIterNew4(a, b, c, d):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(3, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(3, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777
+ /* "numpy.pxd":774
* return PyArray_MultiIterNew(2, <void*>a, <void*>b)
*
* cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<<
@@ -20936,7 +20890,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":780
+/* "numpy.pxd":777
* return PyArray_MultiIterNew(3, <void*>a, <void*>b, <void*> c)
*
* cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<<
@@ -20953,7 +20907,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("PyArray_MultiIterNew4", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":781
+ /* "numpy.pxd":778
*
* cdef inline object PyArray_MultiIterNew4(a, b, c, d):
* return PyArray_MultiIterNew(4, <void*>a, <void*>b, <void*>c, <void*> d) # <<<<<<<<<<<<<<
@@ -20961,13 +20915,13 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__
* cdef inline object PyArray_MultiIterNew5(a, b, c, d, e):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(4, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(4, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":780
+ /* "numpy.pxd":777
* return PyArray_MultiIterNew(3, <void*>a, <void*>b, <void*> c)
*
* cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<<
@@ -20986,7 +20940,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783
+/* "numpy.pxd":780
* return PyArray_MultiIterNew(4, <void*>a, <void*>b, <void*>c, <void*> d)
*
* cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<<
@@ -21003,7 +20957,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("PyArray_MultiIterNew5", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":784
+ /* "numpy.pxd":781
*
* cdef inline object PyArray_MultiIterNew5(a, b, c, d, e):
* return PyArray_MultiIterNew(5, <void*>a, <void*>b, <void*>c, <void*> d, <void*> e) # <<<<<<<<<<<<<<
@@ -21011,13 +20965,13 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__
* cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(5, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d), ((void *)__pyx_v_e)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(5, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d), ((void *)__pyx_v_e)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783
+ /* "numpy.pxd":780
* return PyArray_MultiIterNew(4, <void*>a, <void*>b, <void*>c, <void*> d)
*
* cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<<
@@ -21036,7 +20990,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":786
+/* "numpy.pxd":783
* return PyArray_MultiIterNew(5, <void*>a, <void*>b, <void*>c, <void*> d, <void*> e)
*
* cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<<
@@ -21058,7 +21012,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
Py_ssize_t __pyx_t_2;
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
- int __pyx_t_5;
+ PyObject *__pyx_t_5 = NULL;
int __pyx_t_6;
int __pyx_t_7;
long __pyx_t_8;
@@ -21068,7 +21022,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("_util_dtypestring", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":793
+ /* "numpy.pxd":790
* cdef int delta_offset
* cdef tuple i
* cdef int endian_detector = 1 # <<<<<<<<<<<<<<
@@ -21077,7 +21031,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
__pyx_v_endian_detector = 1;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":794
+ /* "numpy.pxd":791
* cdef tuple i
* cdef int endian_detector = 1
* cdef bint little_endian = ((<char*>&endian_detector)[0] != 0) # <<<<<<<<<<<<<<
@@ -21086,7 +21040,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
__pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":797
+ /* "numpy.pxd":794
* cdef tuple fields
*
* for childname in descr.names: # <<<<<<<<<<<<<<
@@ -21095,42 +21049,38 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
if (unlikely(__pyx_v_descr->names == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
for (;;) {
if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
#if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
__Pyx_XDECREF_SET(__pyx_v_childname, __pyx_t_3);
__pyx_t_3 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":798
+ /* "numpy.pxd":795
*
* for childname in descr.names:
* fields = descr.fields[childname] # <<<<<<<<<<<<<<
* child, new_offset = fields
*
*/
- if (unlikely(__pyx_v_descr->fields == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_t_3 = PyObject_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__Pyx_GOTREF(__pyx_t_3);
- if (!(likely(PyTuple_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "tuple", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyTuple_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "tuple", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_fields, ((PyObject*)__pyx_t_3));
__pyx_t_3 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":799
+ /* "numpy.pxd":796
* for childname in descr.names:
* fields = descr.fields[childname]
* child, new_offset = fields # <<<<<<<<<<<<<<
*
- * if (end - f) - <int>(new_offset - offset[0]) < 15:
+ * if (end - f) - (new_offset - offset[0]) < 15:
*/
if (likely(__pyx_v_fields != Py_None)) {
PyObject* sequence = __pyx_v_fields;
@@ -21142,7 +21092,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
if (unlikely(size != 2)) {
if (size > 2) __Pyx_RaiseTooManyValuesError(2);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
@@ -21150,52 +21100,59 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__Pyx_INCREF(__pyx_t_3);
__Pyx_INCREF(__pyx_t_4);
#else
- __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
#endif
} else {
- __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_dtype))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_dtype))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_child, ((PyArray_Descr *)__pyx_t_3));
__pyx_t_3 = 0;
__Pyx_XDECREF_SET(__pyx_v_new_offset, __pyx_t_4);
__pyx_t_4 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801
+ /* "numpy.pxd":798
* child, new_offset = fields
*
- * if (end - f) - <int>(new_offset - offset[0]) < 15: # <<<<<<<<<<<<<<
+ * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<<
* raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd")
*
*/
- __pyx_t_4 = __Pyx_PyInt_From_int((__pyx_v_offset[0])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_From_ptrdiff_t((__pyx_v_end - __pyx_v_f)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyNumber_Subtract(__pyx_v_new_offset, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_From_int((__pyx_v_offset[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyNumber_Subtract(__pyx_v_new_offset, __pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyNumber_Subtract(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_5 = __Pyx_PyInt_As_int(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_3, __pyx_int_15, Py_LT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0);
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802
+ /* "numpy.pxd":799
*
- * if (end - f) - <int>(new_offset - offset[0]) < 15:
+ * if (end - f) - (new_offset - offset[0]) < 15:
* raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<<
*
* if ((child.byteorder == c'>' and little_endian) or
*/
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__96, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_Raise(__pyx_t_3, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__96, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":804
+ /* "numpy.pxd":801
* raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd")
*
* if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<<
@@ -21215,7 +21172,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
}
__pyx_L8_next_or:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":805
+ /* "numpy.pxd":802
*
* if ((child.byteorder == c'>' and little_endian) or
* (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<<
@@ -21233,21 +21190,21 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__pyx_L7_bool_binop_done:;
if (__pyx_t_6) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":806
+ /* "numpy.pxd":803
* if ((child.byteorder == c'>' and little_endian) or
* (child.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<<
* # One could encode it in the format string and have Cython
* # complain instead, BUT: < and > in format strings also imply
*/
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__97, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_Raise(__pyx_t_3, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__97, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816
+ /* "numpy.pxd":813
*
* # Output padding bytes
* while offset[0] < new_offset: # <<<<<<<<<<<<<<
@@ -21255,15 +21212,15 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* f += 1
*/
while (1) {
- __pyx_t_3 = __Pyx_PyInt_From_int((__pyx_v_offset[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_t_3, __pyx_v_new_offset, Py_LT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_From_int((__pyx_v_offset[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_5, __pyx_v_new_offset, Py_LT); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (!__pyx_t_6) break;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":817
+ /* "numpy.pxd":814
* # Output padding bytes
* while offset[0] < new_offset:
* f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<<
@@ -21272,7 +21229,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
(__pyx_v_f[0]) = 120;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":818
+ /* "numpy.pxd":815
* while offset[0] < new_offset:
* f[0] = 120 # "x"; pad byte
* f += 1 # <<<<<<<<<<<<<<
@@ -21281,7 +21238,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
__pyx_v_f = (__pyx_v_f + 1);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":819
+ /* "numpy.pxd":816
* f[0] = 120 # "x"; pad byte
* f += 1
* offset[0] += 1 # <<<<<<<<<<<<<<
@@ -21292,7 +21249,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
(__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1);
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":821
+ /* "numpy.pxd":818
* offset[0] += 1
*
* offset[0] += child.itemsize # <<<<<<<<<<<<<<
@@ -21302,7 +21259,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__pyx_t_8 = 0;
(__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823
+ /* "numpy.pxd":820
* offset[0] += child.itemsize
*
* if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<<
@@ -21312,19 +21269,19 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0);
if (__pyx_t_6) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":824
+ /* "numpy.pxd":821
*
* if not PyDataType_HASFIELDS(child):
* t = child.type_num # <<<<<<<<<<<<<<
* if end - f < 5:
* raise RuntimeError(u"Format string allocated too short.")
*/
- __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_child->type_num); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_child->type_num); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_3);
+ __pyx_t_3 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":825
+ /* "numpy.pxd":822
* if not PyDataType_HASFIELDS(child):
* t = child.type_num
* if end - f < 5: # <<<<<<<<<<<<<<
@@ -21334,267 +21291,267 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0);
if (__pyx_t_6) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826
+ /* "numpy.pxd":823
* t = child.type_num
* if end - f < 5:
* raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<<
*
* # Until ticket #99 is fixed, use integers to avoid warnings
*/
- __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__98, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_Raise(__pyx_t_4, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__98, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_Raise(__pyx_t_3, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":829
+ /* "numpy.pxd":826
*
* # Until ticket #99 is fixed, use integers to avoid warnings
* if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<<
* elif t == NPY_UBYTE: f[0] = 66 #"B"
* elif t == NPY_SHORT: f[0] = 104 #"h"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_BYTE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_BYTE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 98;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":830
+ /* "numpy.pxd":827
* # Until ticket #99 is fixed, use integers to avoid warnings
* if t == NPY_BYTE: f[0] = 98 #"b"
* elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<<
* elif t == NPY_SHORT: f[0] = 104 #"h"
* elif t == NPY_USHORT: f[0] = 72 #"H"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_UBYTE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_UBYTE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 66;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":831
+ /* "numpy.pxd":828
* if t == NPY_BYTE: f[0] = 98 #"b"
* elif t == NPY_UBYTE: f[0] = 66 #"B"
* elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<<
* elif t == NPY_USHORT: f[0] = 72 #"H"
* elif t == NPY_INT: f[0] = 105 #"i"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_SHORT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_SHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 104;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":832
+ /* "numpy.pxd":829
* elif t == NPY_UBYTE: f[0] = 66 #"B"
* elif t == NPY_SHORT: f[0] = 104 #"h"
* elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<<
* elif t == NPY_INT: f[0] = 105 #"i"
* elif t == NPY_UINT: f[0] = 73 #"I"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_USHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_USHORT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 72;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833
+ /* "numpy.pxd":830
* elif t == NPY_SHORT: f[0] = 104 #"h"
* elif t == NPY_USHORT: f[0] = 72 #"H"
* elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<<
* elif t == NPY_UINT: f[0] = 73 #"I"
* elif t == NPY_LONG: f[0] = 108 #"l"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_INT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_INT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 105;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":834
+ /* "numpy.pxd":831
* elif t == NPY_USHORT: f[0] = 72 #"H"
* elif t == NPY_INT: f[0] = 105 #"i"
* elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<<
* elif t == NPY_LONG: f[0] = 108 #"l"
* elif t == NPY_ULONG: f[0] = 76 #"L"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_UINT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_UINT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 73;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":835
+ /* "numpy.pxd":832
* elif t == NPY_INT: f[0] = 105 #"i"
* elif t == NPY_UINT: f[0] = 73 #"I"
* elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<<
* elif t == NPY_ULONG: f[0] = 76 #"L"
* elif t == NPY_LONGLONG: f[0] = 113 #"q"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_LONG); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_LONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 108;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836
+ /* "numpy.pxd":833
* elif t == NPY_UINT: f[0] = 73 #"I"
* elif t == NPY_LONG: f[0] = 108 #"l"
* elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<<
* elif t == NPY_LONGLONG: f[0] = 113 #"q"
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_ULONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_ULONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 76;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":837
+ /* "numpy.pxd":834
* elif t == NPY_LONG: f[0] = 108 #"l"
* elif t == NPY_ULONG: f[0] = 76 #"L"
* elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<<
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q"
* elif t == NPY_FLOAT: f[0] = 102 #"f"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_LONGLONG); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_LONGLONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 113;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":838
+ /* "numpy.pxd":835
* elif t == NPY_ULONG: f[0] = 76 #"L"
* elif t == NPY_LONGLONG: f[0] = 113 #"q"
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<<
* elif t == NPY_FLOAT: f[0] = 102 #"f"
* elif t == NPY_DOUBLE: f[0] = 100 #"d"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_ULONGLONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_ULONGLONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 81;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":839
+ /* "numpy.pxd":836
* elif t == NPY_LONGLONG: f[0] = 113 #"q"
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q"
* elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<<
* elif t == NPY_DOUBLE: f[0] = 100 #"d"
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_FLOAT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_FLOAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 102;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":840
+ /* "numpy.pxd":837
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q"
* elif t == NPY_FLOAT: f[0] = 102 #"f"
* elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<<
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g"
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf
*/
- __pyx_t_3 = PyInt_FromLong(NPY_DOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_DOUBLE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 100;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":841
+ /* "numpy.pxd":838
* elif t == NPY_FLOAT: f[0] = 102 #"f"
* elif t == NPY_DOUBLE: f[0] = 100 #"d"
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<<
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd
*/
- __pyx_t_4 = PyInt_FromLong(NPY_LONGDOUBLE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_LONGDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 103;
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842
+ /* "numpy.pxd":839
* elif t == NPY_DOUBLE: f[0] = 100 #"d"
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g"
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<<
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg
*/
- __pyx_t_3 = PyInt_FromLong(NPY_CFLOAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_CFLOAT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 90;
(__pyx_v_f[1]) = 102;
@@ -21602,19 +21559,19 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":843
+ /* "numpy.pxd":840
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g"
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<<
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg
* elif t == NPY_OBJECT: f[0] = 79 #"O"
*/
- __pyx_t_4 = PyInt_FromLong(NPY_CDOUBLE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_CDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 90;
(__pyx_v_f[1]) = 100;
@@ -21622,19 +21579,19 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":844
+ /* "numpy.pxd":841
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<<
* elif t == NPY_OBJECT: f[0] = 79 #"O"
* else:
*/
- __pyx_t_3 = PyInt_FromLong(NPY_CLONGDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_CLONGDOUBLE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 90;
(__pyx_v_f[1]) = 103;
@@ -21642,49 +21599,49 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
goto __pyx_L15;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":845
+ /* "numpy.pxd":842
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg
* elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<<
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
*/
- __pyx_t_4 = PyInt_FromLong(NPY_OBJECT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_OBJECT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
(__pyx_v_f[0]) = 79;
goto __pyx_L15;
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":847
+ /* "numpy.pxd":844
* elif t == NPY_OBJECT: f[0] = 79 #"O"
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<<
* f += 1
* else:
*/
- __pyx_t_3 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_v_t); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_v_t); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0, 0);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_5 = 0;
+ __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_L15:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":848
+ /* "numpy.pxd":845
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
* f += 1 # <<<<<<<<<<<<<<
@@ -21696,19 +21653,19 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":852
+ /* "numpy.pxd":849
* # Cython ignores struct boundary information ("T{...}"),
* # so don't output it
* f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<<
* return f
*
*/
- __pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_child, __pyx_v_f, __pyx_v_end, __pyx_v_offset); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_child, __pyx_v_f, __pyx_v_end, __pyx_v_offset); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_f = __pyx_t_9;
}
__pyx_L13:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":797
+ /* "numpy.pxd":794
* cdef tuple fields
*
* for childname in descr.names: # <<<<<<<<<<<<<<
@@ -21718,7 +21675,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":853
+ /* "numpy.pxd":850
* # so don't output it
* f = _util_dtypestring(child, f, end, offset)
* return f # <<<<<<<<<<<<<<
@@ -21728,7 +21685,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__pyx_r = __pyx_v_f;
goto __pyx_L0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":786
+ /* "numpy.pxd":783
* return PyArray_MultiIterNew(5, <void*>a, <void*>b, <void*>c, <void*> d, <void*> e)
*
* cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<<
@@ -21741,6 +21698,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_t_5);
__Pyx_AddTraceback("numpy._util_dtypestring", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
@@ -21753,7 +21711,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
return __pyx_r;
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":969
+/* "numpy.pxd":965
*
*
* cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<<
@@ -21768,7 +21726,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
int __pyx_t_2;
__Pyx_RefNannySetupContext("set_array_base", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":971
+ /* "numpy.pxd":967
* cdef inline void set_array_base(ndarray arr, object base):
* cdef PyObject* baseptr
* if base is None: # <<<<<<<<<<<<<<
@@ -21779,7 +21737,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
__pyx_t_2 = (__pyx_t_1 != 0);
if (__pyx_t_2) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":972
+ /* "numpy.pxd":968
* cdef PyObject* baseptr
* if base is None:
* baseptr = NULL # <<<<<<<<<<<<<<
@@ -21791,7 +21749,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":974
+ /* "numpy.pxd":970
* baseptr = NULL
* else:
* Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<<
@@ -21800,7 +21758,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
*/
Py_INCREF(__pyx_v_base);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":975
+ /* "numpy.pxd":971
* else:
* Py_INCREF(base) # important to do this before decref below!
* baseptr = <PyObject*>base # <<<<<<<<<<<<<<
@@ -21811,7 +21769,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
}
__pyx_L3:;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976
+ /* "numpy.pxd":972
* Py_INCREF(base) # important to do this before decref below!
* baseptr = <PyObject*>base
* Py_XDECREF(arr.base) # <<<<<<<<<<<<<<
@@ -21820,7 +21778,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
*/
Py_XDECREF(__pyx_v_arr->base);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":977
+ /* "numpy.pxd":973
* baseptr = <PyObject*>base
* Py_XDECREF(arr.base)
* arr.base = baseptr # <<<<<<<<<<<<<<
@@ -21829,7 +21787,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
*/
__pyx_v_arr->base = __pyx_v_baseptr;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":969
+ /* "numpy.pxd":965
*
*
* cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<<
@@ -21841,7 +21799,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
__Pyx_RefNannyFinishContext();
}
-/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979
+/* "numpy.pxd":975
* arr.base = baseptr
*
* cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<<
@@ -21855,7 +21813,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
int __pyx_t_1;
__Pyx_RefNannySetupContext("get_array_base", 0);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":980
+ /* "numpy.pxd":976
*
* cdef inline object get_array_base(ndarray arr):
* if arr.base is NULL: # <<<<<<<<<<<<<<
@@ -21865,7 +21823,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
__pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0);
if (__pyx_t_1) {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":981
+ /* "numpy.pxd":977
* cdef inline object get_array_base(ndarray arr):
* if arr.base is NULL:
* return None # <<<<<<<<<<<<<<
@@ -21879,7 +21837,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
}
/*else*/ {
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":983
+ /* "numpy.pxd":979
* return None
* else:
* return <object>arr.base # <<<<<<<<<<<<<<
@@ -21890,7 +21848,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
goto __pyx_L0;
}
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979
+ /* "numpy.pxd":975
* arr.base = baseptr
*
* cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<<
@@ -23114,7 +23072,7 @@ static int __Pyx_InitCachedBuiltins(void) {
__pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_zip = __Pyx_GetBuiltinName(__pyx_n_s_zip); if (!__pyx_builtin_zip) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_StopIteration = __Pyx_GetBuiltinName(__pyx_n_s_StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
return -1;
@@ -24059,69 +24017,69 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GOTREF(__pyx_tuple__92);
__Pyx_GIVEREF(__pyx_tuple__92);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218
+ /* "numpy.pxd":215
* if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)):
* raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<<
*
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
*/
- __pyx_tuple__93 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple__93)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__93 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple__93)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__93);
__Pyx_GIVEREF(__pyx_tuple__93);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222
+ /* "numpy.pxd":219
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)):
* raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<<
*
* info.buf = PyArray_DATA(self)
*/
- __pyx_tuple__94 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__94)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__94 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__94)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__94);
__Pyx_GIVEREF(__pyx_tuple__94);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260
+ /* "numpy.pxd":257
* if ((descr.byteorder == c'>' and little_endian) or
* (descr.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<<
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B"
*/
- __pyx_tuple__95 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__95)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__95 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__95)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__95);
__Pyx_GIVEREF(__pyx_tuple__95);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802
+ /* "numpy.pxd":799
*
- * if (end - f) - <int>(new_offset - offset[0]) < 15:
+ * if (end - f) - (new_offset - offset[0]) < 15:
* raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<<
*
* if ((child.byteorder == c'>' and little_endian) or
*/
- __pyx_tuple__96 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__96)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__96 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__96)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__96);
__Pyx_GIVEREF(__pyx_tuple__96);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":806
+ /* "numpy.pxd":803
* if ((child.byteorder == c'>' and little_endian) or
* (child.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<<
* # One could encode it in the format string and have Cython
* # complain instead, BUT: < and > in format strings also imply
*/
- __pyx_tuple__97 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__97)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__97 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__97)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__97);
__Pyx_GIVEREF(__pyx_tuple__97);
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826
+ /* "numpy.pxd":823
* t = child.type_num
* if end - f < 5:
* raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<<
*
* # Until ticket #99 is fixed, use integers to avoid warnings
*/
- __pyx_tuple__98 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__98)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__98 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__98)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__98);
__Pyx_GIVEREF(__pyx_tuple__98);
@@ -24165,6 +24123,7 @@ static int __Pyx_InitGlobals(void) {
__pyx_int_9 = PyInt_FromLong(9); if (unlikely(!__pyx_int_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_int_10 = PyInt_FromLong(10); if (unlikely(!__pyx_int_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_int_12 = PyInt_FromLong(12); if (unlikely(!__pyx_int_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_int_15 = PyInt_FromLong(15); if (unlikely(!__pyx_int_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_int_16 = PyInt_FromLong(16); if (unlikely(!__pyx_int_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_int_20 = PyInt_FromLong(20); if (unlikely(!__pyx_int_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_int_32 = PyInt_FromLong(32); if (unlikely(!__pyx_int_32)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -24417,10 +24376,10 @@ PyMODINIT_FUNC PyInit_Parser(void)
__pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
@@ -24764,7 +24723,7 @@ PyMODINIT_FUNC PyInit_Parser(void)
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
/* "MACS2/IO/Parser.pyx":1
- * # Time-stamp: <2015-06-02 23:21:25 Tao Liu> # <<<<<<<<<<<<<<
+ * # Time-stamp: <2015-08-14 14:29:30 Tao Liu> # <<<<<<<<<<<<<<
*
* """Module for all MACS Parser classes for input.
*/
@@ -24773,7 +24732,7 @@ PyMODINIT_FUNC PyInit_Parser(void)
if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979
+ /* "numpy.pxd":975
* arr.base = baseptr
*
* cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<<
@@ -27425,6 +27384,32 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_short(short value) {
#endif
#endif
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_ptrdiff_t(ptrdiff_t value) {
+ const ptrdiff_t neg_one = (ptrdiff_t) -1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (is_unsigned) {
+ if (sizeof(ptrdiff_t) < sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(ptrdiff_t) <= sizeof(unsigned long)) {
+ return PyLong_FromUnsignedLong((unsigned long) value);
+ } else if (sizeof(ptrdiff_t) <= sizeof(unsigned long long)) {
+ return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ }
+ } else {
+ if (sizeof(ptrdiff_t) <= sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(ptrdiff_t) <= sizeof(long long)) {
+ return PyLong_FromLongLong((long long) value);
+ }
+ }
+ {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&value;
+ return _PyLong_FromByteArray(bytes, sizeof(ptrdiff_t),
+ little, !is_unsigned);
+ }
+}
+
static CYTHON_INLINE int __Pyx_StrEq(const char *s1, const char *s2) {
while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
return *s1 == *s2;
diff --git a/MACS2/IO/Parser.pyx b/MACS2/IO/Parser.pyx
index d486d8c..9ebf665 100644
--- a/MACS2/IO/Parser.pyx
+++ b/MACS2/IO/Parser.pyx
@@ -1,4 +1,4 @@
-# Time-stamp: <2015-06-02 23:21:25 Tao Liu>
+# Time-stamp: <2015-08-14 14:29:30 Tao Liu>
"""Module for all MACS Parser classes for input.
@@ -1242,8 +1242,8 @@ cdef class BAMPEParser(BAMParser):
(n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] )
if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
return ret #unmapped sequence or bad sequence or 2nd or sup alignment
- if bwflag & 256 or bwflag & 2048:
- return ret # secondary or supplementary alignment
+ #if bwflag & 256 or bwflag & 2048:
+ # return ret # secondary or supplementary alignment
if bwflag & 1:
# paired read. We should only keep sequence if the mate is mapped
# and if this is the left mate, all is within the flag!
diff --git a/MACS2/callpeak_cmd.py b/MACS2/callpeak_cmd.py
index 7f8d245..00462cd 100644
--- a/MACS2/callpeak_cmd.py
+++ b/MACS2/callpeak_cmd.py
@@ -1,4 +1,4 @@
-# Time-stamp: <2015-07-27 12:31:14 Tao Liu>
+# Time-stamp: <2015-12-22 11:55:15 Tao Liu>
"""Description: MACS 2 main executable
@@ -286,9 +286,9 @@ def run( args ):
ofhd_xls.write(tagsinfo)
if options.shift > 0:
- ofhd_xls.write("#2 Sequencing ends will be shifted towards 3' by %d bp(s)\n" % (options.shift))
+ ofhd_xls.write("# Sequencing ends will be shifted towards 3' by %d bp(s)\n" % (options.shift))
elif options.shift < 0:
- ofhd_xls.write("#2 Sequencing ends will be shifted towards 5' by %d bp(s)\n" % (options.shift * -1))
+ ofhd_xls.write("# Sequencing ends will be shifted towards 5' by %d bp(s)\n" % (options.shift * -1))
ofhd_xls.write("# d = %d\n" % (options.d))
try:
diff --git a/PKG-INFO b/PKG-INFO
index 7875ec9..af49a01 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: MACS2
-Version: 2.1.0.20150731
+Version: 2.1.0.20151222
Summary: Model Based Analysis for ChIP-Seq data
Home-page: http://github.com/taoliu/MACS/
Author: Tao Liu
diff --git a/setup.py b/setup.py
index 9518c69..733d87b 100644
--- a/setup.py
+++ b/setup.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-# Time-stamp: <2015-07-31 14:55:55 Tao Liu>
+# Time-stamp: <2015-12-22 16:21:04 Tao Liu>
"""Description
@@ -57,7 +57,7 @@ def main():
]
setup(name="MACS2",
- version="2.1.0.20150731",
+ version="2.1.0.20151222",
description="Model Based Analysis for ChIP-Seq data",
author='Tao Liu',
author_email='vladimir.liu at gmail.com',
diff --git a/setup_w_cython.py b/setup_w_cython.py
index 4ec5ab6..f9898b6 100644
--- a/setup_w_cython.py
+++ b/setup_w_cython.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-# Time-stamp: <2015-07-31 14:55:49 Tao Liu>
+# Time-stamp: <2015-12-22 16:21:12 Tao Liu>
"""Description:
@@ -80,7 +80,7 @@ def main():
]
setup(name="MACS2",
- version="2.1.0.20150731",
+ version="2.1.0.20151222",
description="Model Based Analysis for ChIP-Seq data",
author='Tao Liu',
author_email='vladimir.liu at gmail.com',
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/macs.git
More information about the debian-med-commit
mailing list