[med-svn] [macs] 01/03: Imported Upstream version 2.1.1.20160226
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Mar 5 17:54:14 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 68b18f1f11c34912932018c440adc1c43a21b61f
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Sat Mar 5 09:24:01 2016 -0800
Imported Upstream version 2.1.1.20160226
---
ChangeLog | 35 +
MACS2.egg-info/PKG-INFO | 2 +-
MACS2/Constants.py | 2 +-
MACS2/IO/BedGraph.c | 112 +-
MACS2/IO/BedGraph.pyx | 4 +-
MACS2/IO/CallPeakUnit.c | 4932 ++++-----
MACS2/IO/CallPeakUnit.pyx | 9 +-
MACS2/IO/PairedEndTrack.c | 260 +-
MACS2/IO/PairedEndTrack.pyx | 15 +-
MACS2/IO/Parser.c | 22751 +++++++++++++++++++-----------------------
MACS2/IO/Parser.pyx | 584 +-
MACS2/IO/PeakIO.c | 4438 ++++----
MACS2/IO/PeakIO.pyx | 4 +-
MACS2/IO/ScoreTrack.c | 5465 +++++-----
MACS2/IO/ScoreTrack.pyx | 20 +-
MACS2/OptValidator.py | 21 +-
MACS2/Pileup.c | 2 +-
MACS2/Pileup.pyx | 2 +-
MACS2/bdgcmp_cmd.py | 4 +-
MACS2/bdgopt_cmd.py | 18 +-
MACS2/callpeak_cmd.py | 11 +-
PKG-INFO | 2 +-
README.rst | 30 +-
bin/macs2 | 23 +-
setup.py | 37 +-
setup_w_cython.py | 67 +-
26 files changed, 18085 insertions(+), 20765 deletions(-)
diff --git a/ChangeLog b/ChangeLog
index 3757a5c..1e26e7c 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,38 @@
+2016-02-26 Tao Liu <vladimir.liu at gmail.com>
+ MACS version 2.1.1 20160226 (tag:rc Zhengyue)
+
+ * Bug fixes
+
+ 1) Now "-Ofast" has been replaced by "-O3 --ffast-math", because
+ the former option is not supported by older GCC. Related to issues
+ #91, #109.
+
+ 2) Issue #108 is fixed. If no peak can be found in a chromosome,
+ the PeakIO won't throw an error.
+
+ * New features
+
+ 1) callpeak
+
+ a) A more flexible format, BEDPE, is supported. Now users can
+ define the left and right position of the ChIPed fragment, and
+ MACS2 will skip model building and directly pileup the
+ fragments. Related to issue #112.
+
+ b) The 'tempdir' can be specified, to save cached pileup
+ tracks. Originially, the temporary files were stored in
+ /tmp. Thank @daler! Related to issues #97 and #105.
+
+ 2) bdgopt
+
+ New operations are added, to calculate the maximum or minimum value between
+ values in BEDGRAPH and given value.
+
+ 3) bdgcmp
+
+ New method is added, to calculate the maximum value between values
+ defined in two BEDGRAPH files.
+
2015-12-22 Tao Liu <vladimir.liu at gmail.com>
MACS version 2.1.0 20151222 (tag:rc Dongzhi)
diff --git a/MACS2.egg-info/PKG-INFO b/MACS2.egg-info/PKG-INFO
index af49a01..cf74d85 100644
--- a/MACS2.egg-info/PKG-INFO
+++ b/MACS2.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: MACS2
-Version: 2.1.0.20151222
+Version: 2.1.1.20160226
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 de57fab..6afe067 100644
--- a/MACS2/Constants.py
+++ b/MACS2/Constants.py
@@ -1,4 +1,4 @@
-MACS_VERSION = "2.1.0.20151222"
+MACS_VERSION = "2.1.1.20160226"
#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/BedGraph.c b/MACS2/IO/BedGraph.c
index 652364b..800439c 100644
--- a/MACS2/IO/BedGraph.c
+++ b/MACS2/IO/BedGraph.c
@@ -1180,7 +1180,7 @@ static char __pyx_k_add_broadpeak_locals_lambda[] = "__add_broadpeak.<locals>.<l
static char __pyx_k_bedRegionTrackI_safe_add_loc[] = "bedRegionTrackI.safe_add_loc";
static char __pyx_k_pscore_npeaks_lpeaks_avelpeak[] = "pscore\tnpeaks\tlpeaks\tavelpeak\n";
static char __pyx_k_Tao_Liu_vladimir_liu_gmail_com[] = "Tao Liu <vladimir.liu at gmail.com>";
-static char __pyx_k_Users_taoliu_Dropbox_projects_m[] = "/Users/taoliu/Dropbox/projects/macs2/MACS/MACS2/IO/BedGraph.pyx";
+static char __pyx_k_Users_taoliu_Dropbox_Projects_M[] = "/Users/taoliu/Dropbox/Projects/MACS2/MACS/MACS2/IO/BedGraph.pyx";
static char __pyx_k_level_1_cutoff_should_be_larger[] = "level 1 cutoff should be larger than level 2.";
static char __pyx_k_A_similar_class_to_bedGraphTrack[] = "A similar class to bedGraphTrackI, but is designed to save\n traditional 3-fields BED format data.\n\n ";
static char __pyx_k_Module_for_Feature_IO_classes_Co[] = "Module for Feature IO classes.\n\nCopyright (c) 2010,2011 Tao Liu <taoliu at jimmy.harvard.edu>\n\nThis code is free software; you can redistribute it and/or modify it\nunder the terms of the BSD License (see the file COPYING included\nwith the distribution).\n\n at status: experimental\n at version: $Revision$\n at author: Tao Liu\n at contact: taoliu at jimmy.harvard.edu\n";
@@ -1210,7 +1210,7 @@ static PyObject *__pyx_n_s_MACS2_IO_ScoreTrack;
static PyObject *__pyx_n_s_PeakIO;
static PyObject *__pyx_n_s_StopIteration;
static PyObject *__pyx_kp_s_Tao_Liu_vladimir_liu_gmail_com;
-static PyObject *__pyx_kp_s_Users_taoliu_Dropbox_projects_m;
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static PyObject *__pyx_kp_s__2;
static PyObject *__pyx_kp_s__5;
static PyObject *__pyx_kp_s__6;
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*
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@@ -18632,7 +18626,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_PeakIO, __pyx_k_PeakIO, sizeof(__pyx_k_PeakIO), 0, 0, 1, 1},
{&__pyx_n_s_StopIteration, __pyx_k_StopIteration, sizeof(__pyx_k_StopIteration), 0, 0, 1, 1},
{&__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_kp_s__2, __pyx_k__2, sizeof(__pyx_k__2), 0, 0, 1, 0},
{&__pyx_kp_s__5, __pyx_k__5, sizeof(__pyx_k__5), 0, 0, 1, 0},
{&__pyx_kp_s__6, __pyx_k__6, sizeof(__pyx_k__6), 0, 0, 1, 0},
@@ -18844,7 +18838,7 @@ static int __Pyx_InitCachedConstants(void) {
__pyx_tuple__9 = PyTuple_Pack(12, __pyx_n_s_scoretrack, __pyx_n_s_colname, __pyx_n_s_pre, __pyx_n_s_i, __pyx_n_s_chrom, __pyx_n_s_bdgtrack, __pyx_n_s_flag100, __pyx_n_s_chrs, __pyx_n_s_d, __pyx_n_s_l, __pyx_n_s_pos, __pyx_n_s_value); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__9);
__Pyx_GIVEREF(__pyx_tuple__9);
- __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(2, 0, 12, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_projects_m, __pyx_n_s_scoreTracktoBedGraph, 1222, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__10 = (PyObject*)__Pyx_PyCode_New(2, 0, 12, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__9, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_scoreTracktoBedGraph, 1222, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MACS2/IO/BedGraph.pyx":1260
*
@@ -18856,7 +18850,7 @@ static int __Pyx_InitCachedConstants(void) {
__pyx_tuple__11 = PyTuple_Pack(1, __pyx_n_s_self); if (unlikely(!__pyx_tuple__11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__11);
__Pyx_GIVEREF(__pyx_tuple__11);
- __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__11, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_projects_m, __pyx_n_s_init, 1260, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__11, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_init, 1260, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MACS2/IO/BedGraph.pyx":1266
* self.baseline_value = 0
@@ -18868,7 +18862,7 @@ static int __Pyx_InitCachedConstants(void) {
__pyx_tuple__13 = PyTuple_Pack(7, __pyx_n_s_self, __pyx_n_s_chromosome, __pyx_n_s_startpos, __pyx_n_s_endpos, __pyx_n_s_pre_pos, __pyx_n_s_pre_v, __pyx_n_s_c); if (unlikely(!__pyx_tuple__13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__13);
__Pyx_GIVEREF(__pyx_tuple__13);
- __pyx_codeobj__14 = (PyObject*)__Pyx_PyCode_New(4, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__13, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_projects_m, __pyx_n_s_safe_add_loc, 1266, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__14 = (PyObject*)__Pyx_PyCode_New(4, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__13, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_safe_add_loc, 1266, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_RefNannyFinishContext();
return 0;
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@@ -19246,7 +19240,7 @@ PyMODINIT_FUNC PyInit_BedGraph(void)
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "MACS2/IO/BedGraph.pyx":1
- * # Time-stamp: <2015-05-19 13:46:49 Tao Liu> # <<<<<<<<<<<<<<
+ * # Time-stamp: <2016-02-12 00:39:32 Tao Liu> # <<<<<<<<<<<<<<
*
* """Module for Feature IO classes.
*/
diff --git a/MACS2/IO/BedGraph.pyx b/MACS2/IO/BedGraph.pyx
index 3f37ff1..80a6d06 100644
--- a/MACS2/IO/BedGraph.pyx
+++ b/MACS2/IO/BedGraph.pyx
@@ -1,4 +1,4 @@
-# Time-stamp: <2015-05-19 13:46:49 Tao Liu>
+# Time-stamp: <2016-02-12 00:39:32 Tao Liu>
"""Module for Feature IO classes.
@@ -827,7 +827,7 @@ cdef class bedGraphTrackI:
for (p,s) in self.__data.values():
for i in xrange(len(s)):
- s[i][1] = func(s[i][1])
+ s[i] = func(s[i])
self.maxvalue = func(self.maxvalue)
self.minvalue = func(self.minvalue)
return True
diff --git a/MACS2/IO/CallPeakUnit.c b/MACS2/IO/CallPeakUnit.c
index 040da78..796db62 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":706
+/* "MACS2/IO/CallPeakUnit.pyx":709
*
*
* 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":858
+/* "MACS2/IO/CallPeakUnit.pyx":861
*
*
* 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":1063
+/* "MACS2/IO/CallPeakUnit.pyx":1066
* 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":1123
+/* "MACS2/IO/CallPeakUnit.pyx":1126
* 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":1428
+/* "MACS2/IO/CallPeakUnit.pyx":1431
* 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":1712
+/* "MACS2/IO/CallPeakUnit.pyx":1715
* 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":1818
+/* "MACS2/IO/CallPeakUnit.pyx":1821
* return bpeaks
*
* cpdef refine_peak_from_tags_distribution ( self, peaks, int window_size = 100, float cutoff = 5 ): # <<<<<<<<<<<<<<
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*
* if not self.no_lambda_flag: # <<<<<<<<<<<<<<
* if self.PE_mode:
- * ctrl_pv = self.ctrl.pileup_a_chromosome_c( chrom, self.ctrl_d_s, self.ctrl_scaling_factor_s, baseline_value = self.lambda_bg )
+ * # note, we pileup up PE control as SE control because
*/
__pyx_t_3 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_self->no_lambda_flag)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 489; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- * ctrl_pv = self.ctrl.pileup_a_chromosome_c( chrom, self.ctrl_d_s, self.ctrl_scaling_factor_s, baseline_value = self.lambda_bg )
- * else:
+ * # note, we pileup up PE control as SE control because
+ * # we assume the bias only can be captured at the
*/
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if (__pyx_t_1) {
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- * if not self.no_lambda_flag:
- * if self.PE_mode:
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+ * # we assume the bias only can be captured at the
+ * # surrounding regions of cutting sites from control experiments.
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+ __pyx_t_8 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->ctrl, __pyx_n_s_pileup_a_chromosome_c); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (!(likely(PyList_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_2 = 0;
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+ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_self->ctrl, __pyx_n_s_pileup_a_chromosome); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_9);
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* ret_p_ptr = <int32_t *> ret_p.data
* ret_t_ptr = <float32_t *>ret_t.data
* ret_c_ptr = <float32_t *>ret_c.data # <<<<<<<<<<<<<<
@@ -8082,7 +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":557
+ /* "MACS2/IO/CallPeakUnit.pyx":560
* ret_c_ptr = <float32_t *>ret_c.data
*
* pre_p = 0 # <<<<<<<<<<<<<<
@@ -8091,7 +8091,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_pre_p = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":558
+ /* "MACS2/IO/CallPeakUnit.pyx":561
*
* pre_p = 0
* index_ret = 0 # <<<<<<<<<<<<<<
@@ -8100,7 +8100,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_index_ret = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":559
+ /* "MACS2/IO/CallPeakUnit.pyx":562
* pre_p = 0
* index_ret = 0
* it = 0 # <<<<<<<<<<<<<<
@@ -8109,7 +8109,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_it = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":560
+ /* "MACS2/IO/CallPeakUnit.pyx":563
* index_ret = 0
* it = 0
* ic = 0 # <<<<<<<<<<<<<<
@@ -8118,7 +8118,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ic = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":562
+ /* "MACS2/IO/CallPeakUnit.pyx":565
* ic = 0
*
* while it < lt and ic < lc: # <<<<<<<<<<<<<<
@@ -8137,7 +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":563
+ /* "MACS2/IO/CallPeakUnit.pyx":566
*
* while it < lt and ic < lc:
* if t_p_ptr[0] < c_p_ptr[0]: # <<<<<<<<<<<<<<
@@ -8147,7 +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":565
+ /* "MACS2/IO/CallPeakUnit.pyx":568
* 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] # <<<<<<<<<<<<<<
@@ -8156,7 +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":566
+ /* "MACS2/IO/CallPeakUnit.pyx":569
* # 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] # <<<<<<<<<<<<<<
@@ -8165,7 +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":567
+ /* "MACS2/IO/CallPeakUnit.pyx":570
* ret_p_ptr[0] = t_p_ptr[0]
* ret_t_ptr[0] = t_v_ptr[0]
* ret_c_ptr[0] = c_v_ptr[0] # <<<<<<<<<<<<<<
@@ -8174,7 +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":568
+ /* "MACS2/IO/CallPeakUnit.pyx":571
* ret_t_ptr[0] = t_v_ptr[0]
* ret_c_ptr[0] = c_v_ptr[0]
* ret_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8183,7 +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":569
+ /* "MACS2/IO/CallPeakUnit.pyx":572
* ret_c_ptr[0] = c_v_ptr[0]
* ret_p_ptr += 1
* ret_t_ptr += 1 # <<<<<<<<<<<<<<
@@ -8192,7 +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":570
+ /* "MACS2/IO/CallPeakUnit.pyx":573
* ret_p_ptr += 1
* ret_t_ptr += 1
* ret_c_ptr += 1 # <<<<<<<<<<<<<<
@@ -8201,7 +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":571
+ /* "MACS2/IO/CallPeakUnit.pyx":574
* ret_t_ptr += 1
* ret_c_ptr += 1
* pre_p = t_p_ptr[0] # <<<<<<<<<<<<<<
@@ -8210,7 +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":572
+ /* "MACS2/IO/CallPeakUnit.pyx":575
* ret_c_ptr += 1
* pre_p = t_p_ptr[0]
* index_ret += 1 # <<<<<<<<<<<<<<
@@ -8219,7 +8219,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_index_ret = (__pyx_v_index_ret + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":574
+ /* "MACS2/IO/CallPeakUnit.pyx":577
* index_ret += 1
* # call for the next p1 and v1
* it += 1 # <<<<<<<<<<<<<<
@@ -8228,7 +8228,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_it = (__pyx_v_it + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":575
+ /* "MACS2/IO/CallPeakUnit.pyx":578
* # call for the next p1 and v1
* it += 1
* t_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8237,7 +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":576
+ /* "MACS2/IO/CallPeakUnit.pyx":579
* it += 1
* t_p_ptr += 1
* t_v_ptr += 1 # <<<<<<<<<<<<<<
@@ -8248,7 +8248,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
goto __pyx_L11;
}
- /* "MACS2/IO/CallPeakUnit.pyx":577
+ /* "MACS2/IO/CallPeakUnit.pyx":580
* t_p_ptr += 1
* t_v_ptr += 1
* elif t_p_ptr[0] > c_p_ptr[0]: # <<<<<<<<<<<<<<
@@ -8258,7 +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":579
+ /* "MACS2/IO/CallPeakUnit.pyx":582
* 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] # <<<<<<<<<<<<<<
@@ -8267,7 +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":580
+ /* "MACS2/IO/CallPeakUnit.pyx":583
* # 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] # <<<<<<<<<<<<<<
@@ -8276,7 +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":581
+ /* "MACS2/IO/CallPeakUnit.pyx":584
* ret_p_ptr[0] = c_p_ptr[0]
* ret_t_ptr[0] = t_v_ptr[0]
* ret_c_ptr[0] = c_v_ptr[0] # <<<<<<<<<<<<<<
@@ -8285,7 +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":582
+ /* "MACS2/IO/CallPeakUnit.pyx":585
* ret_t_ptr[0] = t_v_ptr[0]
* ret_c_ptr[0] = c_v_ptr[0]
* ret_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8294,7 +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":583
+ /* "MACS2/IO/CallPeakUnit.pyx":586
* ret_c_ptr[0] = c_v_ptr[0]
* ret_p_ptr += 1
* ret_t_ptr += 1 # <<<<<<<<<<<<<<
@@ -8303,7 +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":584
+ /* "MACS2/IO/CallPeakUnit.pyx":587
* ret_p_ptr += 1
* ret_t_ptr += 1
* ret_c_ptr += 1 # <<<<<<<<<<<<<<
@@ -8312,7 +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":585
+ /* "MACS2/IO/CallPeakUnit.pyx":588
* ret_t_ptr += 1
* ret_c_ptr += 1
* pre_p = c_p_ptr[0] # <<<<<<<<<<<<<<
@@ -8321,7 +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":586
+ /* "MACS2/IO/CallPeakUnit.pyx":589
* ret_c_ptr += 1
* pre_p = c_p_ptr[0]
* index_ret += 1 # <<<<<<<<<<<<<<
@@ -8330,7 +8330,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_index_ret = (__pyx_v_index_ret + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":588
+ /* "MACS2/IO/CallPeakUnit.pyx":591
* index_ret += 1
* # call for the next p2 and v2
* ic += 1 # <<<<<<<<<<<<<<
@@ -8339,7 +8339,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ic = (__pyx_v_ic + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":589
+ /* "MACS2/IO/CallPeakUnit.pyx":592
* # call for the next p2 and v2
* ic += 1
* c_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8348,7 +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":590
+ /* "MACS2/IO/CallPeakUnit.pyx":593
* ic += 1
* c_p_ptr += 1
* c_v_ptr += 1 # <<<<<<<<<<<<<<
@@ -8360,7 +8360,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":593
+ /* "MACS2/IO/CallPeakUnit.pyx":596
* else:
* # from pre_p to p1 or p2, then set pre_p as p1 or p2.
* ret_p_ptr[0] = t_p_ptr[0] # <<<<<<<<<<<<<<
@@ -8369,7 +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":594
+ /* "MACS2/IO/CallPeakUnit.pyx":597
* # 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] # <<<<<<<<<<<<<<
@@ -8378,7 +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":595
+ /* "MACS2/IO/CallPeakUnit.pyx":598
* ret_p_ptr[0] = t_p_ptr[0]
* ret_t_ptr[0] = t_v_ptr[0]
* ret_c_ptr[0] = c_v_ptr[0] # <<<<<<<<<<<<<<
@@ -8387,7 +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":596
+ /* "MACS2/IO/CallPeakUnit.pyx":599
* ret_t_ptr[0] = t_v_ptr[0]
* ret_c_ptr[0] = c_v_ptr[0]
* ret_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8396,7 +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":597
+ /* "MACS2/IO/CallPeakUnit.pyx":600
* ret_c_ptr[0] = c_v_ptr[0]
* ret_p_ptr += 1
* ret_t_ptr += 1 # <<<<<<<<<<<<<<
@@ -8405,7 +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":598
+ /* "MACS2/IO/CallPeakUnit.pyx":601
* ret_p_ptr += 1
* ret_t_ptr += 1
* ret_c_ptr += 1 # <<<<<<<<<<<<<<
@@ -8414,7 +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":599
+ /* "MACS2/IO/CallPeakUnit.pyx":602
* ret_t_ptr += 1
* ret_c_ptr += 1
* pre_p = t_p_ptr[0] # <<<<<<<<<<<<<<
@@ -8423,7 +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":600
+ /* "MACS2/IO/CallPeakUnit.pyx":603
* ret_c_ptr += 1
* pre_p = t_p_ptr[0]
* index_ret += 1 # <<<<<<<<<<<<<<
@@ -8432,7 +8432,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_index_ret = (__pyx_v_index_ret + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":602
+ /* "MACS2/IO/CallPeakUnit.pyx":605
* index_ret += 1
* # call for the next p1, v1, p2, v2.
* it += 1 # <<<<<<<<<<<<<<
@@ -8441,7 +8441,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_it = (__pyx_v_it + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":603
+ /* "MACS2/IO/CallPeakUnit.pyx":606
* # call for the next p1, v1, p2, v2.
* it += 1
* ic += 1 # <<<<<<<<<<<<<<
@@ -8450,7 +8450,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
__pyx_v_ic = (__pyx_v_ic + 1);
- /* "MACS2/IO/CallPeakUnit.pyx":604
+ /* "MACS2/IO/CallPeakUnit.pyx":607
* it += 1
* ic += 1
* t_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8459,7 +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":605
+ /* "MACS2/IO/CallPeakUnit.pyx":608
* ic += 1
* t_p_ptr += 1
* t_v_ptr += 1 # <<<<<<<<<<<<<<
@@ -8468,7 +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":606
+ /* "MACS2/IO/CallPeakUnit.pyx":609
* t_p_ptr += 1
* t_v_ptr += 1
* c_p_ptr += 1 # <<<<<<<<<<<<<<
@@ -8477,7 +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":607
+ /* "MACS2/IO/CallPeakUnit.pyx":610
* t_v_ptr += 1
* c_p_ptr += 1
* c_v_ptr += 1 # <<<<<<<<<<<<<<
@@ -8489,85 +8489,85 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_L11:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":609
+ /* "MACS2/IO/CallPeakUnit.pyx":612
* 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 = 609; __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 = 612; __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 = 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 = 612; __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 = 612; __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 = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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fprintf(__pyx_v_self->bedGraph_treat_f, __pyx_t_12);
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__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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+ 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 = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":907
+ /* "MACS2/IO/CallPeakUnit.pyx":910
* 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 = 907; __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 = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
fprintf(__pyx_v_self->bedGraph_ctrl_f, __pyx_t_12);
goto __pyx_L7;
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@@ -12034,24 +12034,24 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
}
__pyx_L5:;
- /* "MACS2/IO/CallPeakUnit.pyx":909
+ /* "MACS2/IO/CallPeakUnit.pyx":912
* fprintf( self.bedGraph_ctrl_f, tmp_bytes )
*
* logging.info("#3 Call peaks for each chromosome...") # <<<<<<<<<<<<<<
* for chrom in self.chromosomes:
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*/
- __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_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_logging); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 912; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 912; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ __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 = 912; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":910
+ /* "MACS2/IO/CallPeakUnit.pyx":913
*
* logging.info("#3 Call peaks for each chromosome...")
* for chrom in self.chromosomes: # <<<<<<<<<<<<<<
@@ -12060,21 +12060,21 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
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if (unlikely(__pyx_v_self->chromosomes == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 913; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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for (;;) {
if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_1)) break;
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- __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;}
+ __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 = 913; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ 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 = 913; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_chrom, ((PyObject*)__pyx_t_4));
__pyx_t_4 = 0;
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+ /* "MACS2/IO/CallPeakUnit.pyx":915
* for chrom in self.chromosomes:
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@@ -12083,12 +12083,12 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
*/
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__Pyx_INCREF(__pyx_t_4);
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+ __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 = 915; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":910
+ /* "MACS2/IO/CallPeakUnit.pyx":913
*
* logging.info("#3 Call peaks for each chromosome...")
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@@ -12098,17 +12098,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
}
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+ /* "MACS2/IO/CallPeakUnit.pyx":919
*
* # close bedGraph file
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* fclose(self.bedGraph_treat_f)
* fclose(self.bedGraph_ctrl_f)
*/
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+ __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 = 919; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_10) {
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*/
fclose(__pyx_v_self->bedGraph_treat_f);
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+ /* "MACS2/IO/CallPeakUnit.pyx":921
* if self.save_bedGraph:
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@@ -12126,7 +12126,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
*/
fclose(__pyx_v_self->bedGraph_ctrl_f);
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}
__pyx_L10:;
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+ /* "MACS2/IO/CallPeakUnit.pyx":926
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__pyx_r = __pyx_v_peaks;
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":858
+ /* "MACS2/IO/CallPeakUnit.pyx":861
*
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@@ -12184,7 +12184,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_p
/* Python wrapper */
static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_9call_peaks(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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+static char __pyx_doc_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_8call_peaks[] = "Call peaks for all chromosomes. Return a PeakIO object.\n \n scoring_function_s: symbols of functions to calculate score. 'p' for pscore, 'q' for qscore, 'f' for fold change, 's' for subtraction. for example: ['p', 'q']\n score_cutoff_s : cutoff values corresponding to scoring functions\n min_length : minimum length of peak\n max_gap : maximum gap [...]
static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_9call_peaks(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_scoring_function_symbols = 0;
PyObject *__pyx_v_score_cutoff_s = 0;
@@ -12202,7 +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};
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+ /* "MACS2/IO/CallPeakUnit.pyx":862
*
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@@ -12232,7 +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 = 858; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("call_peaks", 0, 2, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (kw_args > 0) {
@@ -12256,7 +12256,7 @@ static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_9call
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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 = 858; __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 = 861; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -12273,12 +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]);
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+ __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 = 861; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_min_length = ((int)200);
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+ __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 = 862; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
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+ 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 = 862; __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":858
+ /* "MACS2/IO/CallPeakUnit.pyx":861
*
*
* cpdef call_peaks ( self, list scoring_function_symbols, list score_cutoff_s, int min_length = 200, # <<<<<<<<<<<<<<
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__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 = 858; __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 = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -12348,7 +12348,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_8call
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":925
+/* "MACS2/IO/CallPeakUnit.pyx":928
* return peaks
*
* cdef __chrom_call_peak_using_certain_criteria ( self, peaks, str chrom, list scoring_function_s, list score_cutoff_s, int min_length, # <<<<<<<<<<<<<<
@@ -12444,7 +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":961
+ /* "MACS2/IO/CallPeakUnit.pyx":964
*
*
* assert len(scoring_function_s) == len(score_cutoff_s), "number of functions and cutoffs should be the same!" # <<<<<<<<<<<<<<
@@ -12455,45 +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 = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __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;}
+ __pyx_t_1 = PyList_GET_SIZE(__pyx_v_scoring_function_s); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __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 = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __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;}
+ __pyx_t_2 = PyList_GET_SIZE(__pyx_v_score_cutoff_s); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __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 = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
}
#endif
- /* "MACS2/IO/CallPeakUnit.pyx":963
+ /* "MACS2/IO/CallPeakUnit.pyx":966
* assert len(scoring_function_s) == len(score_cutoff_s), "number of functions and cutoffs should be the same!"
*
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*
* # 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 = 963; __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 = 966; __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":967
+ /* "MACS2/IO/CallPeakUnit.pyx":970
* # first, build pileup, self.chr_pos_treat_ctrl
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* 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 = 967; __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 = 970; __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":968
+ /* "MACS2/IO/CallPeakUnit.pyx":971
* # 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 # <<<<<<<<<<<<<<
@@ -12512,7 +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 = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#if CYTHON_COMPILING_IN_CPYTHON
__pyx_t_4 = PyList_GET_ITEM(sequence, 0);
@@ -12522,20 +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 = 968; __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 = 971; __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 = 968; __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 = 971; __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 = 968; __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 = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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- __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __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;}
+ if (!(likely(((__pyx_t_4) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_4, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __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 = 971; __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 = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = ((PyArrayObject *)__pyx_t_4);
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
@@ -12551,7 +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];
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+ if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_7 = 0;
__pyx_v_pos_array = ((PyArrayObject *)__pyx_t_4);
@@ -12571,7 +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];
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+ if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_12 = 0;
__pyx_v_treat_array = ((PyArrayObject *)__pyx_t_5);
@@ -12591,49 +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];
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+ if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
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__pyx_v_ctrl_array = ((PyArrayObject *)__pyx_t_6);
__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":971
+ /* "MACS2/IO/CallPeakUnit.pyx":974
*
* # while save_bedGraph is true, invoke __write_bedGraph_for_a_chromosome
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+ __pyx_t_13 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_save_bedGraph)); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 974; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_13) {
- /* "MACS2/IO/CallPeakUnit.pyx":972
+ /* "MACS2/IO/CallPeakUnit.pyx":975
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+ __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 = 975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L3;
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__pyx_L3:;
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+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 979; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_score_array_s = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":977
+ /* "MACS2/IO/CallPeakUnit.pyx":980
* #t0 = ttime()
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 980; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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* peak_content = [ ( ts, te, tp, cp, ti ), ] # <<<<<<<<<<<<<<
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*/
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+ __pyx_t_6 = __Pyx_PyInt_From_long(__pyx_v_ts); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_4 = __Pyx_PyInt_From_long(__pyx_v_ti); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __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_t_18 = PyTuple_New(5); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1052; __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);
@@ -13385,7 +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 = 1049; __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 = 1052; __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);
@@ -13393,7 +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":1050
+ /* "MACS2/IO/CallPeakUnit.pyx":1053
* 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] # <<<<<<<<<<<<<<
@@ -13405,7 +13405,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_L11:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1052
+ /* "MACS2/IO/CallPeakUnit.pyx":1055
* lastp = te #above_cutoff_endpos[i]
* # save the last peak
* if not peak_content: # <<<<<<<<<<<<<<
@@ -13416,7 +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":1053
+ /* "MACS2/IO/CallPeakUnit.pyx":1056
* # save the last peak
* if not peak_content:
* return peaks # <<<<<<<<<<<<<<
@@ -13430,17 +13430,17 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1055
+ /* "MACS2/IO/CallPeakUnit.pyx":1058
* 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 = 1055; __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 = 1058; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_14) {
- /* "MACS2/IO/CallPeakUnit.pyx":1056
+ /* "MACS2/IO/CallPeakUnit.pyx":1059
* 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' # <<<<<<<<<<<<<<
@@ -13449,14 +13449,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
*/
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__pyx_t_20.score_cutoff_s = __pyx_v_score_cutoff_s;
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+ __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 = 1059; __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":1058
+ /* "MACS2/IO/CallPeakUnit.pyx":1061
* 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' # <<<<<<<<<<<<<<
@@ -13465,14 +13465,14 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
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__pyx_t_21.score_cutoff_s = __pyx_v_score_cutoff_s;
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+ __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 = 1061; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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__pyx_L14:;
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- /* "MACS2/IO/CallPeakUnit.pyx":1061
+ /* "MACS2/IO/CallPeakUnit.pyx":1064
*
* #print "close peaks -- chrom:",chrom," time:", ttime() - t0
* return peaks # <<<<<<<<<<<<<<
@@ -13484,7 +13484,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_r = __pyx_v_peaks;
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":925
+ /* "MACS2/IO/CallPeakUnit.pyx":928
* return peaks
*
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@@ -13535,7 +13535,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1063
+/* "MACS2/IO/CallPeakUnit.pyx":1066
* return peaks
*
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@@ -13593,7 +13593,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
}
- /* "MACS2/IO/CallPeakUnit.pyx":1078
+ /* "MACS2/IO/CallPeakUnit.pyx":1081
* int tlist_scores_p
*
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@@ -13602,57 +13602,57 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1078; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1081; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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+ __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 = 1082; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_4) {
- /* "MACS2/IO/CallPeakUnit.pyx":1080
+ /* "MACS2/IO/CallPeakUnit.pyx":1083
* peak_length = peak_content[ -1 ][ 1 ] - peak_content[ 0 ][ 0 ]
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- __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_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_tsummit = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1081
+ /* "MACS2/IO/CallPeakUnit.pyx":1084
* if peak_length >= min_length: # if the peak is too small, reject it
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* summit_pos = 0 # <<<<<<<<<<<<<<
@@ -13661,7 +13661,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_summit_pos = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1082
+ /* "MACS2/IO/CallPeakUnit.pyx":1085
* tsummit = []
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@@ -13670,7 +13670,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
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- /* "MACS2/IO/CallPeakUnit.pyx":1083
+ /* "MACS2/IO/CallPeakUnit.pyx":1086
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@@ -13679,13 +13679,13 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1084; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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goto __pyx_L0;
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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@@ -14980,7 +14980,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
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@@ -14994,24 +14994,24 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
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*/
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if (__pyx_t_4) {
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+ /* "MACS2/IO/CallPeakUnit.pyx":1182
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__pyx_t_22.__pyx_n = 1;
__pyx_t_22.score_cutoff_s = __pyx_v_score_cutoff_s;
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+ __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 = 1182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_1 = 0;
goto __pyx_L0;
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+ /* "MACS2/IO/CallPeakUnit.pyx":1184
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+ __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 = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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__pyx_v_summit_indices = __pyx_t_1;
__pyx_t_1 = 0;
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+ __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 = 1185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -15159,20 +15159,20 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
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__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];
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}
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__Pyx_DECREF_SET(__pyx_v_summit_offsets, ((PyArrayObject *)__pyx_t_3));
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+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_INCREF(((PyObject *)__pyx_v_summit_offsets));
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_summit_offsets));
@@ -15180,16 +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 = 1184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_23 = Py_TYPE(__pyx_t_3)->tp_iternext; if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -15197,16 +15197,16 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
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+ __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 = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -15215,7 +15215,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
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@@ -16704,7 +16704,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
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* a1_ptr = <float32_t *> array1.data
* a2_ptr = <float32_t *> array2.data
* s_ptr = <float32_t *> s.data # <<<<<<<<<<<<<<
@@ -16722,7 +16722,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
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* s_ptr = <float32_t *> s.data
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@@ -16733,7 +16733,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
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__pyx_v_i = __pyx_t_11;
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@@ -16742,7 +16742,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
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+ /* "MACS2/IO/CallPeakUnit.pyx":1297
* for i in range(array1.shape[0]):
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@@ -16751,7 +16751,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
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* s_ptr[0] = get_logFE( a1_ptr[0] + self.pseudocount, a2_ptr[0] + self.pseudocount )
* s_ptr += 1
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@@ -16760,7 +16760,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
*/
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@@ -16770,7 +16770,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_v_a2_ptr = (__pyx_v_a2_ptr + 1);
}
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+ /* "MACS2/IO/CallPeakUnit.pyx":1300
* a1_ptr += 1
* a2_ptr += 1
* return s # <<<<<<<<<<<<<<
@@ -16782,7 +16782,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_r = ((PyArrayObject *)__pyx_v_s);
goto __pyx_L0;
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+ /* "MACS2/IO/CallPeakUnit.pyx":1280
* return s
*
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@@ -16816,7 +16816,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
return __pyx_r;
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*
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*
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* a1_ptr = <float32_t *> array1.data
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__pyx_v_i = __pyx_t_11;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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* for i in range(array1.shape[0]):
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@@ -17042,7 +17042,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
__pyx_r = ((PyArrayObject *)__pyx_v_s);
goto __pyx_L0;
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+ /* "MACS2/IO/CallPeakUnit.pyx":1302
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@@ -17076,7 +17076,7 @@ static PyArrayObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments__
return __pyx_r;
}
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+ /* "MACS2/IO/CallPeakUnit.pyx":1336
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* a1_ptr = <float32_t *> array1.data
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__pyx_v_i = __pyx_t_11;
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+ /* "MACS2/IO/CallPeakUnit.pyx":1341
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__pyx_v_s_ptr = (__pyx_v_s_ptr + 1);
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__pyx_v_a1_ptr = (__pyx_v_a1_ptr + 1);
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__pyx_r = ((PyArrayObject *)__pyx_v_s);
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__pyx_pybuffernd_ctrl_array.rcbuffer = &__pyx_pybuffer_ctrl_array;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__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];
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+ if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __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":1364
+ /* "MACS2/IO/CallPeakUnit.pyx":1367
*
* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl
* pos_array_ptr = <int32_t *> pos_array.data # <<<<<<<<<<<<<<
@@ -17504,7 +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":1365
+ /* "MACS2/IO/CallPeakUnit.pyx":1368
* [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 # <<<<<<<<<<<<<<
@@ -17513,7 +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":1366
+ /* "MACS2/IO/CallPeakUnit.pyx":1369
* pos_array_ptr = <int32_t *> pos_array.data
* treat_array_ptr = <float32_t *> treat_array.data
* ctrl_array_ptr = <float32_t *> ctrl_array.data # <<<<<<<<<<<<<<
@@ -17522,17 +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":1368
+ /* "MACS2/IO/CallPeakUnit.pyx":1371
* 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 = 1368; __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 = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_11) {
- /* "MACS2/IO/CallPeakUnit.pyx":1369
+ /* "MACS2/IO/CallPeakUnit.pyx":1372
*
* if self.save_SPMR:
* if self.treat_scaling_factor == 1: # <<<<<<<<<<<<<<
@@ -17542,38 +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":1371
+ /* "MACS2/IO/CallPeakUnit.pyx":1374
* 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 = 1371; __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 = 1374; __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 = 1371; __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 = 1374; __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 = 1371; __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 = 1374; __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":1374
+ /* "MACS2/IO/CallPeakUnit.pyx":1377
* 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 = 1374; __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 = 1377; __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 = 1374; __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 = 1377; __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 = 1374; __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 = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_denominator = __pyx_t_12;
}
@@ -17582,7 +17582,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1376
+ /* "MACS2/IO/CallPeakUnit.pyx":1379
* denominator = self.ctrl.total/1e6
* else:
* denominator = 1.0 # <<<<<<<<<<<<<<
@@ -17593,7 +17593,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
}
__pyx_L3:;
- /* "MACS2/IO/CallPeakUnit.pyx":1378
+ /* "MACS2/IO/CallPeakUnit.pyx":1381
* denominator = 1.0
*
* l = pos_array.shape[ 0 ] # <<<<<<<<<<<<<<
@@ -17602,7 +17602,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_l = (__pyx_v_pos_array->dimensions[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1380
+ /* "MACS2/IO/CallPeakUnit.pyx":1383
* l = pos_array.shape[ 0 ]
*
* if l == 0: # if there is no data, return # <<<<<<<<<<<<<<
@@ -17612,7 +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":1381
+ /* "MACS2/IO/CallPeakUnit.pyx":1384
*
* if l == 0: # if there is no data, return
* return False # <<<<<<<<<<<<<<
@@ -17625,7 +17625,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
goto __pyx_L0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1383
+ /* "MACS2/IO/CallPeakUnit.pyx":1386
* return False
*
* ft = self.bedGraph_treat_f # <<<<<<<<<<<<<<
@@ -17635,7 +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":1384
+ /* "MACS2/IO/CallPeakUnit.pyx":1387
*
* ft = self.bedGraph_treat_f
* fc = self.bedGraph_ctrl_f # <<<<<<<<<<<<<<
@@ -17645,7 +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":1388
+ /* "MACS2/IO/CallPeakUnit.pyx":1391
* #c_write_func = self.bedGraph_ctrl.write
*
* pre_p_t = 0 # <<<<<<<<<<<<<<
@@ -17654,7 +17654,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_pre_p_t = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1389
+ /* "MACS2/IO/CallPeakUnit.pyx":1392
*
* pre_p_t = 0
* pre_p_c = 0 # <<<<<<<<<<<<<<
@@ -17663,7 +17663,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_pre_p_c = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1390
+ /* "MACS2/IO/CallPeakUnit.pyx":1393
* pre_p_t = 0
* pre_p_c = 0
* pre_v_t = treat_array_ptr[ 0 ]/denominator # <<<<<<<<<<<<<<
@@ -17678,11 +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 = 1390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1393; __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":1391
+ /* "MACS2/IO/CallPeakUnit.pyx":1394
* pre_p_c = 0
* pre_v_t = treat_array_ptr[ 0 ]/denominator
* pre_v_c = ctrl_array_ptr [ 0 ]/denominator # <<<<<<<<<<<<<<
@@ -17697,11 +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 = 1391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1394; __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":1392
+ /* "MACS2/IO/CallPeakUnit.pyx":1395
* pre_v_t = treat_array_ptr[ 0 ]/denominator
* pre_v_c = ctrl_array_ptr [ 0 ]/denominator
* treat_array_ptr += 1 # <<<<<<<<<<<<<<
@@ -17710,7 +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":1393
+ /* "MACS2/IO/CallPeakUnit.pyx":1396
* pre_v_c = ctrl_array_ptr [ 0 ]/denominator
* treat_array_ptr += 1
* ctrl_array_ptr += 1 # <<<<<<<<<<<<<<
@@ -17719,7 +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":1395
+ /* "MACS2/IO/CallPeakUnit.pyx":1398
* ctrl_array_ptr += 1
*
* for i in range( 1, l ): # <<<<<<<<<<<<<<
@@ -17730,7 +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":1396
+ /* "MACS2/IO/CallPeakUnit.pyx":1399
*
* for i in range( 1, l ):
* v_t = treat_array_ptr[ 0 ]/denominator # <<<<<<<<<<<<<<
@@ -17745,11 +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 = 1396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1399; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_v_v_t = ((__pyx_v_treat_array_ptr[0]) / __pyx_v_denominator);
- /* "MACS2/IO/CallPeakUnit.pyx":1397
+ /* "MACS2/IO/CallPeakUnit.pyx":1400
* for i in range( 1, l ):
* v_t = treat_array_ptr[ 0 ]/denominator
* v_c = ctrl_array_ptr [ 0 ]/denominator # <<<<<<<<<<<<<<
@@ -17764,11 +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 = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_v_v_c = ((__pyx_v_ctrl_array_ptr[0]) / __pyx_v_denominator);
- /* "MACS2/IO/CallPeakUnit.pyx":1398
+ /* "MACS2/IO/CallPeakUnit.pyx":1401
* v_t = treat_array_ptr[ 0 ]/denominator
* v_c = ctrl_array_ptr [ 0 ]/denominator
* p = pos_array_ptr [ 0 ] # <<<<<<<<<<<<<<
@@ -17777,7 +17777,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
*/
__pyx_v_p = (__pyx_v_pos_array_ptr[0]);
- /* "MACS2/IO/CallPeakUnit.pyx":1399
+ /* "MACS2/IO/CallPeakUnit.pyx":1402
* v_c = ctrl_array_ptr [ 0 ]/denominator
* p = pos_array_ptr [ 0 ]
* pos_array_ptr += 1 # <<<<<<<<<<<<<<
@@ -17786,7 +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":1400
+ /* "MACS2/IO/CallPeakUnit.pyx":1403
* p = pos_array_ptr [ 0 ]
* pos_array_ptr += 1
* treat_array_ptr += 1 # <<<<<<<<<<<<<<
@@ -17795,7 +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":1401
+ /* "MACS2/IO/CallPeakUnit.pyx":1404
* pos_array_ptr += 1
* treat_array_ptr += 1
* ctrl_array_ptr += 1 # <<<<<<<<<<<<<<
@@ -17804,7 +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":1403
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* ctrl_array_ptr += 1
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@@ -17814,20 +17814,20 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
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if (__pyx_t_11) {
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*
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+ __pyx_t_2 = PyFloat_FromDouble(__pyx_v_pre_v_t); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1407; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_v_chrom);
@@ -17841,10 +17841,10 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
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+ /* "MACS2/IO/CallPeakUnit.pyx":1515
* lvl2 = lvl2peakschrom[i]
*
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@@ -19081,50 +19081,50 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
*/
while (1) {
- /* "MACS2/IO/CallPeakUnit.pyx":1513
+ /* "MACS2/IO/CallPeakUnit.pyx":1516
*
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* tmppeakset.append(lvl1)
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+ /* "MACS2/IO/CallPeakUnit.pyx":1517
* while True:
* if lvl2["start"] <= lvl1["start"] and lvl1["end"] <= lvl2["end"]:
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* lvl1 = lvl1peakschrom_next()
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*/
- __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;}
+ __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 = 1517; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
- /* "MACS2/IO/CallPeakUnit.pyx":1515
+ /* "MACS2/IO/CallPeakUnit.pyx":1518
* if lvl2["start"] <= lvl1["start"] and lvl1["end"] <= lvl2["end"]:
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}
}
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- __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_t_5 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_9); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1518; __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 = 1515; __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 = 1518; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -19156,30 +19156,30 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
}
/*else*/ {
- /* "MACS2/IO/CallPeakUnit.pyx":1519
+ /* "MACS2/IO/CallPeakUnit.pyx":1522
* # make a hierarchical broad peak
* #print lvl2["start"], lvl2["end"], lvl2["score"]
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* #tmp_n += 1
* tmppeakset = []
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- __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_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 = 1522; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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+ /* "MACS2/IO/CallPeakUnit.pyx":1524
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*/
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+ __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1524; __pyx_clineno = __LINE__; goto __pyx_L12_error;}
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__Pyx_DECREF_SET(__pyx_v_tmppeakset, ((PyObject*)__pyx_t_5));
__pyx_t_5 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1522
+ /* "MACS2/IO/CallPeakUnit.pyx":1525
* #tmp_n += 1
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__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
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+ /* "MACS2/IO/CallPeakUnit.pyx":1526
* tmppeakset = []
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__Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_9);
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+ /* "MACS2/IO/CallPeakUnit.pyx":1528
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__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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+ /* "MACS2/IO/CallPeakUnit.pyx":1530
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+ __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1530; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;}
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__pyx_t_6 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1529
+ /* "MACS2/IO/CallPeakUnit.pyx":1532
* tmppeakset = []
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__pyx_v_j = __pyx_t_18;
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+ /* "MACS2/IO/CallPeakUnit.pyx":1533
* # add the rest lvl2 peaks
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+ __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 = 1533; __pyx_clineno = __LINE__; goto __pyx_L14_except_error;}
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@@ -19290,7 +19290,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
__pyx_L19_try_end:;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1498
+ /* "MACS2/IO/CallPeakUnit.pyx":1501
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}
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- /* "MACS2/IO/CallPeakUnit.pyx":1534
+ /* "MACS2/IO/CallPeakUnit.pyx":1537
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__pyx_r = __pyx_v_broadpeaks;
goto __pyx_L0;
- /* "MACS2/IO/CallPeakUnit.pyx":1428
+ /* "MACS2/IO/CallPeakUnit.pyx":1431
* return True
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@@ -19352,7 +19352,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_call_b
/* Python wrapper */
static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_11call_broadpeaks(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
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+static char __pyx_doc_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_10call_broadpeaks[] = "This function try to find enriched regions within which,\n scores are continuously higher than a given cutoff for level\n 1, and link them using the gap above level 2 cutoff with a\n maximum length of lvl2_max_gap.\n\n scoring_function_s: symbols of functions to calculate score. 'p' for pscore, 'q' for qscore, 'f' for fold change, 's' for subtraction. for example: ['p [...]
static PyObject *__pyx_pw_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_11call_broadpeaks(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_scoring_function_symbols = 0;
PyObject *__pyx_v_lvl1_cutoff_s = 0;
@@ -19393,12 +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 = 1428; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("call_broadpeaks", 0, 3, 7, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1431; __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 = 1428; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("call_broadpeaks", 0, 3, 7, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1431; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
if (kw_args > 0) {
@@ -19422,7 +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 = 1428; __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 = 1431; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -19441,17 +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 = 1428; __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 = 1431; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_min_length = ((int)200);
}
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- __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;}
+ __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 = 1431; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_lvl1_max_gap = ((int)50);
}
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- __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;}
+ __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 = 1431; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_lvl2_max_gap = ((int)400);
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@@ -19459,16 +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 = 1428; __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 = 1431; __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;
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- 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;}
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_scoring_function_symbols), (&PyList_Type), 1, "scoring_function_symbols", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_lvl2_cutoff_s), (&PyList_Type), 1, "lvl2_cutoff_s", 1))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1431; __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 = 1431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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/* function exit code */
@@ -19495,7 +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;
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+ __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 = 1431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -19512,7 +19512,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments_10cal
return __pyx_r;
}
-/* "MACS2/IO/CallPeakUnit.pyx":1536
+/* "MACS2/IO/CallPeakUnit.pyx":1539
* 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, # <<<<<<<<<<<<<<
@@ -19563,7 +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":1560
+ /* "MACS2/IO/CallPeakUnit.pyx":1563
* float32_t * ctrl_array_ptr
*
* assert len(scoring_function_s) == len(lvl1_cutoff_s), "number of functions and cutoffs should be the same!" # <<<<<<<<<<<<<<
@@ -19574,22 +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 = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1563; __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;}
+ __pyx_t_1 = PyList_GET_SIZE(__pyx_v_scoring_function_s); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1563; __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 = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
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+ __pyx_t_2 = PyList_GET_SIZE(__pyx_v_lvl1_cutoff_s); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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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;}
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- /* "MACS2/IO/CallPeakUnit.pyx":1561
+ /* "MACS2/IO/CallPeakUnit.pyx":1564
*
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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 = 1561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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+ __pyx_t_2 = PyList_GET_SIZE(__pyx_v_scoring_function_s); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1564; __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 = 1561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_1 = PyList_GET_SIZE(__pyx_v_lvl2_cutoff_s); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1564; __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 = 1561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- /* "MACS2/IO/CallPeakUnit.pyx":1564
+ /* "MACS2/IO/CallPeakUnit.pyx":1567
*
* # first, build pileup, self.chr_pos_treat_ctrl
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* [pos_array, treat_array, ctrl_array] = self.chr_pos_treat_ctrl
*
*/
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+ __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 = 1567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_4 = PyList_GET_ITEM(sequence, 0);
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+ __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1568; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -19676,43 +19676,43 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
__pyx_v_ctrl_array = ((PyArrayObject *)__pyx_t_6);
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if (__pyx_t_7) {
- /* "MACS2/IO/CallPeakUnit.pyx":1569
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L3;
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+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1575; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_score_array_s = ((PyObject*)__pyx_t_3);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ 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 = 1577; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 1578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ /* "MACS2/IO/CallPeakUnit.pyx":1580
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goto __pyx_L6;
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L6;
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goto __pyx_L6;
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* acs_ptr = <int32_t *>above_cutoff_startpos.data
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__Pyx_DECREF_SET(__pyx_v_ts, __pyx_t_11);
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*/
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__pyx_L17:;
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goto __pyx_L0;
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@@ -21093,7 +21093,7 @@ static PyObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___chro
return __pyx_r;
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@@ -21143,7 +21143,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
if (__pyx_optional_args) {
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__pyx_v_tlist_control = ((PyObject*)__pyx_t_3);
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+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_tlist_length = ((PyObject*)__pyx_t_3);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1734; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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+ __pyx_t_5 = PyList_GET_SIZE(__pyx_v_peak_content); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1737; __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;
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if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyObject* sequence = __pyx_t_3;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -21290,7 +21290,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
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goto __pyx_L7_unpacking_done;
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* tarray_fc = self.__cal_FE ( tarray_pileup, tarray_control )
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* peak_content[0][0], # start
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+ __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 = 1750; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- /* "MACS2/IO/CallPeakUnit.pyx":1748
+ /* "MACS2/IO/CallPeakUnit.pyx":1751
*
* peaks.add( chrom, # chromosome
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@@ -21486,15 +21486,15 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1748; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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+ /* "MACS2/IO/CallPeakUnit.pyx":1752
* peaks.add( chrom, # chromosome
* peak_content[0][0], # start
* peak_content[-1][1], # end # <<<<<<<<<<<<<<
@@ -21503,22 +21503,22 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
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if (unlikely(__pyx_v_peak_content == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1749; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1752; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- /* "MACS2/IO/CallPeakUnit.pyx":1747
+ /* "MACS2/IO/CallPeakUnit.pyx":1750
* tarray_fc = self.__cal_FE ( tarray_pileup, tarray_control )
*
* peaks.add( chrom, # chromosome # <<<<<<<<<<<<<<
* peak_content[0][0], # start
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*/
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+ __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1750; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_chrom);
@@ -21529,85 +21529,85 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_12CallPeakUnit_20CallerFromAlignments___
__Pyx_GIVEREF(__pyx_t_8);
__pyx_t_7 = 0;
__pyx_t_8 = 0;
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+ __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1750; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- /* "MACS2/IO/CallPeakUnit.pyx":1751
+ /* "MACS2/IO/CallPeakUnit.pyx":1754
* peak_content[-1][1], # end
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+ if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_peak_score, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1750; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ /* "MACS2/IO/CallPeakUnit.pyx":1755
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+ if (PyDict_SetItem(__pyx_t_8, __pyx_n_s_pileup, __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1750; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ /* "MACS2/IO/CallPeakUnit.pyx":1756
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__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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goto __pyx_L0;
}
- /* "MACS2/IO/CallPeakUnit.pyx":1712
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return __pyx_r;
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int __pyx_clineno = 0;
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__pyx_v_start = __pyx_t_2;
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__Pyx_GOTREF(__pyx_slice__13);
__Pyx_GIVEREF(__pyx_slice__13);
- /* "MACS2/IO/CallPeakUnit.pyx":647
+ /* "MACS2/IO/CallPeakUnit.pyx":650
* float32_t * ctrl_value_ptr
*
* logging.debug ( "Start to calculate pvalue stat..." ) # <<<<<<<<<<<<<<
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* for i in range( len( self.chromosomes ) ):
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- __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_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 = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__14);
__Pyx_GIVEREF(__pyx_tuple__14);
- /* "MACS2/IO/CallPeakUnit.pyx":736
+ /* "MACS2/IO/CallPeakUnit.pyx":739
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* logging.debug ( "Start to calculate pvalue stat..." ) # <<<<<<<<<<<<<<
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* tmplist = sorted( list(np.arange(0.3, 10.0, 0.3)), reverse = True )
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__Pyx_GIVEREF(__pyx_tuple__15);
- /* "MACS2/IO/CallPeakUnit.pyx":738
+ /* "MACS2/IO/CallPeakUnit.pyx":741
* logging.debug ( "Start to calculate pvalue stat..." )
*
* tmplist = sorted( list(np.arange(0.3, 10.0, 0.3)), reverse = True ) # <<<<<<<<<<<<<<
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* for i in range( len( self.chromosomes ) ):
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__Pyx_GIVEREF(__pyx_tuple__16);
- /* "MACS2/IO/CallPeakUnit.pyx":843
+ /* "MACS2/IO/CallPeakUnit.pyx":846
* # write pvalue and total length of predicted peaks
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__Pyx_GOTREF(__pyx_tuple__17);
__Pyx_GIVEREF(__pyx_tuple__17);
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+ /* "MACS2/IO/CallPeakUnit.pyx":855
* 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..." ) # <<<<<<<<<<<<<<
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__Pyx_GIVEREF(__pyx_tuple__18);
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+ /* "MACS2/IO/CallPeakUnit.pyx":881
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__Pyx_GOTREF(__pyx_tuple__19);
__Pyx_GIVEREF(__pyx_tuple__19);
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__Pyx_GOTREF(__pyx_tuple__20);
__Pyx_GIVEREF(__pyx_tuple__20);
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* logging.info ( "#3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads." )
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*/
- __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_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 = 912; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__25);
__Pyx_GIVEREF(__pyx_tuple__25);
- /* "MACS2/IO/CallPeakUnit.pyx":1459
+ /* "MACS2/IO/CallPeakUnit.pyx":1462
* # 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 = 1459; __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 = 1462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__28);
__Pyx_GIVEREF(__pyx_tuple__28);
- /* "MACS2/IO/CallPeakUnit.pyx":1461
+ /* "MACS2/IO/CallPeakUnit.pyx":1464
* 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 = 1461; __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 = 1464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__29);
__Pyx_GIVEREF(__pyx_tuple__29);
- /* "MACS2/IO/CallPeakUnit.pyx":1471
+ /* "MACS2/IO/CallPeakUnit.pyx":1474
* 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 = 1471; __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 = 1474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__30);
__Pyx_GIVEREF(__pyx_tuple__30);
- /* "MACS2/IO/CallPeakUnit.pyx":1483
+ /* "MACS2/IO/CallPeakUnit.pyx":1486
*
*
* 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 = 1483; __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 = 1486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__31);
__Pyx_GIVEREF(__pyx_tuple__31);
- /* "MACS2/IO/CallPeakUnit.pyx":1795
+ /* "MACS2/IO/CallPeakUnit.pyx":1798
* 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 = 1795; __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 = 1798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__33);
__Pyx_GIVEREF(__pyx_tuple__33);
@@ -27186,47 +27186,47 @@ PyMODINIT_FUNC PyInit_CallPeakUnit(void)
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- /* "MACS2/IO/CallPeakUnit.pyx":1064
+ /* "MACS2/IO/CallPeakUnit.pyx":1067
*
* 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 = 1064; __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 = 1067; __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":1124
+ /* "MACS2/IO/CallPeakUnit.pyx":1127
*
* 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 = 1124; __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 = 1127; __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":1713
+ /* "MACS2/IO/CallPeakUnit.pyx":1716
*
* 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 = 1713; __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 = 1716; __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: <2015-12-22 16:06:56 Tao Liu> # <<<<<<<<<<<<<<
+ * # Time-stamp: <2016-02-15 15:23:38 Tao Liu> # <<<<<<<<<<<<<<
*
* """Module for Calculate Scores.
*/
diff --git a/MACS2/IO/CallPeakUnit.pyx b/MACS2/IO/CallPeakUnit.pyx
index 9fa6dd9..5b53dd2 100644
--- a/MACS2/IO/CallPeakUnit.pyx
+++ b/MACS2/IO/CallPeakUnit.pyx
@@ -1,4 +1,4 @@
-# Time-stamp: <2015-12-22 16:06:56 Tao Liu>
+# Time-stamp: <2016-02-15 15:23:38 Tao Liu>
"""Module for Calculate Scores.
@@ -488,6 +488,9 @@ cdef class CallerFromAlignments:
if not self.no_lambda_flag:
if self.PE_mode:
+ # note, we pileup up PE control as SE control because
+ # we assume the bias only can be captured at the
+ # surrounding regions of cutting sites from control experiments.
ctrl_pv = self.ctrl.pileup_a_chromosome_c( chrom, self.ctrl_d_s, self.ctrl_scaling_factor_s, baseline_value = self.lambda_bg )
else:
ctrl_pv = self.ctrl.pileup_a_chromosome( chrom, self.ctrl_d_s, self.ctrl_scaling_factor_s,
@@ -862,7 +865,7 @@ cdef class CallerFromAlignments:
scoring_function_s: symbols of functions to calculate score. 'p' for pscore, 'q' for qscore, 'f' for fold change, 's' for subtraction. for example: ['p', 'q']
score_cutoff_s : cutoff values corresponding to scoring functions
min_length : minimum length of peak
- max_gap : maximum gap of 'insignificant' regions within a peak
+ max_gap : maximum gap of 'insignificant' regions within a peak. Note, for PE_mode, max_gap and max_length are both set as fragment length.
call_summits : boolean. Whether or not call sub-peaks.
save_bedGraph : whether or not to save pileup and control into a bedGraph file
"""
@@ -1435,7 +1438,7 @@ cdef class CallerFromAlignments:
lvl1_cutoff_s: list of cutoffs at highly enriched regions, corresponding to scoring functions.
lvl2_cutoff_s: list of cutoffs at less enriched regions, corresponding to scoring functions.
- min_length : minimum peak length, default 200.
+ min_length : minimum peak length, default 200.
lvl1_max_gap : maximum gap to merge nearby enriched peaks, default 50.
lvl2_max_gap : maximum length of linkage regions, default 400.
diff --git a/MACS2/IO/PairedEndTrack.c b/MACS2/IO/PairedEndTrack.c
index 7ce73ed..f36b784 100644
--- a/MACS2/IO/PairedEndTrack.c
+++ b/MACS2/IO/PairedEndTrack.c
@@ -1468,7 +1468,6 @@ static char __pyx_k_destroy[] = "destroy";
static char __pyx_k_float64[] = "float64";
static char __pyx_k_logging[] = "logging";
static char __pyx_k_percent[] = "percent";
-static char __pyx_k_rlength[] = "rlength";
static char __pyx_k_shuffle[] = "shuffle";
static char __pyx_k_bincount[] = "bincount";
static char __pyx_k_refcheck[] = "refcheck";
@@ -1565,7 +1564,6 @@ static PyObject *__pyx_n_s_random;
static PyObject *__pyx_n_s_range;
static PyObject *__pyx_n_s_refcheck;
static PyObject *__pyx_n_s_resize;
-static PyObject *__pyx_n_s_rlength;
static PyObject *__pyx_n_s_round;
static PyObject *__pyx_kp_s_s_d_d;
static PyObject *__pyx_n_s_sample_percent;
@@ -3138,7 +3136,7 @@ static int __pyx_f_5MACS2_2IO_14PairedEndTrack_8PETrackI_set_rlengths(struct __p
* self.rlengths[chrom] = rlengths[chrom]
* missed_chroms = set(self.__locations.keys()).difference(rlengths.keys()) # <<<<<<<<<<<<<<
* for chrom in missed_chroms:
- * self.rlength[chrom] = INT_MAX
+ * self.rlengths[chrom] = INT_MAX
*/
if (unlikely(__pyx_v_self->__locations == Py_None)) {
PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "keys");
@@ -3192,7 +3190,7 @@ static int __pyx_f_5MACS2_2IO_14PairedEndTrack_8PETrackI_set_rlengths(struct __p
* self.rlengths[chrom] = rlengths[chrom]
* missed_chroms = set(self.__locations.keys()).difference(rlengths.keys())
* for chrom in missed_chroms: # <<<<<<<<<<<<<<
- * self.rlength[chrom] = INT_MAX
+ * self.rlengths[chrom] = INT_MAX
* return True
*/
__pyx_t_1 = PyObject_GetIter(__pyx_v_missed_chroms); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -3218,20 +3216,21 @@ static int __pyx_f_5MACS2_2IO_14PairedEndTrack_8PETrackI_set_rlengths(struct __p
/* "MACS2/IO/PairedEndTrack.pyx":142
* missed_chroms = set(self.__locations.keys()).difference(rlengths.keys())
* for chrom in missed_chroms:
- * self.rlength[chrom] = INT_MAX # <<<<<<<<<<<<<<
+ * self.rlengths[chrom] = INT_MAX # <<<<<<<<<<<<<<
* return True
*
*/
- __pyx_t_2 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s_rlength); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (unlikely(PyObject_SetItem(__pyx_t_2, __pyx_v_chrom, __pyx_v_5MACS2_2IO_14PairedEndTrack_INT_MAX) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (unlikely(__pyx_v_self->rlengths == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ if (unlikely(PyDict_SetItem(__pyx_v_self->rlengths, __pyx_v_chrom, __pyx_v_5MACS2_2IO_14PairedEndTrack_INT_MAX) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MACS2/IO/PairedEndTrack.pyx":141
* self.rlengths[chrom] = rlengths[chrom]
* missed_chroms = set(self.__locations.keys()).difference(rlengths.keys())
* for chrom in missed_chroms: # <<<<<<<<<<<<<<
- * self.rlength[chrom] = INT_MAX
+ * self.rlengths[chrom] = INT_MAX
* return True
*/
}
@@ -3239,7 +3238,7 @@ static int __pyx_f_5MACS2_2IO_14PairedEndTrack_8PETrackI_set_rlengths(struct __p
/* "MACS2/IO/PairedEndTrack.pyx":143
* for chrom in missed_chroms:
- * self.rlength[chrom] = INT_MAX
+ * self.rlengths[chrom] = INT_MAX
* return True # <<<<<<<<<<<<<<
*
* cpdef dict get_rlengths ( self ):
@@ -3513,7 +3512,7 @@ static PyObject *__pyx_f_5MACS2_2IO_14PairedEndTrack_8PETrackI_get_rlengths(stru
/* Python wrapper */
static PyObject *__pyx_pw_5MACS2_2IO_14PairedEndTrack_8PETrackI_11get_rlengths(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_5MACS2_2IO_14PairedEndTrack_8PETrackI_10get_rlengths[] = "Get reference chromosome lengths dictionary.\n\n If self.rlength is empty, create a new dict where the length of\n chromosome will be set as the maximum integer.\n ";
+static char __pyx_doc_5MACS2_2IO_14PairedEndTrack_8PETrackI_10get_rlengths[] = "Get reference chromosome lengths dictionary.\n\n If self.rlengths is empty, create a new dict where the length of\n chromosome will be set as the maximum integer.\n ";
static PyObject *__pyx_pw_5MACS2_2IO_14PairedEndTrack_8PETrackI_11get_rlengths(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
@@ -5197,7 +5196,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
* else:
* 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_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;}
__Pyx_GOTREF(__pyx_t_1);
@@ -5243,8 +5242,8 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
* else:
* 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);
@@ -5289,86 +5288,86 @@ static PyObject *__pyx_pf_5MACS2_2IO_14PairedEndTrack_8PETrackI_22separate_dups(
/* "MACS2/IO/PairedEndTrack.pyx":306
* 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_v_i_new = (__pyx_v_i_new + 1);
-
- /* "MACS2/IO/PairedEndTrack.pyx":307
- * 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 # <<<<<<<<<<<<<<
*
* current_loc_start = locs[0][0] # same as locs[0]['l']
*/
__pyx_v_n = 1;
- /* "MACS2/IO/PairedEndTrack.pyx":309
+ /* "MACS2/IO/PairedEndTrack.pyx":308
* n = 1
*
* current_loc_start = locs[0][0] # same as locs[0]['l'] # <<<<<<<<<<<<<<
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+ __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 = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 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_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 = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_current_loc_start = __pyx_t_9;
- /* "MACS2/IO/PairedEndTrack.pyx":310
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__pyx_t_14 = 0;
__pyx_t_15 = 0;
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_18, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_18, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(PyList_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyList_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_tmp_pileup, ((PyObject*)__pyx_t_2));
__pyx_t_2 = 0;
- /* "MACS2/IO/PairedEndTrack.pyx":568
+ /* "MACS2/IO/PairedEndTrack.pyx":571
* tmp_pileup = se_all_in_one_pileup ( self.__locations[chrom]['l'], self.__locations[chrom]['r'], five_shift, three_shift, rlength, scale_factor, baseline_value )
*
* if prev_pileup: # <<<<<<<<<<<<<<
@@ -8602,14 +8601,14 @@ static PyObject *__pyx_f_5MACS2_2IO_14PairedEndTrack_8PETrackI_pileup_a_chromoso
__pyx_t_10 = (__pyx_v_prev_pileup != Py_None) && (PyList_GET_SIZE(__pyx_v_prev_pileup) != 0);
if (__pyx_t_10) {
- /* "MACS2/IO/PairedEndTrack.pyx":569
+ /* "MACS2/IO/PairedEndTrack.pyx":572
*
* if prev_pileup:
* prev_pileup = max_over_two_pv_array ( prev_pileup, tmp_pileup ) # <<<<<<<<<<<<<<
* else:
* prev_pileup = tmp_pileup
*/
- __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_max_over_two_pv_array); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_max_over_two_pv_array); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_18 = NULL;
__pyx_t_17 = 0;
@@ -8623,7 +8622,7 @@ static PyObject *__pyx_f_5MACS2_2IO_14PairedEndTrack_8PETrackI_pileup_a_chromoso
__pyx_t_17 = 1;
}
}
- __pyx_t_15 = PyTuple_New(2+__pyx_t_17); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = PyTuple_New(2+__pyx_t_17); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
if (__pyx_t_18) {
PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_t_18); __Pyx_GIVEREF(__pyx_t_18); __pyx_t_18 = NULL;
@@ -8634,18 +8633,18 @@ static PyObject *__pyx_f_5MACS2_2IO_14PairedEndTrack_8PETrackI_pileup_a_chromoso
__Pyx_INCREF(__pyx_v_tmp_pileup);
PyTuple_SET_ITEM(__pyx_t_15, 1+__pyx_t_17, __pyx_v_tmp_pileup);
__Pyx_GIVEREF(__pyx_v_tmp_pileup);
- __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_15, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_1, __pyx_t_15, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(PyList_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyList_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "list", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF_SET(__pyx_v_prev_pileup, ((PyObject*)__pyx_t_2));
__pyx_t_2 = 0;
goto __pyx_L6;
}
/*else*/ {
- /* "MACS2/IO/PairedEndTrack.pyx":571
+ /* "MACS2/IO/PairedEndTrack.pyx":574
* prev_pileup = max_over_two_pv_array ( prev_pileup, tmp_pileup )
* else:
* prev_pileup = tmp_pileup # <<<<<<<<<<<<<<
@@ -8658,7 +8657,7 @@ static PyObject *__pyx_f_5MACS2_2IO_14PairedEndTrack_8PETrackI_pileup_a_chromoso
__pyx_L6:;
}
- /* "MACS2/IO/PairedEndTrack.pyx":573
+ /* "MACS2/IO/PairedEndTrack.pyx":576
* prev_pileup = tmp_pileup
*
* return prev_pileup # <<<<<<<<<<<<<<
@@ -8703,7 +8702,7 @@ static PyObject *__pyx_f_5MACS2_2IO_14PairedEndTrack_8PETrackI_pileup_a_chromoso
/* Python wrapper */
static PyObject *__pyx_pw_5MACS2_2IO_14PairedEndTrack_8PETrackI_35pileup_a_chromosome_c(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_5MACS2_2IO_14PairedEndTrack_8PETrackI_34pileup_a_chromosome_c[] = "pileup a certain chromosome, return [p,v] (end position and value) list.\n\n This function is for control track. Basically, here is a simplified function from FixWidthTrack.\n \n ds : tag will be extended to this value to 3' direction,\n unless directional is False. Can contain multiple extension\n values. Final pileup w [...]
+static char __pyx_doc_5MACS2_2IO_14PairedEndTrack_8PETrackI_34pileup_a_chromosome_c[] = "pileup a certain chromosome, return [p,v] (end position and value) list.\n\n This function is for control track. Basically, here is a\n simplified function from FixWidthTrack. We pretend the PE is\n SE data and left read is on plus strand and right read is on\n minus strand.\n \n ds : tag will be extended to this value to 3' direction,\n [...]
static PyObject *__pyx_pw_5MACS2_2IO_14PairedEndTrack_8PETrackI_35pileup_a_chromosome_c(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_chrom = 0;
PyObject *__pyx_v_ds = 0;
@@ -12840,7 +12839,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 0, 0, 1, 1},
{&__pyx_n_s_refcheck, __pyx_k_refcheck, sizeof(__pyx_k_refcheck), 0, 0, 1, 1},
{&__pyx_n_s_resize, __pyx_k_resize, sizeof(__pyx_k_resize), 0, 0, 1, 1},
- {&__pyx_n_s_rlength, __pyx_k_rlength, sizeof(__pyx_k_rlength), 0, 0, 1, 1},
{&__pyx_n_s_round, __pyx_k_round, sizeof(__pyx_k_round), 0, 0, 1, 1},
{&__pyx_kp_s_s_d_d, __pyx_k_s_d_d, sizeof(__pyx_k_s_d_d), 0, 0, 1, 0},
{&__pyx_n_s_sample_percent, __pyx_k_sample_percent, sizeof(__pyx_k_sample_percent), 0, 0, 1, 1},
@@ -12945,7 +12943,7 @@ static int __Pyx_InitCachedConstants(void) {
* else:
* 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_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;}
__Pyx_GOTREF(__pyx_tuple__9);
@@ -12958,8 +12956,8 @@ static int __Pyx_InitCachedConstants(void) {
* else:
* 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_tuple__11 = PyTuple_Pack(2, __pyx_n_s_l, __pyx_n_s_int32); if (unlikely(!__pyx_tuple__11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__11);
@@ -12983,8 +12981,8 @@ static int __Pyx_InitCachedConstants(void) {
* new_locs = locs
* else:
* 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
+ *
*/
__pyx_tuple__14 = PyTuple_Pack(2, __pyx_n_s_l, __pyx_n_s_int32); if (unlikely(!__pyx_tuple__14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__14);
@@ -13354,7 +13352,7 @@ PyMODINIT_FUNC PyInit_PairedEndTrack(void)
__pyx_t_1 = 0;
/* "MACS2/IO/PairedEndTrack.pyx":1
- * # Time-stamp: <2015-07-27 12:37:26 Tao Liu> # <<<<<<<<<<<<<<
+ * # Time-stamp: <2016-02-15 16:12:19 Tao Liu> # <<<<<<<<<<<<<<
*
* """Module for filter duplicate tags from paired-end data
*/
diff --git a/MACS2/IO/PairedEndTrack.pyx b/MACS2/IO/PairedEndTrack.pyx
index 27c3023..df9ba7e 100644
--- a/MACS2/IO/PairedEndTrack.pyx
+++ b/MACS2/IO/PairedEndTrack.pyx
@@ -1,4 +1,4 @@
-# Time-stamp: <2015-07-27 12:37:26 Tao Liu>
+# Time-stamp: <2016-02-15 16:12:19 Tao Liu>
"""Module for filter duplicate tags from paired-end data
@@ -139,13 +139,13 @@ cdef class PETrackI:
self.rlengths[chrom] = rlengths[chrom]
missed_chroms = set(self.__locations.keys()).difference(rlengths.keys())
for chrom in missed_chroms:
- self.rlength[chrom] = INT_MAX
+ self.rlengths[chrom] = INT_MAX
return True
cpdef dict get_rlengths ( self ):
"""Get reference chromosome lengths dictionary.
- If self.rlength is empty, create a new dict where the length of
+ If self.rlengths is empty, create a new dict where the length of
chromosome will be set as the maximum integer.
"""
if not self.rlengths:
@@ -303,13 +303,13 @@ cdef class PETrackI:
else:
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
current_loc_start = locs[0][0] # same as locs[0]['l']
current_loc_end = locs[0][1]# same as locs[0]['r']
new_locs[i_new][0] = current_loc_start
new_locs[i_new][1] = current_loc_end
+ i_new += 1
self.length += current_loc_end - current_loc_start
for i_old in range(1, size):
loc_start = locs[i_old][0]
@@ -389,13 +389,13 @@ cdef class PETrackI:
new_locs = locs
else:
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
current_loc_start = locs[0][0]
current_loc_end = locs[0][1]
new_locs[i_new][0] = current_loc_start
new_locs[i_new][1] = current_loc_end
+ i_new += 1
self.length += current_loc_end - current_loc_start
for i_old in range(1, size):
loc_start = locs[i_old][0]
@@ -537,7 +537,10 @@ cdef class PETrackI:
cpdef pileup_a_chromosome_c ( self, str chrom, list ds, list scale_factor_s, float baseline_value = 0.0 ):
"""pileup a certain chromosome, return [p,v] (end position and value) list.
- This function is for control track. Basically, here is a simplified function from FixWidthTrack.
+ This function is for control track. Basically, here is a
+ simplified function from FixWidthTrack. We pretend the PE is
+ SE data and left read is on plus strand and right read is on
+ minus strand.
ds : tag will be extended to this value to 3' direction,
unless directional is False. Can contain multiple extension
diff --git a/MACS2/IO/Parser.c b/MACS2/IO/Parser.c
index e8ba81e..4bd0b03 100644
--- a/MACS2/IO/Parser.c
+++ b/MACS2/IO/Parser.c
@@ -672,6 +672,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
/*--- Type declarations ---*/
struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser;
struct __pyx_obj_5MACS2_2IO_6Parser_BEDParser;
+struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser;
struct __pyx_obj_5MACS2_2IO_6Parser_ELANDResultParser;
struct __pyx_obj_5MACS2_2IO_6Parser_ELANDMultiParser;
struct __pyx_obj_5MACS2_2IO_6Parser_ELANDExportParser;
@@ -679,7 +680,6 @@ struct __pyx_obj_5MACS2_2IO_6Parser_SAMParser;
struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser;
struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser;
struct __pyx_obj_5MACS2_2IO_6Parser_BowtieParser;
-struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser;
/* "numpy.pxd":762
* ctypedef npy_longdouble longdouble_t
@@ -719,19 +719,19 @@ typedef npy_cdouble __pyx_t_5numpy_complex_t;
struct __pyx_opt_args_5MACS2_2IO_6Parser_guess_parser;
struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed;
-/* "MACS2/IO/Parser.pyx":68
+/* "MACS2/IO/Parser.pyx":58
* # ------------------------------------
*
* cpdef guess_parser ( fhd, long buffer_size = 100000 ): # <<<<<<<<<<<<<<
+ * # Note: BAMPE and BEDPE can't be automatically detected.
* order_list = ("BAM",
- * "BED",
*/
struct __pyx_opt_args_5MACS2_2IO_6Parser_guess_parser {
int __pyx_n;
long buffer_size;
};
-/* "MACS2/IO/Parser.pyx":1274
+/* "MACS2/IO/Parser.pyx":1168
* return ret
*
* cdef struct _BAMPEParsed: # <<<<<<<<<<<<<<
@@ -744,7 +744,7 @@ struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed {
int tlen;
};
-/* "MACS2/IO/Parser.pyx":120
+/* "MACS2/IO/Parser.pyx":111
* return repr( "Strand information can not be recognized in this line: \"%s\",\"%s\"" % ( self.string, self.strand ) )
*
* cdef class GenericParser: # <<<<<<<<<<<<<<
@@ -762,11 +762,11 @@ struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser {
};
-/* "MACS2/IO/Parser.pyx":300
+/* "MACS2/IO/Parser.pyx":291
* self.fhd.close()
*
* cdef class BEDParser( GenericParser ): # <<<<<<<<<<<<<<
- * """File Parser Class for tabular File.
+ * """File Parser Class for BED File.
*
*/
struct __pyx_obj_5MACS2_2IO_6Parser_BEDParser {
@@ -774,9 +774,23 @@ struct __pyx_obj_5MACS2_2IO_6Parser_BEDParser {
};
-/* "MACS2/IO/Parser.pyx":354
+/* "MACS2/IO/Parser.pyx":345
* 0 )
*
+ * cdef class BEDPEParser(GenericParser): # <<<<<<<<<<<<<<
+ * """Parser for BED format file containing PE information, and also
+ * can be used for the cases when users predefine the fragment
+ */
+struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser {
+ struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser __pyx_base;
+ int n;
+ int d;
+};
+
+
+/* "MACS2/IO/Parser.pyx":459
+ * return petrack
+ *
* cdef class ELANDResultParser( GenericParser ): # <<<<<<<<<<<<<<
* """File Parser Class for tabular File.
*
@@ -786,7 +800,7 @@ struct __pyx_obj_5MACS2_2IO_6Parser_ELANDResultParser {
};
-/* "MACS2/IO/Parser.pyx":406
+/* "MACS2/IO/Parser.pyx":511
* return ( "", -1, -1 )
*
* cdef class ELANDMultiParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -798,7 +812,7 @@ struct __pyx_obj_5MACS2_2IO_6Parser_ELANDMultiParser {
};
-/* "MACS2/IO/Parser.pyx":479
+/* "MACS2/IO/Parser.pyx":584
*
*
* cdef class ELANDExportParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -810,7 +824,7 @@ struct __pyx_obj_5MACS2_2IO_6Parser_ELANDExportParser {
};
-/* "MACS2/IO/Parser.pyx":522
+/* "MACS2/IO/Parser.pyx":627
*
* ### Contributed by Davide, modified by Tao
* cdef class SAMParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -822,7 +836,7 @@ struct __pyx_obj_5MACS2_2IO_6Parser_SAMParser {
};
-/* "MACS2/IO/Parser.pyx":630
+/* "MACS2/IO/Parser.pyx":735
* return ( thisref, thisstart, thisstrand )
*
* cdef class BAMParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -834,7 +848,7 @@ struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser {
};
-/* "MACS2/IO/Parser.pyx":1014
+/* "MACS2/IO/Parser.pyx":994
* return ( thisref, thisstart, thisstrand )
*
* cdef class BAMPEParser(BAMParser): # <<<<<<<<<<<<<<
@@ -848,7 +862,7 @@ struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser {
};
-/* "MACS2/IO/Parser.pyx":1281
+/* "MACS2/IO/Parser.pyx":1175
* ### End ###
*
* cdef class BowtieParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -860,25 +874,8 @@ struct __pyx_obj_5MACS2_2IO_6Parser_BowtieParser {
};
-/* "MACS2/IO/Parser.pyx":1365
- * raise StrandFormatError( thisline, thisfields[ 1 ] )
- *
- * cdef class PySAMParser: # <<<<<<<<<<<<<<
- * """Parser using PySAM to parse SAM or BAM
- *
- */
-struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser {
- PyObject_HEAD
- struct __pyx_vtabstruct_5MACS2_2IO_6Parser_PySAMParser *__pyx_vtab;
- PyObject *filename;
- PyBoolObject *gzipped;
- int tag_size;
- PyObject *fhd;
-};
-
-
-/* "MACS2/IO/Parser.pyx":120
+/* "MACS2/IO/Parser.pyx":111
* return repr( "Strand information can not be recognized in this line: \"%s\",\"%s\"" % ( self.string, self.strand ) )
*
* cdef class GenericParser: # <<<<<<<<<<<<<<
@@ -898,11 +895,11 @@ struct __pyx_vtabstruct_5MACS2_2IO_6Parser_GenericParser {
static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_GenericParser *__pyx_vtabptr_5MACS2_2IO_6Parser_GenericParser;
-/* "MACS2/IO/Parser.pyx":300
+/* "MACS2/IO/Parser.pyx":291
* self.fhd.close()
*
* cdef class BEDParser( GenericParser ): # <<<<<<<<<<<<<<
- * """File Parser Class for tabular File.
+ * """File Parser Class for BED File.
*
*/
@@ -912,9 +909,26 @@ struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BEDParser {
static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BEDParser *__pyx_vtabptr_5MACS2_2IO_6Parser_BEDParser;
-/* "MACS2/IO/Parser.pyx":354
+/* "MACS2/IO/Parser.pyx":345
* 0 )
*
+ * cdef class BEDPEParser(GenericParser): # <<<<<<<<<<<<<<
+ * """Parser for BED format file containing PE information, and also
+ * can be used for the cases when users predefine the fragment
+ */
+
+struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BEDPEParser {
+ struct __pyx_vtabstruct_5MACS2_2IO_6Parser_GenericParser __pyx_base;
+ PyObject *(*__pyx___pe_parse_line)(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *, PyObject *);
+ PyObject *(*build_petrack)(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *, int __pyx_skip_dispatch);
+ PyObject *(*append_petrack)(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *, PyObject *, int __pyx_skip_dispatch);
+};
+static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BEDPEParser *__pyx_vtabptr_5MACS2_2IO_6Parser_BEDPEParser;
+
+
+/* "MACS2/IO/Parser.pyx":459
+ * return petrack
+ *
* cdef class ELANDResultParser( GenericParser ): # <<<<<<<<<<<<<<
* """File Parser Class for tabular File.
*
@@ -926,7 +940,7 @@ struct __pyx_vtabstruct_5MACS2_2IO_6Parser_ELANDResultParser {
static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_ELANDResultParser *__pyx_vtabptr_5MACS2_2IO_6Parser_ELANDResultParser;
-/* "MACS2/IO/Parser.pyx":406
+/* "MACS2/IO/Parser.pyx":511
* return ( "", -1, -1 )
*
* cdef class ELANDMultiParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -940,7 +954,7 @@ struct __pyx_vtabstruct_5MACS2_2IO_6Parser_ELANDMultiParser {
static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_ELANDMultiParser *__pyx_vtabptr_5MACS2_2IO_6Parser_ELANDMultiParser;
-/* "MACS2/IO/Parser.pyx":479
+/* "MACS2/IO/Parser.pyx":584
*
*
* cdef class ELANDExportParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -954,7 +968,7 @@ struct __pyx_vtabstruct_5MACS2_2IO_6Parser_ELANDExportParser {
static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_ELANDExportParser *__pyx_vtabptr_5MACS2_2IO_6Parser_ELANDExportParser;
-/* "MACS2/IO/Parser.pyx":522
+/* "MACS2/IO/Parser.pyx":627
*
* ### Contributed by Davide, modified by Tao
* cdef class SAMParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -968,7 +982,7 @@ struct __pyx_vtabstruct_5MACS2_2IO_6Parser_SAMParser {
static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_SAMParser *__pyx_vtabptr_5MACS2_2IO_6Parser_SAMParser;
-/* "MACS2/IO/Parser.pyx":630
+/* "MACS2/IO/Parser.pyx":735
* return ( thisref, thisstart, thisstrand )
*
* cdef class BAMParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -979,18 +993,12 @@ static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_SAMParser *__pyx_vtabptr_5MACS
struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BAMParser {
struct __pyx_vtabstruct_5MACS2_2IO_6Parser_GenericParser __pyx_base;
PyObject *(*get_references)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *, int __pyx_skip_dispatch);
- PyObject *(*__pyx___get_references_w_pysam)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *);
- PyObject *(*__pyx___get_references_wo_pysam)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *);
- PyObject *(*__pyx___build_fwtrack_w_pysam)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *);
- PyObject *(*__pyx___build_fwtrack_wo_pysam)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *);
- PyObject *(*__pyx___append_fwtrack_w_pysam)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *, PyObject *);
- PyObject *(*__pyx___append_fwtrack_wo_pysam)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *, PyObject *);
- PyObject *(*__pyx___fw_binary_parse_wo_pysam)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *, PyObject *);
+ PyObject *(*__pyx___fw_binary_parse)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *, PyObject *);
};
static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BAMParser *__pyx_vtabptr_5MACS2_2IO_6Parser_BAMParser;
-/* "MACS2/IO/Parser.pyx":1014
+/* "MACS2/IO/Parser.pyx":994
* return ( thisref, thisstart, thisstrand )
*
* cdef class BAMPEParser(BAMParser): # <<<<<<<<<<<<<<
@@ -1001,15 +1009,13 @@ static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BAMParser *__pyx_vtabptr_5MACS
struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BAMPEParser {
struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BAMParser __pyx_base;
PyObject *(*build_petrack)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *, int __pyx_skip_dispatch);
- PyObject *(*__pyx___build_petrack_w_pysam)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *);
- PyObject *(*__pyx___build_petrack_wo_pysam)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *);
PyObject *(*append_petrack)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *, PyObject *, int __pyx_skip_dispatch);
struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed (*__pyx___pe_binary_parse)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *, PyObject *);
};
static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BAMPEParser *__pyx_vtabptr_5MACS2_2IO_6Parser_BAMPEParser;
-/* "MACS2/IO/Parser.pyx":1281
+/* "MACS2/IO/Parser.pyx":1175
* ### End ###
*
* cdef class BowtieParser( GenericParser ): # <<<<<<<<<<<<<<
@@ -1022,22 +1028,6 @@ struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BowtieParser {
};
static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_BowtieParser *__pyx_vtabptr_5MACS2_2IO_6Parser_BowtieParser;
-
-/* "MACS2/IO/Parser.pyx":1365
- * raise StrandFormatError( thisline, thisfields[ 1 ] )
- *
- * cdef class PySAMParser: # <<<<<<<<<<<<<<
- * """Parser using PySAM to parse SAM or BAM
- *
- */
-
-struct __pyx_vtabstruct_5MACS2_2IO_6Parser_PySAMParser {
- PyObject *(*__pyx___tlen_parse_line)(struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *, PyObject *);
- PyObject *(*__pyx___fw_parse_line)(struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *, PyObject *);
- PyObject *(*sniff)(struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *, int __pyx_skip_dispatch);
-};
-static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_PySAMParser *__pyx_vtabptr_5MACS2_2IO_6Parser_PySAMParser;
-
/* --- Runtime support code (head) --- */
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
@@ -1232,6 +1222,8 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
int is_list, int wraparound, int boundscheck);
+static CYTHON_INLINE long __Pyx_mod_long(long, long); /* proto */
+
static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
PyObject** py_start, PyObject** py_stop, PyObject** py_slice,
@@ -1512,6 +1504,9 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_13GenericParser_sniff(struct __pyx_o
static PyObject *__pyx_f_5MACS2_2IO_6Parser_13GenericParser_close(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self, int __pyx_skip_dispatch); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BEDParser___tlen_parse_line(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_BEDParser *__pyx_v_self, PyObject *__pyx_v_thisline); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BEDParser___fw_parse_line(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_BEDParser *__pyx_v_self, PyObject *__pyx_v_thisline); /* proto*/
+static PyObject *__pyx_f_5MACS2_2IO_6Parser_11BEDPEParser___pe_parse_line(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self, PyObject *__pyx_v_thisline); /* proto*/
+static PyObject *__pyx_f_5MACS2_2IO_6Parser_11BEDPEParser_build_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self, int __pyx_skip_dispatch); /* proto*/
+static PyObject *__pyx_f_5MACS2_2IO_6Parser_11BEDPEParser_append_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self, PyObject *__pyx_v_petrack, int __pyx_skip_dispatch); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_6Parser_17ELANDResultParser___tlen_parse_line(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_ELANDResultParser *__pyx_v_self, PyObject *__pyx_v_thisline); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_6Parser_17ELANDResultParser___fw_parse_line(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_ELANDResultParser *__pyx_v_self, PyObject *__pyx_v_thisline); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_6Parser_16ELANDMultiParser___tlen_parse_line(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_ELANDMultiParser *__pyx_v_self, PyObject *__pyx_v_thisline); /* proto*/
@@ -1523,25 +1518,14 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_9SAMParser___fw_parse_line(CYTHON_UN
static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BAMParser_sniff(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, int __pyx_skip_dispatch); /* proto*/
static int __pyx_f_5MACS2_2IO_6Parser_9BAMParser_tsize(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, int __pyx_skip_dispatch); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BAMParser_get_references(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, int __pyx_skip_dispatch); /* proto*/
-static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BAMParser___get_references_w_pysam(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto*/
-static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BAMParser___get_references_wo_pysam(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BAMParser_build_fwtrack(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, int __pyx_skip_dispatch); /* proto*/
-static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BAMParser___build_fwtrack_w_pysam(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto*/
-static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BAMParser___build_fwtrack_wo_pysam(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BAMParser_append_fwtrack(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, PyObject *__pyx_v_fwtrack, int __pyx_skip_dispatch); /* proto*/
-static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BAMParser___append_fwtrack_w_pysam(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, PyObject *__pyx_v_fwtrack); /* proto*/
-static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BAMParser___append_fwtrack_wo_pysam(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, PyObject *__pyx_v_fwtrack); /* proto*/
-static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BAMParser___fw_binary_parse_wo_pysam(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, PyObject *__pyx_v_data); /* proto*/
+static PyObject *__pyx_f_5MACS2_2IO_6Parser_9BAMParser___fw_binary_parse(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, PyObject *__pyx_v_data); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_6Parser_11BAMPEParser_build_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self, int __pyx_skip_dispatch); /* proto*/
-static PyObject *__pyx_f_5MACS2_2IO_6Parser_11BAMPEParser___build_petrack_w_pysam(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self); /* proto*/
-static PyObject *__pyx_f_5MACS2_2IO_6Parser_11BAMPEParser___build_petrack_wo_pysam(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_6Parser_11BAMPEParser_append_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self, PyObject *__pyx_v_petrack, int __pyx_skip_dispatch); /* proto*/
static struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed __pyx_f_5MACS2_2IO_6Parser_11BAMPEParser___pe_binary_parse(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self, PyObject *__pyx_v_data); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_6Parser_12BowtieParser___tlen_parse_line(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_BowtieParser *__pyx_v_self, PyObject *__pyx_v_thisline); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_6Parser_12BowtieParser___fw_parse_line(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_BowtieParser *__pyx_v_self, PyObject *__pyx_v_thisline); /* proto*/
-static PyObject *__pyx_f_5MACS2_2IO_6Parser_11PySAMParser___tlen_parse_line(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_thisline); /* proto*/
-static PyObject *__pyx_f_5MACS2_2IO_6Parser_11PySAMParser___fw_parse_line(CYTHON_UNUSED struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_thisline); /* proto*/
-static PyObject *__pyx_f_5MACS2_2IO_6Parser_11PySAMParser_sniff(struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *__pyx_v_self, int __pyx_skip_dispatch); /* proto*/
/* Module declarations from 'cpython.version' */
@@ -1641,6 +1625,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, cha
/* Module declarations from 'MACS2.IO.Parser' */
static PyTypeObject *__pyx_ptype_5MACS2_2IO_6Parser_GenericParser = 0;
static PyTypeObject *__pyx_ptype_5MACS2_2IO_6Parser_BEDParser = 0;
+static PyTypeObject *__pyx_ptype_5MACS2_2IO_6Parser_BEDPEParser = 0;
static PyTypeObject *__pyx_ptype_5MACS2_2IO_6Parser_ELANDResultParser = 0;
static PyTypeObject *__pyx_ptype_5MACS2_2IO_6Parser_ELANDMultiParser = 0;
static PyTypeObject *__pyx_ptype_5MACS2_2IO_6Parser_ELANDExportParser = 0;
@@ -1648,8 +1633,6 @@ static PyTypeObject *__pyx_ptype_5MACS2_2IO_6Parser_SAMParser = 0;
static PyTypeObject *__pyx_ptype_5MACS2_2IO_6Parser_BAMParser = 0;
static PyTypeObject *__pyx_ptype_5MACS2_2IO_6Parser_BAMPEParser = 0;
static PyTypeObject *__pyx_ptype_5MACS2_2IO_6Parser_BowtieParser = 0;
-static PyTypeObject *__pyx_ptype_5MACS2_2IO_6Parser_PySAMParser = 0;
-__PYX_EXTERN_C DL_EXPORT(int) HAS_PYSAM;
static PyObject *__pyx_f_5MACS2_2IO_6Parser_guess_parser(PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5MACS2_2IO_6Parser_guess_parser *__pyx_optional_args); /*proto*/
#define __Pyx_MODULE_NAME "MACS2.IO.Parser"
int __pyx_module_is_main_MACS2__IO__Parser = 0;
@@ -1663,8 +1646,6 @@ static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_sum;
static PyObject *__pyx_builtin_map;
static PyObject *__pyx_builtin_range;
-static PyObject *__pyx_builtin_zip;
-static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_RuntimeError;
static PyObject *__pyx_pf_5MACS2_2IO_6Parser_guess_parser(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_fhd, long __pyx_v_buffer_size); /* proto */
static PyObject *__pyx_pf_5MACS2_2IO_6Parser_17StrandFormatError___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_string, PyObject *__pyx_v_strand); /* proto */
@@ -1675,6 +1656,12 @@ static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_4build_fwtrack(stru
static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_6append_fwtrack(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self, PyObject *__pyx_v_fwtrack); /* proto */
static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_8sniff(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5MACS2_2IO_6Parser_13GenericParser_10close(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_build_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_2append_petrack(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self, PyObject *__pyx_v_petrack); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_1n___get__(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_1n_2__set__(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_1d___get__(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self); /* proto */
+static int __pyx_pf_5MACS2_2IO_6Parser_11BEDPEParser_1d_2__set__(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
static int __pyx_pf_5MACS2_2IO_6Parser_9BAMParser___init__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self, PyObject *__pyx_v_filename, long __pyx_v_buffer_size); /* proto */
static PyObject *__pyx_pf_5MACS2_2IO_6Parser_9BAMParser_2sniff(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto */
static PyObject *__pyx_pf_5MACS2_2IO_6Parser_9BAMParser_4tsize(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *__pyx_v_self); /* proto */
@@ -1687,16 +1674,11 @@ static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_1n___get__(struct __p
static int __pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_1n_2__set__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_1d___get__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self); /* proto */
static int __pyx_pf_5MACS2_2IO_6Parser_11BAMPEParser_1d_2__set__(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_5MACS2_2IO_6Parser_11PySAMParser___init__(struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *__pyx_v_self, PyObject *__pyx_v_filename, long __pyx_v_buffer_size); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11PySAMParser_2tsize(struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11PySAMParser_4build_fwtrack(struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11PySAMParser_6append_fwtrack(struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *__pyx_v_self, PyObject *__pyx_v_fwtrack); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11PySAMParser_8sniff(struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5MACS2_2IO_6Parser_11PySAMParser_10close(struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *__pyx_v_self); /* proto */
static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_GenericParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BEDParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BEDPEParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_ELANDResultParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_ELANDMultiParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_ELANDExportParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
@@ -1704,7 +1686,6 @@ static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_SAMParser(PyTypeObject *t, PyOb
static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BAMParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BAMPEParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BowtieParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_PySAMParser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static char __pyx_k_B[] = "<B";
static char __pyx_k_F[] = "F";
static char __pyx_k_H[] = "H";
@@ -1743,29 +1724,22 @@ static char __pyx_k_SAM[] = "SAM";
static char __pyx_k__10[] = "\t";
static char __pyx_k__14[] = "+";
static char __pyx_k__15[] = "-";
-static char __pyx_k__27[] = ":";
-static char __pyx_k__36[] = "@";
-static char __pyx_k__99[] = "*";
+static char __pyx_k__29[] = ":";
+static char __pyx_k__38[] = "@";
+static char __pyx_k__94[] = "*";
static char __pyx_k_d_2[] = "d";
static char __pyx_k_doc[] = "__doc__";
static char __pyx_k_fhd[] = "fhd";
static char __pyx_k_i_2[] = "i";
static char __pyx_k_map[] = "map";
-static char __pyx_k_pos[] = "pos";
static char __pyx_k_str[] = "__str__";
static char __pyx_k_sum[] = "sum";
-static char __pyx_k_sys[] = "sys";
-static char __pyx_k_tid[] = "tid";
-static char __pyx_k_zip[] = "zip";
-static char __pyx_k_aend[] = "aend";
-static char __pyx_k_exit[] = "exit";
static char __pyx_k_gzip[] = "gzip";
static char __pyx_k_info[] = "info";
static char __pyx_k_init[] = "__init__";
static char __pyx_k_join[] = "join";
static char __pyx_k_main[] = "__main__";
static char __pyx_k_mode[] = "mode";
-static char __pyx_k_next[] = "next";
static char __pyx_k_open[] = "open";
static char __pyx_k_read[] = "read";
static char __pyx_k_seek[] = "seek";
@@ -1777,9 +1751,7 @@ static char __pyx_k_close[] = "close";
static char __pyx_k_debug[] = "debug";
static char __pyx_k_error[] = "error";
static char __pyx_k_numpy[] = "numpy";
-static char __pyx_k_pysam[] = "pysam";
static char __pyx_k_range[] = "range";
-static char __pyx_k_reset[] = "reset";
static char __pyx_k_sniff[] = "sniff";
static char __pyx_k_split[] = "split";
static char __pyx_k_track[] = "track";
@@ -1797,37 +1769,29 @@ static char __pyx_k_struct[] = "struct";
static char __pyx_k_unpack[] = "unpack";
static char __pyx_k_FWTrack[] = "FWTrack";
static char __pyx_k_IOError[] = "IOError";
-static char __pyx_k_Samfile[] = "Samfile";
static char __pyx_k_add_loc[] = "add_loc";
static char __pyx_k_browser[] = "browser";
static char __pyx_k_findall[] = "findall";
static char __pyx_k_isdigit[] = "isdigit";
-static char __pyx_k_lengths[] = "lengths";
static char __pyx_k_logging[] = "logging";
static char __pyx_k_prepare[] = "__prepare__";
static char __pyx_k_version[] = "__version__";
static char __pyx_k_PETrackI[] = "PETrackI";
static char __pyx_k_filename[] = "filename";
-static char __pyx_k_finalize[] = "finalize";
-static char __pyx_k_is_read2[] = "is_read2";
static char __pyx_k_qualname[] = "__qualname__";
static char __pyx_k_readline[] = "readline";
-static char __pyx_k_rlengths[] = "rlengths";
+static char __pyx_k_righ_pos[] = "righ_pos";
static char __pyx_k_Exception[] = "Exception";
-static char __pyx_k_is_paired[] = "is_paired";
static char __pyx_k_metaclass[] = "__metaclass__";
+static char __pyx_k_DUMMYCHROM[] = "DUMMYCHROM";
static char __pyx_k_ELANDMULTI[] = "ELANDMULTI";
static char __pyx_k_IndexError[] = "IndexError";
static char __pyx_k_ValueError[] = "ValueError";
-static char __pyx_k_is_reverse[] = "is_reverse";
static char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
-static char __pyx_k_references[] = "references";
static char __pyx_k_ELANDEXPORT[] = "ELANDEXPORT";
static char __pyx_k_buffer_size[] = "buffer_size";
-static char __pyx_k_is_unmapped[] = "is_unmapped";
static char __pyx_k_RuntimeError[] = "RuntimeError";
static char __pyx_k_set_rlengths[] = "set_rlengths";
-static char __pyx_k_StopIteration[] = "StopIteration";
static char __pyx_k_build_fwtrack[] = "build_fwtrack";
static char __pyx_k_build_petrack[] = "build_petrack";
static char __pyx_k_BufferedReader[] = "BufferedReader";
@@ -1835,7 +1799,6 @@ static char __pyx_k_NotImplemented[] = "NotImplemented";
static char __pyx_k_append_fwtrack[] = "append_fwtrack";
static char __pyx_k_append_petrack[] = "append_petrack";
static char __pyx_k_get_references[] = "get_references";
-static char __pyx_k_is_proper_pair[] = "is_proper_pair";
static char __pyx_k_MACS2_Constants[] = "MACS2.Constants";
static char __pyx_k_MACS2_IO_Parser[] = "MACS2.IO.Parser";
static char __pyx_k_Parser_Revision[] = "Parser $Revision$";
@@ -1850,14 +1813,15 @@ static char __pyx_k_MACS2_IO_PairedEndTrack[] = "MACS2.IO.PairedEndTrack";
static char __pyx_k_StrandFormatError___str[] = "StrandFormatError.__str__";
static char __pyx_k_StrandFormatError___init[] = "StrandFormatError.__init__";
static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous";
-static char __pyx_k_BAM_files_might_be_corrupted[] = "BAM files might be corrupted!";
static char __pyx_k_Users_taoliu_Dropbox_Projects_M[] = "/Users/taoliu/Dropbox/Projects/MACS2/MACS/MACS2/IO/Parser.pyx";
static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
static char __pyx_k_Exception_about_strand_format_er[] = "Exception about strand format error.\n\n Example:\n raise StrandFormatError('Must be F or R','X')\n ";
static char __pyx_k_File_is_not_of_a_valid_BAM_forma[] = "File is not of a valid BAM format! %d";
static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd";
+static char __pyx_k_Less_than_3_columns_found_at_thi[] = "Less than 3 columns found at this line: %s\n";
static char __pyx_k_Module_for_all_MACS_Parser_class[] = "Module for all MACS Parser classes for input.\n\nCopyright (c) 2010,2011 Tao Liu <taoliu at jimmy.harvard.edu>\n\nThis code is free software; you can redistribute it and/or modify it\nunder the terms of the BSD License (see the file COPYING included\nwith the distribution).\n\n at status: experimental\n at version: $Revision$\n at author: Tao Liu\n at contact: taoliu at jimmy.harvard.edu\n";
static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported";
+static char __pyx_k_Right_position_must_be_larger_th[] = "Right position must be larger than left position, check your BED file at line: %s";
static char __pyx_k_Something_went_wrong_mean_fragme[] = "Something went wrong (mean fragment size was negative)";
static char __pyx_k_Strand_information_can_not_be_re[] = "Strand information can not be recognized in this line: \"%s\",\"%s\"";
static char __pyx_k_Tao_Liu_taoliu_jimmy_harvard_edu[] = "Tao Liu <taoliu at jimmy.harvard.edu>";
@@ -1866,11 +1830,11 @@ static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string alloca
static PyObject *__pyx_kp_s_All_Parser_classes;
static PyObject *__pyx_kp_s_B;
static PyObject *__pyx_n_s_BAM;
-static PyObject *__pyx_kp_s_BAM_files_might_be_corrupted;
static PyObject *__pyx_n_s_BED;
static PyObject *__pyx_n_s_BOWTIE;
static PyObject *__pyx_n_s_BufferedReader;
static PyObject *__pyx_kp_s_Can_t_detect_format;
+static PyObject *__pyx_n_s_DUMMYCHROM;
static PyObject *__pyx_kp_s_Detected_format_is_s;
static PyObject *__pyx_n_s_ELAND;
static PyObject *__pyx_n_s_ELANDEXPORT;
@@ -1886,6 +1850,7 @@ static PyObject *__pyx_kp_s_HH;
static PyObject *__pyx_n_s_IOError;
static PyObject *__pyx_n_s_IndexError;
static PyObject *__pyx_kp_s_Input_file_is_gzipped;
+static PyObject *__pyx_kp_s_Less_than_3_columns_found_at_thi;
static PyObject *__pyx_n_s_MACS2_Constants;
static PyObject *__pyx_n_s_MACS2_IO_FixWidthTrack;
static PyObject *__pyx_n_s_MACS2_IO_PairedEndTrack;
@@ -1895,11 +1860,10 @@ static PyObject *__pyx_n_s_NotImplemented;
static PyObject *__pyx_n_s_PETrackI;
static PyObject *__pyx_kp_s_Parser_Revision;
static PyObject *__pyx_n_s_R;
+static PyObject *__pyx_kp_s_Right_position_must_be_larger_th;
static PyObject *__pyx_n_s_RuntimeError;
static PyObject *__pyx_n_s_SAM;
-static PyObject *__pyx_n_s_Samfile;
static PyObject *__pyx_kp_s_Something_went_wrong_mean_fragme;
-static PyObject *__pyx_n_s_StopIteration;
static PyObject *__pyx_n_s_StrandFormatError;
static PyObject *__pyx_n_s_StrandFormatError___init;
static PyObject *__pyx_n_s_StrandFormatError___str;
@@ -1914,13 +1878,12 @@ static PyObject *__pyx_n_s_ValueError;
static PyObject *__pyx_kp_s__10;
static PyObject *__pyx_kp_s__14;
static PyObject *__pyx_kp_s__15;
-static PyObject *__pyx_kp_s__27;
-static PyObject *__pyx_kp_s__36;
+static PyObject *__pyx_kp_s__29;
+static PyObject *__pyx_kp_s__38;
static PyObject *__pyx_kp_s__6;
static PyObject *__pyx_kp_s__9;
-static PyObject *__pyx_n_s__99;
+static PyObject *__pyx_n_s__94;
static PyObject *__pyx_n_s_add_loc;
-static PyObject *__pyx_n_s_aend;
static PyObject *__pyx_n_s_append_fwtrack;
static PyObject *__pyx_n_s_append_petrack;
static PyObject *__pyx_n_s_author;
@@ -1935,11 +1898,9 @@ static PyObject *__pyx_kp_s_d_MDNX;
static PyObject *__pyx_n_s_debug;
static PyObject *__pyx_n_s_doc;
static PyObject *__pyx_n_s_error;
-static PyObject *__pyx_n_s_exit;
static PyObject *__pyx_kp_s_fa;
static PyObject *__pyx_n_s_fhd;
static PyObject *__pyx_n_s_filename;
-static PyObject *__pyx_n_s_finalize;
static PyObject *__pyx_n_s_findall;
static PyObject *__pyx_n_s_get_references;
static PyObject *__pyx_n_s_gzip;
@@ -1948,14 +1909,8 @@ static PyObject *__pyx_n_s_import;
static PyObject *__pyx_n_s_info;
static PyObject *__pyx_n_s_init;
static PyObject *__pyx_n_s_io;
-static PyObject *__pyx_n_s_is_paired;
-static PyObject *__pyx_n_s_is_proper_pair;
-static PyObject *__pyx_n_s_is_read2;
-static PyObject *__pyx_n_s_is_reverse;
-static PyObject *__pyx_n_s_is_unmapped;
static PyObject *__pyx_n_s_isdigit;
static PyObject *__pyx_n_s_join;
-static PyObject *__pyx_n_s_lengths;
static PyObject *__pyx_n_s_logging;
static PyObject *__pyx_n_s_main;
static PyObject *__pyx_n_s_map;
@@ -1964,13 +1919,10 @@ static PyObject *__pyx_n_s_mode;
static PyObject *__pyx_n_s_module;
static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous;
static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou;
-static PyObject *__pyx_n_s_next;
static PyObject *__pyx_n_s_np;
static PyObject *__pyx_n_s_numpy;
static PyObject *__pyx_n_s_open;
-static PyObject *__pyx_n_s_pos;
static PyObject *__pyx_n_s_prepare;
-static PyObject *__pyx_n_s_pysam;
static PyObject *__pyx_n_s_pyx_vtable;
static PyObject *__pyx_n_s_qualname;
static PyObject *__pyx_n_s_range;
@@ -1978,10 +1930,8 @@ static PyObject *__pyx_n_s_rb;
static PyObject *__pyx_n_s_re;
static PyObject *__pyx_n_s_read;
static PyObject *__pyx_n_s_readline;
-static PyObject *__pyx_n_s_references;
-static PyObject *__pyx_n_s_reset;
+static PyObject *__pyx_n_s_righ_pos;
static PyObject *__pyx_n_s_rindex;
-static PyObject *__pyx_n_s_rlengths;
static PyObject *__pyx_n_s_rstrip;
static PyObject *__pyx_n_s_seek;
static PyObject *__pyx_n_s_self;
@@ -1993,16 +1943,13 @@ static PyObject *__pyx_n_s_strand;
static PyObject *__pyx_n_s_string;
static PyObject *__pyx_n_s_struct;
static PyObject *__pyx_n_s_sum;
-static PyObject *__pyx_n_s_sys;
static PyObject *__pyx_n_s_tell;
static PyObject *__pyx_n_s_test;
-static PyObject *__pyx_n_s_tid;
static PyObject *__pyx_n_s_track;
static PyObject *__pyx_n_s_tsize;
static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd;
static PyObject *__pyx_n_s_unpack;
static PyObject *__pyx_n_s_version;
-static PyObject *__pyx_n_s_zip;
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_3;
@@ -2024,8 +1971,8 @@ static PyObject *__pyx_tuple__4;
static PyObject *__pyx_tuple__5;
static PyObject *__pyx_tuple__7;
static PyObject *__pyx_tuple__8;
-static PyObject *__pyx_slice__56;
-static PyObject *__pyx_slice__62;
+static PyObject *__pyx_slice__58;
+static PyObject *__pyx_slice__64;
static PyObject *__pyx_slice__69;
static PyObject *__pyx_slice__70;
static PyObject *__pyx_slice__71;
@@ -2044,16 +1991,16 @@ static PyObject *__pyx_tuple__23;
static PyObject *__pyx_tuple__24;
static PyObject *__pyx_tuple__25;
static PyObject *__pyx_tuple__26;
+static PyObject *__pyx_tuple__27;
static PyObject *__pyx_tuple__28;
-static PyObject *__pyx_tuple__29;
static PyObject *__pyx_tuple__30;
static PyObject *__pyx_tuple__31;
static PyObject *__pyx_tuple__32;
static PyObject *__pyx_tuple__33;
static PyObject *__pyx_tuple__34;
static PyObject *__pyx_tuple__35;
+static PyObject *__pyx_tuple__36;
static PyObject *__pyx_tuple__37;
-static PyObject *__pyx_tuple__38;
static PyObject *__pyx_tuple__39;
static PyObject *__pyx_tuple__40;
static PyObject *__pyx_tuple__41;
@@ -2071,13 +2018,13 @@ static PyObject *__pyx_tuple__52;
static PyObject *__pyx_tuple__53;
static PyObject *__pyx_tuple__54;
static PyObject *__pyx_tuple__55;
+static PyObject *__pyx_tuple__56;
static PyObject *__pyx_tuple__57;
-static PyObject *__pyx_tuple__58;
static PyObject *__pyx_tuple__59;
static PyObject *__pyx_tuple__60;
static PyObject *__pyx_tuple__61;
+static PyObject *__pyx_tuple__62;
static PyObject *__pyx_tuple__63;
-static PyObject *__pyx_tuple__64;
static PyObject *__pyx_tuple__65;
static PyObject *__pyx_tuple__66;
static PyObject *__pyx_tuple__67;
@@ -2103,23 +2050,17 @@ static PyObject *__pyx_tuple__90;
static PyObject *__pyx_tuple__91;
static PyObject *__pyx_tuple__92;
static PyObject *__pyx_tuple__93;
-static PyObject *__pyx_tuple__94;
static PyObject *__pyx_tuple__95;
-static PyObject *__pyx_tuple__96;
static PyObject *__pyx_tuple__97;
-static PyObject *__pyx_tuple__98;
-static PyObject *__pyx_tuple__100;
-static PyObject *__pyx_tuple__102;
-static PyObject *__pyx_codeobj__101;
-static PyObject *__pyx_codeobj__103;
-int HAS_PYSAM;
-
-/* "MACS2/IO/Parser.pyx":68
+static PyObject *__pyx_codeobj__96;
+static PyObject *__pyx_codeobj__98;
+
+/* "MACS2/IO/Parser.pyx":58
* # ------------------------------------
*
* cpdef guess_parser ( fhd, long buffer_size = 100000 ): # <<<<<<<<<<<<<<
+ * # Note: BAMPE and BEDPE can't be automatically detected.
* order_list = ("BAM",
- * "BED",
*/
static PyObject *__pyx_pw_5MACS2_2IO_6Parser_1guess_parser(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
@@ -2149,9 +2090,9 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_guess_parser(PyObject *__pyx_v_fhd,
}
}
- /* "MACS2/IO/Parser.pyx":69
- *
+ /* "MACS2/IO/Parser.pyx":60
* cpdef guess_parser ( fhd, long buffer_size = 100000 ):
+ * # Note: BAMPE and BEDPE can't be automatically detected.
* order_list = ("BAM", # <<<<<<<<<<<<<<
* "BED",
* "ELAND",
@@ -2159,7 +2100,7 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_guess_parser(PyObject *__pyx_v_fhd,
__Pyx_INCREF(__pyx_tuple_);
__pyx_v_order_list = __pyx_tuple_;
- /* "MACS2/IO/Parser.pyx":78
+ /* "MACS2/IO/Parser.pyx":69
* )
*
* for f in order_list: # <<<<<<<<<<<<<<
@@ -2170,42 +2111,42 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_guess_parser(PyObject *__pyx_v_fhd,
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[0]; __pyx_lineno = 78; __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[0]; __pyx_lineno = 69; __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[0]; __pyx_lineno = 78; __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[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
__Pyx_XDECREF_SET(__pyx_v_f, __pyx_t_3);
__pyx_t_3 = 0;
- /* "MACS2/IO/Parser.pyx":79
+ /* "MACS2/IO/Parser.pyx":70
*
* for f in order_list:
* if f == 'BED': # <<<<<<<<<<<<<<
* p = BEDParser( fhd, buffer_size = buffer_size )
* elif f == "ELAND":
*/
- __pyx_t_4 = (__Pyx_PyString_Equals(__pyx_v_f, __pyx_n_s_BED, Py_EQ)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (__Pyx_PyString_Equals(__pyx_v_f, __pyx_n_s_BED, Py_EQ)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
- /* "MACS2/IO/Parser.pyx":80
+ /* "MACS2/IO/Parser.pyx":71
* for f in order_list:
* if f == 'BED':
* p = BEDParser( fhd, buffer_size = buffer_size ) # <<<<<<<<<<<<<<
* elif f == "ELAND":
* p = ELANDResultParser( fhd, buffer_size = buffer_size )
*/
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __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 = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_fhd);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_fhd);
__Pyx_GIVEREF(__pyx_v_fhd);
- __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = __Pyx_PyInt_From_long(__pyx_v_buffer_size); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_6 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5MACS2_2IO_6Parser_BEDParser)), __pyx_t_3, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2214,35 +2155,35 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_guess_parser(PyObject *__pyx_v_fhd,
goto __pyx_L5;
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- /* "MACS2/IO/Parser.pyx":81
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if (__pyx_t_4) {
- /* "MACS2/IO/Parser.pyx":82
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__Pyx_INCREF(__pyx_v_fhd);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_fhd);
__Pyx_GIVEREF(__pyx_v_fhd);
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+ __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_3 = __Pyx_PyInt_From_long(__pyx_v_buffer_size); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_buffer_size, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5MACS2_2IO_6Parser_ELANDResultParser)), __pyx_t_6, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -2251,35 +2192,35 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_guess_parser(PyObject *__pyx_v_fhd,
goto __pyx_L5;
}
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+ __pyx_t_4 = (__Pyx_PyString_Equals(__pyx_v_f, __pyx_n_s_ELANDMULTI, Py_EQ)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
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* p = ELANDResultParser( fhd, buffer_size = buffer_size )
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+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_INCREF(__pyx_v_fhd);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_fhd);
__Pyx_GIVEREF(__pyx_v_fhd);
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+ __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_6 = __Pyx_PyInt_From_long(__pyx_v_buffer_size); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_buffer_size, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_6 = __Pyx_PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5MACS2_2IO_6Parser_ELANDMultiParser)), __pyx_t_3, __pyx_t_5); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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goto __pyx_L5;
}
- /* "MACS2/IO/Parser.pyx":85
+ /* "MACS2/IO/Parser.pyx":76
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+ __pyx_t_4 = (__Pyx_PyString_Equals(__pyx_v_f, __pyx_n_s_ELANDEXPORT, Py_EQ)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
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* p = ELANDMultiParser( fhd, buffer_size = buffer_size )
* elif f == "ELANDEXPORT":
* p = ELANDExportParser( fhd, buffer_size = buffer_size ) # <<<<<<<<<<<<<<
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+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_INCREF(__pyx_v_fhd);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_fhd);
__Pyx_GIVEREF(__pyx_v_fhd);
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+ __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (PyDict_SetItem(__pyx_t_5, __pyx_n_s_buffer_size, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -2325,35 +2266,35 @@ static PyObject *__pyx_f_5MACS2_2IO_6Parser_guess_parser(PyObject *__pyx_v_fhd,
goto __pyx_L5;
}
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if (__pyx_t_4) {
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PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_fhd);
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goto __pyx_L5;
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}
__pyx_L13:;
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return __pyx_r;
}
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/* Check if overridden in Python */
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*/
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*/
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*/
__pyx_v_m = 0;
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goto __pyx_L0;
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#endif
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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goto __pyx_L3_continue;
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0, /*tp_iternext*/
- 0, /*tp_methods*/
+ __pyx_methods_5MACS2_2IO_6Parser_BEDPEParser, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_5MACS2_2IO_6Parser_BEDPEParser, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
@@ -22041,7 +19575,7 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_BEDParser = {
0, /*tp_init*/
#endif
0, /*tp_alloc*/
- __pyx_tp_new_5MACS2_2IO_6Parser_BEDParser, /*tp_new*/
+ __pyx_tp_new_5MACS2_2IO_6Parser_BEDPEParser, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -22353,9 +19887,9 @@ static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_BAMParser(PyTypeObject *t, PyOb
static PyMethodDef __pyx_methods_5MACS2_2IO_6Parser_BAMParser[] = {
{"sniff", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_9BAMParser_3sniff, METH_NOARGS, __pyx_doc_5MACS2_2IO_6Parser_9BAMParser_2sniff},
{"tsize", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_9BAMParser_5tsize, METH_NOARGS, __pyx_doc_5MACS2_2IO_6Parser_9BAMParser_4tsize},
- {"get_references", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_9BAMParser_7get_references, METH_NOARGS, 0},
- {"build_fwtrack", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_9BAMParser_9build_fwtrack, METH_NOARGS, 0},
- {"append_fwtrack", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_9BAMParser_11append_fwtrack, METH_O, 0},
+ {"get_references", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_9BAMParser_7get_references, METH_NOARGS, __pyx_doc_5MACS2_2IO_6Parser_9BAMParser_6get_references},
+ {"build_fwtrack", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_9BAMParser_9build_fwtrack, METH_NOARGS, __pyx_doc_5MACS2_2IO_6Parser_9BAMParser_8build_fwtrack},
+ {"append_fwtrack", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_9BAMParser_11append_fwtrack, METH_O, __pyx_doc_5MACS2_2IO_6Parser_9BAMParser_10append_fwtrack},
{0, 0, 0, 0}
};
@@ -22455,7 +19989,7 @@ static int __pyx_setprop_5MACS2_2IO_6Parser_11BAMPEParser_d(PyObject *o, PyObjec
}
static PyMethodDef __pyx_methods_5MACS2_2IO_6Parser_BAMPEParser[] = {
- {"build_petrack", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_11BAMPEParser_1build_petrack, METH_NOARGS, 0},
+ {"build_petrack", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_11BAMPEParser_1build_petrack, METH_NOARGS, __pyx_doc_5MACS2_2IO_6Parser_11BAMPEParser_build_petrack},
{"append_petrack", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_11BAMPEParser_3append_petrack, METH_O, __pyx_doc_5MACS2_2IO_6Parser_11BAMPEParser_2append_petrack},
{0, 0, 0, 0}
};
@@ -22597,128 +20131,6 @@ static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_BowtieParser = {
0, /*tp_finalize*/
#endif
};
-static struct __pyx_vtabstruct_5MACS2_2IO_6Parser_PySAMParser __pyx_vtable_5MACS2_2IO_6Parser_PySAMParser;
-
-static PyObject *__pyx_tp_new_5MACS2_2IO_6Parser_PySAMParser(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *p;
- PyObject *o;
- if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
- o = (*t->tp_alloc)(t, 0);
- } else {
- o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
- }
- if (unlikely(!o)) return 0;
- p = ((struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *)o);
- p->__pyx_vtab = __pyx_vtabptr_5MACS2_2IO_6Parser_PySAMParser;
- p->filename = ((PyObject*)Py_None); Py_INCREF(Py_None);
- p->gzipped = ((PyBoolObject *)Py_None); Py_INCREF(Py_None);
- p->fhd = Py_None; Py_INCREF(Py_None);
- return o;
-}
-
-static void __pyx_tp_dealloc_5MACS2_2IO_6Parser_PySAMParser(PyObject *o) {
- struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *p = (struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *)o;
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->filename);
- Py_CLEAR(p->gzipped);
- Py_CLEAR(p->fhd);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_5MACS2_2IO_6Parser_PySAMParser(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *p = (struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *)o;
- if (p->gzipped) {
- e = (*v)(((PyObject*)p->gzipped), a); if (e) return e;
- }
- if (p->fhd) {
- e = (*v)(p->fhd, a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_5MACS2_2IO_6Parser_PySAMParser(PyObject *o) {
- PyObject* tmp;
- struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *p = (struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser *)o;
- tmp = ((PyObject*)p->gzipped);
- p->gzipped = ((PyBoolObject *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->fhd);
- p->fhd = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyMethodDef __pyx_methods_5MACS2_2IO_6Parser_PySAMParser[] = {
- {"tsize", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_11PySAMParser_3tsize, METH_NOARGS, __pyx_doc_5MACS2_2IO_6Parser_11PySAMParser_2tsize},
- {"build_fwtrack", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_11PySAMParser_5build_fwtrack, METH_NOARGS, __pyx_doc_5MACS2_2IO_6Parser_11PySAMParser_4build_fwtrack},
- {"append_fwtrack", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_11PySAMParser_7append_fwtrack, METH_O, __pyx_doc_5MACS2_2IO_6Parser_11PySAMParser_6append_fwtrack},
- {"sniff", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_11PySAMParser_9sniff, METH_NOARGS, __pyx_doc_5MACS2_2IO_6Parser_11PySAMParser_8sniff},
- {"close", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_11PySAMParser_11close, METH_NOARGS, __pyx_doc_5MACS2_2IO_6Parser_11PySAMParser_10close},
- {0, 0, 0, 0}
-};
-
-static PyTypeObject __pyx_type_5MACS2_2IO_6Parser_PySAMParser = {
- PyVarObject_HEAD_INIT(0, 0)
- "MACS2.IO.Parser.PySAMParser", /*tp_name*/
- sizeof(struct __pyx_obj_5MACS2_2IO_6Parser_PySAMParser), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_5MACS2_2IO_6Parser_PySAMParser, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- "Parser using PySAM to parse SAM or BAM\n\n ", /*tp_doc*/
- __pyx_tp_traverse_5MACS2_2IO_6Parser_PySAMParser, /*tp_traverse*/
- __pyx_tp_clear_5MACS2_2IO_6Parser_PySAMParser, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_5MACS2_2IO_6Parser_PySAMParser, /*tp_methods*/
- 0, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- __pyx_pw_5MACS2_2IO_6Parser_11PySAMParser_1__init__, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_5MACS2_2IO_6Parser_PySAMParser, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- 0, /*tp_version_tag*/
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
- #endif
-};
static PyMethodDef __pyx_methods[] = {
{"guess_parser", (PyCFunction)__pyx_pw_5MACS2_2IO_6Parser_1guess_parser, METH_VARARGS|METH_KEYWORDS, 0},
@@ -22729,13 +20141,13 @@ static int __pyx_import_star_set(PyObject *o, PyObject* py_name, char *name) {
static const char* internal_type_names[] = {
"BAMPEParser",
"BAMParser",
+ "BEDPEParser",
"BEDParser",
"BowtieParser",
"ELANDExportParser",
"ELANDMultiParser",
"ELANDResultParser",
"GenericParser",
- "PySAMParser",
"SAMParser",
"_BAMPEParsed",
"__pyx_ctuple_char__ptr__and_int__and_long",
@@ -22771,15 +20183,10 @@ static int __pyx_import_star_set(PyObject *o, PyObject* py_name, char *name) {
type_name++;
}
if (0);
- else if (__Pyx_StrEq(name, "HAS_PYSAM")) {
- HAS_PYSAM = __Pyx_PyObject_IsTrue(o); if ((HAS_PYSAM == (int)-1) && PyErr_Occurred()) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 30; __pyx_clineno = __LINE__; goto __pyx_L2_error;};
- }
else {
if (PyObject_SetAttr(__pyx_m, py_name, o) < 0) goto bad;
}
return 0;
- __pyx_L2_error:;
- __Pyx_AddTraceback("MACS2.IO.Parser", __pyx_clineno, __pyx_lineno, __pyx_filename);
bad:
return -1;
}
@@ -22922,11 +20329,11 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s_All_Parser_classes, __pyx_k_All_Parser_classes, sizeof(__pyx_k_All_Parser_classes), 0, 0, 1, 0},
{&__pyx_kp_s_B, __pyx_k_B, sizeof(__pyx_k_B), 0, 0, 1, 0},
{&__pyx_n_s_BAM, __pyx_k_BAM, sizeof(__pyx_k_BAM), 0, 0, 1, 1},
- {&__pyx_kp_s_BAM_files_might_be_corrupted, __pyx_k_BAM_files_might_be_corrupted, sizeof(__pyx_k_BAM_files_might_be_corrupted), 0, 0, 1, 0},
{&__pyx_n_s_BED, __pyx_k_BED, sizeof(__pyx_k_BED), 0, 0, 1, 1},
{&__pyx_n_s_BOWTIE, __pyx_k_BOWTIE, sizeof(__pyx_k_BOWTIE), 0, 0, 1, 1},
{&__pyx_n_s_BufferedReader, __pyx_k_BufferedReader, sizeof(__pyx_k_BufferedReader), 0, 0, 1, 1},
{&__pyx_kp_s_Can_t_detect_format, __pyx_k_Can_t_detect_format, sizeof(__pyx_k_Can_t_detect_format), 0, 0, 1, 0},
+ {&__pyx_n_s_DUMMYCHROM, __pyx_k_DUMMYCHROM, sizeof(__pyx_k_DUMMYCHROM), 0, 0, 1, 1},
{&__pyx_kp_s_Detected_format_is_s, __pyx_k_Detected_format_is_s, sizeof(__pyx_k_Detected_format_is_s), 0, 0, 1, 0},
{&__pyx_n_s_ELAND, __pyx_k_ELAND, sizeof(__pyx_k_ELAND), 0, 0, 1, 1},
{&__pyx_n_s_ELANDEXPORT, __pyx_k_ELANDEXPORT, sizeof(__pyx_k_ELANDEXPORT), 0, 0, 1, 1},
@@ -22942,6 +20349,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_IOError, __pyx_k_IOError, sizeof(__pyx_k_IOError), 0, 0, 1, 1},
{&__pyx_n_s_IndexError, __pyx_k_IndexError, sizeof(__pyx_k_IndexError), 0, 0, 1, 1},
{&__pyx_kp_s_Input_file_is_gzipped, __pyx_k_Input_file_is_gzipped, sizeof(__pyx_k_Input_file_is_gzipped), 0, 0, 1, 0},
+ {&__pyx_kp_s_Less_than_3_columns_found_at_thi, __pyx_k_Less_than_3_columns_found_at_thi, sizeof(__pyx_k_Less_than_3_columns_found_at_thi), 0, 0, 1, 0},
{&__pyx_n_s_MACS2_Constants, __pyx_k_MACS2_Constants, sizeof(__pyx_k_MACS2_Constants), 0, 0, 1, 1},
{&__pyx_n_s_MACS2_IO_FixWidthTrack, __pyx_k_MACS2_IO_FixWidthTrack, sizeof(__pyx_k_MACS2_IO_FixWidthTrack), 0, 0, 1, 1},
{&__pyx_n_s_MACS2_IO_PairedEndTrack, __pyx_k_MACS2_IO_PairedEndTrack, sizeof(__pyx_k_MACS2_IO_PairedEndTrack), 0, 0, 1, 1},
@@ -22951,11 +20359,10 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_PETrackI, __pyx_k_PETrackI, sizeof(__pyx_k_PETrackI), 0, 0, 1, 1},
{&__pyx_kp_s_Parser_Revision, __pyx_k_Parser_Revision, sizeof(__pyx_k_Parser_Revision), 0, 0, 1, 0},
{&__pyx_n_s_R, __pyx_k_R, sizeof(__pyx_k_R), 0, 0, 1, 1},
+ {&__pyx_kp_s_Right_position_must_be_larger_th, __pyx_k_Right_position_must_be_larger_th, sizeof(__pyx_k_Right_position_must_be_larger_th), 0, 0, 1, 0},
{&__pyx_n_s_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 0, 0, 1, 1},
{&__pyx_n_s_SAM, __pyx_k_SAM, sizeof(__pyx_k_SAM), 0, 0, 1, 1},
- {&__pyx_n_s_Samfile, __pyx_k_Samfile, sizeof(__pyx_k_Samfile), 0, 0, 1, 1},
{&__pyx_kp_s_Something_went_wrong_mean_fragme, __pyx_k_Something_went_wrong_mean_fragme, sizeof(__pyx_k_Something_went_wrong_mean_fragme), 0, 0, 1, 0},
- {&__pyx_n_s_StopIteration, __pyx_k_StopIteration, sizeof(__pyx_k_StopIteration), 0, 0, 1, 1},
{&__pyx_n_s_StrandFormatError, __pyx_k_StrandFormatError, sizeof(__pyx_k_StrandFormatError), 0, 0, 1, 1},
{&__pyx_n_s_StrandFormatError___init, __pyx_k_StrandFormatError___init, sizeof(__pyx_k_StrandFormatError___init), 0, 0, 1, 1},
{&__pyx_n_s_StrandFormatError___str, __pyx_k_StrandFormatError___str, sizeof(__pyx_k_StrandFormatError___str), 0, 0, 1, 1},
@@ -22970,13 +20377,12 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s__10, __pyx_k__10, sizeof(__pyx_k__10), 0, 0, 1, 0},
{&__pyx_kp_s__14, __pyx_k__14, sizeof(__pyx_k__14), 0, 0, 1, 0},
{&__pyx_kp_s__15, __pyx_k__15, sizeof(__pyx_k__15), 0, 0, 1, 0},
- {&__pyx_kp_s__27, __pyx_k__27, sizeof(__pyx_k__27), 0, 0, 1, 0},
- {&__pyx_kp_s__36, __pyx_k__36, sizeof(__pyx_k__36), 0, 0, 1, 0},
+ {&__pyx_kp_s__29, __pyx_k__29, sizeof(__pyx_k__29), 0, 0, 1, 0},
+ {&__pyx_kp_s__38, __pyx_k__38, sizeof(__pyx_k__38), 0, 0, 1, 0},
{&__pyx_kp_s__6, __pyx_k__6, sizeof(__pyx_k__6), 0, 0, 1, 0},
{&__pyx_kp_s__9, __pyx_k__9, sizeof(__pyx_k__9), 0, 0, 1, 0},
- {&__pyx_n_s__99, __pyx_k__99, sizeof(__pyx_k__99), 0, 0, 1, 1},
+ {&__pyx_n_s__94, __pyx_k__94, sizeof(__pyx_k__94), 0, 0, 1, 1},
{&__pyx_n_s_add_loc, __pyx_k_add_loc, sizeof(__pyx_k_add_loc), 0, 0, 1, 1},
- {&__pyx_n_s_aend, __pyx_k_aend, sizeof(__pyx_k_aend), 0, 0, 1, 1},
{&__pyx_n_s_append_fwtrack, __pyx_k_append_fwtrack, sizeof(__pyx_k_append_fwtrack), 0, 0, 1, 1},
{&__pyx_n_s_append_petrack, __pyx_k_append_petrack, sizeof(__pyx_k_append_petrack), 0, 0, 1, 1},
{&__pyx_n_s_author, __pyx_k_author, sizeof(__pyx_k_author), 0, 0, 1, 1},
@@ -22991,11 +20397,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_debug, __pyx_k_debug, sizeof(__pyx_k_debug), 0, 0, 1, 1},
{&__pyx_n_s_doc, __pyx_k_doc, sizeof(__pyx_k_doc), 0, 0, 1, 1},
{&__pyx_n_s_error, __pyx_k_error, sizeof(__pyx_k_error), 0, 0, 1, 1},
- {&__pyx_n_s_exit, __pyx_k_exit, sizeof(__pyx_k_exit), 0, 0, 1, 1},
{&__pyx_kp_s_fa, __pyx_k_fa, sizeof(__pyx_k_fa), 0, 0, 1, 0},
{&__pyx_n_s_fhd, __pyx_k_fhd, sizeof(__pyx_k_fhd), 0, 0, 1, 1},
{&__pyx_n_s_filename, __pyx_k_filename, sizeof(__pyx_k_filename), 0, 0, 1, 1},
- {&__pyx_n_s_finalize, __pyx_k_finalize, sizeof(__pyx_k_finalize), 0, 0, 1, 1},
{&__pyx_n_s_findall, __pyx_k_findall, sizeof(__pyx_k_findall), 0, 0, 1, 1},
{&__pyx_n_s_get_references, __pyx_k_get_references, sizeof(__pyx_k_get_references), 0, 0, 1, 1},
{&__pyx_n_s_gzip, __pyx_k_gzip, sizeof(__pyx_k_gzip), 0, 0, 1, 1},
@@ -23004,14 +20408,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_info, __pyx_k_info, sizeof(__pyx_k_info), 0, 0, 1, 1},
{&__pyx_n_s_init, __pyx_k_init, sizeof(__pyx_k_init), 0, 0, 1, 1},
{&__pyx_n_s_io, __pyx_k_io, sizeof(__pyx_k_io), 0, 0, 1, 1},
- {&__pyx_n_s_is_paired, __pyx_k_is_paired, sizeof(__pyx_k_is_paired), 0, 0, 1, 1},
- {&__pyx_n_s_is_proper_pair, __pyx_k_is_proper_pair, sizeof(__pyx_k_is_proper_pair), 0, 0, 1, 1},
- {&__pyx_n_s_is_read2, __pyx_k_is_read2, sizeof(__pyx_k_is_read2), 0, 0, 1, 1},
- {&__pyx_n_s_is_reverse, __pyx_k_is_reverse, sizeof(__pyx_k_is_reverse), 0, 0, 1, 1},
- {&__pyx_n_s_is_unmapped, __pyx_k_is_unmapped, sizeof(__pyx_k_is_unmapped), 0, 0, 1, 1},
{&__pyx_n_s_isdigit, __pyx_k_isdigit, sizeof(__pyx_k_isdigit), 0, 0, 1, 1},
{&__pyx_n_s_join, __pyx_k_join, sizeof(__pyx_k_join), 0, 0, 1, 1},
- {&__pyx_n_s_lengths, __pyx_k_lengths, sizeof(__pyx_k_lengths), 0, 0, 1, 1},
{&__pyx_n_s_logging, __pyx_k_logging, sizeof(__pyx_k_logging), 0, 0, 1, 1},
{&__pyx_n_s_main, __pyx_k_main, sizeof(__pyx_k_main), 0, 0, 1, 1},
{&__pyx_n_s_map, __pyx_k_map, sizeof(__pyx_k_map), 0, 0, 1, 1},
@@ -23020,13 +20418,10 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_module, __pyx_k_module, sizeof(__pyx_k_module), 0, 0, 1, 1},
{&__pyx_kp_u_ndarray_is_not_C_contiguous, __pyx_k_ndarray_is_not_C_contiguous, sizeof(__pyx_k_ndarray_is_not_C_contiguous), 0, 1, 0, 0},
{&__pyx_kp_u_ndarray_is_not_Fortran_contiguou, __pyx_k_ndarray_is_not_Fortran_contiguou, sizeof(__pyx_k_ndarray_is_not_Fortran_contiguou), 0, 1, 0, 0},
- {&__pyx_n_s_next, __pyx_k_next, sizeof(__pyx_k_next), 0, 0, 1, 1},
{&__pyx_n_s_np, __pyx_k_np, sizeof(__pyx_k_np), 0, 0, 1, 1},
{&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1},
{&__pyx_n_s_open, __pyx_k_open, sizeof(__pyx_k_open), 0, 0, 1, 1},
- {&__pyx_n_s_pos, __pyx_k_pos, sizeof(__pyx_k_pos), 0, 0, 1, 1},
{&__pyx_n_s_prepare, __pyx_k_prepare, sizeof(__pyx_k_prepare), 0, 0, 1, 1},
- {&__pyx_n_s_pysam, __pyx_k_pysam, sizeof(__pyx_k_pysam), 0, 0, 1, 1},
{&__pyx_n_s_pyx_vtable, __pyx_k_pyx_vtable, sizeof(__pyx_k_pyx_vtable), 0, 0, 1, 1},
{&__pyx_n_s_qualname, __pyx_k_qualname, sizeof(__pyx_k_qualname), 0, 0, 1, 1},
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{&__pyx_n_s_readline, __pyx_k_readline, sizeof(__pyx_k_readline), 0, 0, 1, 1},
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- {&__pyx_n_s_reset, __pyx_k_reset, sizeof(__pyx_k_reset), 0, 0, 1, 1},
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{&__pyx_n_s_rindex, __pyx_k_rindex, sizeof(__pyx_k_rindex), 0, 0, 1, 1},
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{&__pyx_n_s_rstrip, __pyx_k_rstrip, sizeof(__pyx_k_rstrip), 0, 0, 1, 1},
{&__pyx_n_s_seek, __pyx_k_seek, sizeof(__pyx_k_seek), 0, 0, 1, 1},
{&__pyx_n_s_self, __pyx_k_self, sizeof(__pyx_k_self), 0, 0, 1, 1},
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{&__pyx_n_s_sum, __pyx_k_sum, sizeof(__pyx_k_sum), 0, 0, 1, 1},
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{&__pyx_n_s_tell, __pyx_k_tell, sizeof(__pyx_k_tell), 0, 0, 1, 1},
{&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
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{&__pyx_n_s_track, __pyx_k_track, sizeof(__pyx_k_track), 0, 0, 1, 1},
{&__pyx_n_s_tsize, __pyx_k_tsize, sizeof(__pyx_k_tsize), 0, 0, 1, 1},
{&__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_k_unknown_dtype_code_in_numpy_pxd, sizeof(__pyx_k_unknown_dtype_code_in_numpy_pxd), 0, 1, 0, 0},
{&__pyx_n_s_unpack, __pyx_k_unpack, sizeof(__pyx_k_unpack), 0, 0, 1, 1},
{&__pyx_n_s_version, __pyx_k_version, sizeof(__pyx_k_version), 0, 0, 1, 1},
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__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;}
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__Pyx_GOTREF(__pyx_tuple_);
__Pyx_GIVEREF(__pyx_tuple_);
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__Pyx_GOTREF(__pyx_tuple__2);
__Pyx_GIVEREF(__pyx_tuple__2);
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__Pyx_GOTREF(__pyx_tuple__3);
__Pyx_GIVEREF(__pyx_tuple__3);
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__Pyx_GOTREF(__pyx_tuple__4);
__Pyx_GIVEREF(__pyx_tuple__4);
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__Pyx_GOTREF(__pyx_tuple__5);
__Pyx_GIVEREF(__pyx_tuple__5);
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__Pyx_GOTREF(__pyx_tuple__7);
__Pyx_GIVEREF(__pyx_tuple__7);
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__Pyx_GOTREF(__pyx_tuple__8);
__Pyx_GIVEREF(__pyx_tuple__8);
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__Pyx_GOTREF(__pyx_tuple__11);
__Pyx_GIVEREF(__pyx_tuple__11);
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__Pyx_GOTREF(__pyx_tuple__12);
__Pyx_GIVEREF(__pyx_tuple__12);
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__Pyx_GOTREF(__pyx_tuple__13);
__Pyx_GIVEREF(__pyx_tuple__13);
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+ __Pyx_GIVEREF(__pyx_tuple__16);
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- __Pyx_GOTREF(__pyx_tuple__40);
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- __Pyx_GIVEREF(__pyx_tuple__42);
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- /* "MACS2/IO/Parser.pyx":604
+ /* "MACS2/IO/Parser.pyx":709
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__Pyx_GIVEREF(__pyx_tuple__46);
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__Pyx_GOTREF(__pyx_tuple__47);
__Pyx_GIVEREF(__pyx_tuple__47);
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__Pyx_GOTREF(__pyx_tuple__48);
__Pyx_GIVEREF(__pyx_tuple__48);
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__Pyx_GIVEREF(__pyx_tuple__49);
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__Pyx_GOTREF(__pyx_tuple__50);
__Pyx_GIVEREF(__pyx_tuple__50);
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- __Pyx_GOTREF(__pyx_tuple__57);
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- __Pyx_GOTREF(__pyx_tuple__60);
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__Pyx_GOTREF(__pyx_tuple__65);
__Pyx_GIVEREF(__pyx_tuple__65);
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+ __pyx_tuple__66 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__66);
__Pyx_GIVEREF(__pyx_tuple__66);
- /* "MACS2/IO/Parser.pyx":954
+ /* "MACS2/IO/Parser.pyx":934
* while True:
* try:
* entrylength = unpack( '<i', fread( 4 ) )[ 0 ] # <<<<<<<<<<<<<<
* except struct.error:
* break
*/
- __pyx_tuple__67 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__67 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__67);
__Pyx_GIVEREF(__pyx_tuple__67);
- /* "MACS2/IO/Parser.pyx":978
+ /* "MACS2/IO/Parser.pyx":958
*
* # we skip lot of the available information in data (i.e. tag name, quality etc etc)
* if not data: return ( -1, -1, -1 ) # <<<<<<<<<<<<<<
*
* thisref = unpack( '<i', data[ 0:4 ] )[ 0 ]
*/
- __pyx_tuple__68 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 978; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__68 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__68);
__Pyx_GIVEREF(__pyx_tuple__68);
- /* "MACS2/IO/Parser.pyx":980
+ /* "MACS2/IO/Parser.pyx":960
* if not data: return ( -1, -1, -1 )
*
* thisref = unpack( '<i', data[ 0:4 ] )[ 0 ] # <<<<<<<<<<<<<<
* thisstart = unpack( '<i', data[ 4:8 ] )[ 0 ]
* (n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] )
*/
- __pyx_slice__69 = PySlice_New(__pyx_int_0, __pyx_int_4, Py_None); if (unlikely(!__pyx_slice__69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 980; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_slice__69 = PySlice_New(__pyx_int_0, __pyx_int_4, Py_None); if (unlikely(!__pyx_slice__69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_slice__69);
__Pyx_GIVEREF(__pyx_slice__69);
- /* "MACS2/IO/Parser.pyx":981
+ /* "MACS2/IO/Parser.pyx":961
*
* thisref = unpack( '<i', data[ 0:4 ] )[ 0 ]
* thisstart = unpack( '<i', data[ 4:8 ] )[ 0 ] # <<<<<<<<<<<<<<
* (n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] )
* if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
*/
- __pyx_slice__70 = PySlice_New(__pyx_int_4, __pyx_int_8, Py_None); if (unlikely(!__pyx_slice__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_slice__70 = PySlice_New(__pyx_int_4, __pyx_int_8, Py_None); if (unlikely(!__pyx_slice__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_slice__70);
__Pyx_GIVEREF(__pyx_slice__70);
- /* "MACS2/IO/Parser.pyx":982
+ /* "MACS2/IO/Parser.pyx":962
* thisref = unpack( '<i', data[ 0:4 ] )[ 0 ]
* thisstart = unpack( '<i', data[ 4:8 ] )[ 0 ]
* (n_cigar_op, bwflag ) = unpack( '<HH' , data[ 12:16 ] ) # <<<<<<<<<<<<<<
* if bwflag & 4 or bwflag & 512 or bwflag & 1024 or bwflag & 256 or bwflag & 2048:
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*/
- __pyx_slice__71 = PySlice_New(__pyx_int_12, __pyx_int_16, Py_None); if (unlikely(!__pyx_slice__71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 982; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_slice__71 = PySlice_New(__pyx_int_12, __pyx_int_16, Py_None); if (unlikely(!__pyx_slice__71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 962; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_slice__71);
__Pyx_GIVEREF(__pyx_slice__71);
- /* "MACS2/IO/Parser.pyx":984
+ /* "MACS2/IO/Parser.pyx":964
* (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 ( -1, -1, -1 ) #unmapped sequence or bad sequence or secondary or supplementary alignment # <<<<<<<<<<<<<<
* if bwflag & 1:
* # paired read. We should only keep sequence if the mate is mapped
*/
- __pyx_tuple__72 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 984; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__72 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__72);
__Pyx_GIVEREF(__pyx_tuple__72);
- /* "MACS2/IO/Parser.pyx":989
+ /* "MACS2/IO/Parser.pyx":969
* # and if this is the left mate, all is within the flag!
* if not bwflag & 2:
* return ( -1, -1, -1 ) # not a proper pair # <<<<<<<<<<<<<<
* if bwflag & 8:
* return ( -1, -1, -1 ) # the mate is unmapped
*/
- __pyx_tuple__73 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__73 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__73);
__Pyx_GIVEREF(__pyx_tuple__73);
- /* "MACS2/IO/Parser.pyx":991
+ /* "MACS2/IO/Parser.pyx":971
* return ( -1, -1, -1 ) # not a proper pair
* if bwflag & 8:
* return ( -1, -1, -1 ) # the mate is unmapped # <<<<<<<<<<<<<<
* # From Benjamin Schiller https://github.com/benjschiller
* if bwflag & 128:
*/
- __pyx_tuple__74 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 991; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__74 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__74);
__Pyx_GIVEREF(__pyx_tuple__74);
- /* "MACS2/IO/Parser.pyx":995
+ /* "MACS2/IO/Parser.pyx":975
* if bwflag & 128:
* # this is not the first read in a pair
* return ( -1, -1, -1 ) # <<<<<<<<<<<<<<
* # end of the patch
* # In case of paired-end we have now skipped all possible "bad" pairs
*/
- __pyx_tuple__75 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__75 = PyTuple_Pack(3, __pyx_int_neg_1, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__75);
__Pyx_GIVEREF(__pyx_tuple__75);
- /* "MACS2/IO/Parser.pyx":1003
+ /* "MACS2/IO/Parser.pyx":983
* if bwflag & 16:
* # read mapped to minus strand
* l_read_name = unpack( '<B', data[ 8:9 ] )[ 0 ] # <<<<<<<<<<<<<<
* # need to decipher CIGAR string
* for cigar_code in unpack( '<%dI' % (n_cigar_op) , data[ 32 + l_read_name : 32 + l_read_name + n_cigar_op*4 ] ):
*/
- __pyx_slice__76 = PySlice_New(__pyx_int_8, __pyx_int_9, Py_None); if (unlikely(!__pyx_slice__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1003; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_slice__76 = PySlice_New(__pyx_int_8, __pyx_int_9, Py_None); if (unlikely(!__pyx_slice__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_slice__76);
__Pyx_GIVEREF(__pyx_slice__76);
- /* "MACS2/IO/Parser.pyx":1151
+ /* "MACS2/IO/Parser.pyx":1048
* err = struct.error
* while True:
* try: entrylength = unpack('<i', fread(4))[0] # <<<<<<<<<<<<<<
* except err: break
* rawread = fread(32)
*/
- __pyx_tuple__77 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__77 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__77);
__Pyx_GIVEREF(__pyx_tuple__77);
- /* "MACS2/IO/Parser.pyx":1153
+ /* "MACS2/IO/Parser.pyx":1050
* try: entrylength = unpack('<i', fread(4))[0]
* except err: break
* rawread = fread(32) # <<<<<<<<<<<<<<
* # rawread = <bytes>fread(entrylength)
* read = self.__pe_binary_parse(rawread)
*/
- __pyx_tuple__78 = PyTuple_Pack(1, __pyx_int_32); if (unlikely(!__pyx_tuple__78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__78 = PyTuple_Pack(1, __pyx_int_32); if (unlikely(!__pyx_tuple__78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__78);
__Pyx_GIVEREF(__pyx_tuple__78);
- /* "MACS2/IO/Parser.pyx":1200
+ /* "MACS2/IO/Parser.pyx":1094
* err = struct.error
* while True:
* try: entrylength = unpack('<i', fread(4))[0] # <<<<<<<<<<<<<<
* except err: break
* rawread = fread(32)
*/
- __pyx_tuple__79 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__79 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_tuple__79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__79);
__Pyx_GIVEREF(__pyx_tuple__79);
- /* "MACS2/IO/Parser.pyx":1202
+ /* "MACS2/IO/Parser.pyx":1096
* try: entrylength = unpack('<i', fread(4))[0]
* except err: break
* rawread = fread(32) # <<<<<<<<<<<<<<
* # rawread = <bytes>fread(entrylength)
* read = self.__pe_binary_parse(rawread)
*/
- __pyx_tuple__80 = PyTuple_Pack(1, __pyx_int_32); if (unlikely(!__pyx_tuple__80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__80 = PyTuple_Pack(1, __pyx_int_32); if (unlikely(!__pyx_tuple__80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__80);
__Pyx_GIVEREF(__pyx_tuple__80);
- /* "MACS2/IO/Parser.pyx":1293
+ /* "MACS2/IO/Parser.pyx":1187
*
* thisline = thisline.rstrip()
* if not thisline: return ( "", -1, -1 ) # <<<<<<<<<<<<<<
* if thisline[ 0 ]=="#": return ( "", -1 , -1 ) # comment line is skipped
* thisfields = thisline.split( '\t' ) # I hope it will never bring me more trouble
*/
- __pyx_tuple__81 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__81 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__81);
__Pyx_GIVEREF(__pyx_tuple__81);
- /* "MACS2/IO/Parser.pyx":1294
+ /* "MACS2/IO/Parser.pyx":1188
* thisline = thisline.rstrip()
* if not thisline: return ( "", -1, -1 )
* if thisline[ 0 ]=="#": return ( "", -1 , -1 ) # comment line is skipped # <<<<<<<<<<<<<<
* thisfields = thisline.split( '\t' ) # I hope it will never bring me more trouble
* return len( thisfields[ 4 ] )
*/
- __pyx_tuple__82 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__82 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__82);
__Pyx_GIVEREF(__pyx_tuple__82);
- /* "MACS2/IO/Parser.pyx":1295
+ /* "MACS2/IO/Parser.pyx":1189
* if not thisline: return ( "", -1, -1 )
* if thisline[ 0 ]=="#": return ( "", -1 , -1 ) # comment line is skipped
* thisfields = thisline.split( '\t' ) # I hope it will never bring me more trouble # <<<<<<<<<<<<<<
* return len( thisfields[ 4 ] )
*
*/
- __pyx_tuple__83 = PyTuple_Pack(1, __pyx_kp_s__10); if (unlikely(!__pyx_tuple__83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__83 = PyTuple_Pack(1, __pyx_kp_s__10); if (unlikely(!__pyx_tuple__83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__83);
__Pyx_GIVEREF(__pyx_tuple__83);
- /* "MACS2/IO/Parser.pyx":1344
+ /* "MACS2/IO/Parser.pyx":1238
*
* thisline = thisline.rstrip()
* if not thisline: return ( "", -1, -1 ) # <<<<<<<<<<<<<<
* if thisline[ 0 ]=="#": return ( "", -1, -1 ) # comment line is skipped
* thisfields = thisline.split( '\t' ) # I hope it will never bring me more trouble
*/
- __pyx_tuple__84 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__84)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__84 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__84)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1238; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__84);
__Pyx_GIVEREF(__pyx_tuple__84);
- /* "MACS2/IO/Parser.pyx":1345
+ /* "MACS2/IO/Parser.pyx":1239
* thisline = thisline.rstrip()
* if not thisline: return ( "", -1, -1 )
* if thisline[ 0 ]=="#": return ( "", -1, -1 ) # comment line is skipped # <<<<<<<<<<<<<<
* thisfields = thisline.split( '\t' ) # I hope it will never bring me more trouble
*
*/
- __pyx_tuple__85 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__85 = PyTuple_Pack(3, __pyx_kp_s__6, __pyx_int_neg_1, __pyx_int_neg_1); if (unlikely(!__pyx_tuple__85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__85);
__Pyx_GIVEREF(__pyx_tuple__85);
- /* "MACS2/IO/Parser.pyx":1346
+ /* "MACS2/IO/Parser.pyx":1240
* if not thisline: return ( "", -1, -1 )
* if thisline[ 0 ]=="#": return ( "", -1, -1 ) # comment line is skipped
* thisfields = thisline.split( '\t' ) # I hope it will never bring me more trouble # <<<<<<<<<<<<<<
*
* chromname = thisfields[ 2 ]
*/
- __pyx_tuple__86 = PyTuple_Pack(1, __pyx_kp_s__10); if (unlikely(!__pyx_tuple__86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1346; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__86 = PyTuple_Pack(1, __pyx_kp_s__10); if (unlikely(!__pyx_tuple__86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__86);
__Pyx_GIVEREF(__pyx_tuple__86);
- /* "MACS2/IO/Parser.pyx":1350
+ /* "MACS2/IO/Parser.pyx":1244
* chromname = thisfields[ 2 ]
* try:
* chromname = chromname[ :chromname.rindex( ".fa" ) ] # <<<<<<<<<<<<<<
* except ValueError:
* pass
*/
- __pyx_tuple__87 = PyTuple_Pack(1, __pyx_kp_s_fa); if (unlikely(!__pyx_tuple__87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__87 = PyTuple_Pack(1, __pyx_kp_s_fa); if (unlikely(!__pyx_tuple__87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__87);
__Pyx_GIVEREF(__pyx_tuple__87);
- /* "MACS2/IO/Parser.pyx":1392
- * f = gzip.open( filename )
- * try:
- * f.read( 10 ) # <<<<<<<<<<<<<<
- * except IOError:
- * # not a gzipped file
- */
- __pyx_tuple__88 = PyTuple_Pack(1, __pyx_int_10); if (unlikely(!__pyx_tuple__88)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_tuple__88);
- __Pyx_GIVEREF(__pyx_tuple__88);
-
- /* "MACS2/IO/Parser.pyx":1430
- * n += 1
- * # done
- * self.fhd.seek( 0 ) # <<<<<<<<<<<<<<
- * self.tag_size = s/n
- * return self.tag_size
- */
- __pyx_tuple__89 = PyTuple_Pack(1, __pyx_int_0); if (unlikely(!__pyx_tuple__89)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_tuple__89);
- __Pyx_GIVEREF(__pyx_tuple__89);
-
- /* "MACS2/IO/Parser.pyx":1529
- * else:
- * if t <= 10 or t >= 10000:
- * self.fhd.seek( 0 ) # <<<<<<<<<<<<<<
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/* "numpy.pxd":215
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- __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);
+ __pyx_tuple__88 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple__88)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_tuple__88);
+ __Pyx_GIVEREF(__pyx_tuple__88);
/* "numpy.pxd":219
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
@@ -24035,9 +21368,9 @@ static int __Pyx_InitCachedConstants(void) {
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* info.buf = PyArray_DATA(self)
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- __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);
+ __pyx_tuple__89 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__89)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __Pyx_GIVEREF(__pyx_tuple__89);
/* "numpy.pxd":257
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@@ -24046,9 +21379,9 @@ static int __Pyx_InitCachedConstants(void) {
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- __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);
+ __pyx_tuple__90 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__90)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_tuple__90);
+ __Pyx_GIVEREF(__pyx_tuple__90);
/* "numpy.pxd":799
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@@ -24057,9 +21390,9 @@ static int __Pyx_InitCachedConstants(void) {
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- __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);
+ __pyx_tuple__91 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__91)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __Pyx_GIVEREF(__pyx_tuple__91);
/* "numpy.pxd":803
* if ((child.byteorder == c'>' and little_endian) or
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- __Pyx_GOTREF(__pyx_tuple__97);
- __Pyx_GIVEREF(__pyx_tuple__97);
+ __pyx_tuple__92 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__92)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __Pyx_GIVEREF(__pyx_tuple__92);
/* "numpy.pxd":823
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@@ -24079,33 +21412,33 @@ static int __Pyx_InitCachedConstants(void) {
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- __Pyx_GOTREF(__pyx_tuple__98);
- __Pyx_GIVEREF(__pyx_tuple__98);
+ __pyx_tuple__93 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__93)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_tuple__93);
+ __Pyx_GIVEREF(__pyx_tuple__93);
- /* "MACS2/IO/Parser.pyx":113
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+ __pyx_tuple__95 = PyTuple_Pack(3, __pyx_n_s_self, __pyx_n_s_string, __pyx_n_s_strand); if (unlikely(!__pyx_tuple__95)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_tuple__95);
+ __Pyx_GIVEREF(__pyx_tuple__95);
+ __pyx_codeobj__96 = (PyObject*)__Pyx_PyCode_New(3, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__95, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_init, 104, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__96)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "MACS2/IO/Parser.pyx":117
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+ __pyx_tuple__97 = PyTuple_Pack(1, __pyx_n_s_self); if (unlikely(!__pyx_tuple__97)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __Pyx_GIVEREF(__pyx_tuple__97);
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__pyx_L1_error:;
@@ -24146,9 +21479,6 @@ PyMODINIT_FUNC PyInit_Parser(void)
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -24228,11 +21558,11 @@ PyMODINIT_FUNC PyInit_Parser(void)
__pyx_vtable_5MACS2_2IO_6Parser_GenericParser.__pyx___fw_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_13GenericParser___fw_parse_line;
__pyx_vtable_5MACS2_2IO_6Parser_GenericParser.sniff = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, int __pyx_skip_dispatch))__pyx_f_5MACS2_2IO_6Parser_13GenericParser_sniff;
__pyx_vtable_5MACS2_2IO_6Parser_GenericParser.close = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, int __pyx_skip_dispatch))__pyx_f_5MACS2_2IO_6Parser_13GenericParser_close;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_GenericParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_GenericParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6Parser_GenericParser.tp_print = 0;
#if CYTHON_COMPILING_IN_CPYTHON
{
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+ PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_5MACS2_2IO_6Parser_GenericParser, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_5MACS2_2IO_6Parser_13GenericParser___init__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_5MACS2_2IO_6Parser_13GenericParser___init__.doc = __pyx_doc_5MACS2_2IO_6Parser_13GenericParser___init__;
@@ -24240,58 +21570,69 @@ PyMODINIT_FUNC PyInit_Parser(void)
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- if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_GenericParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_GenericParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "GenericParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_GenericParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_GenericParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_GenericParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "GenericParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_GenericParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6Parser_GenericParser = &__pyx_type_5MACS2_2IO_6Parser_GenericParser;
__pyx_vtabptr_5MACS2_2IO_6Parser_BEDParser = &__pyx_vtable_5MACS2_2IO_6Parser_BEDParser;
__pyx_vtable_5MACS2_2IO_6Parser_BEDParser.__pyx_base = *__pyx_vtabptr_5MACS2_2IO_6Parser_GenericParser;
__pyx_vtable_5MACS2_2IO_6Parser_BEDParser.__pyx_base.__pyx___tlen_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_9BEDParser___tlen_parse_line;
__pyx_vtable_5MACS2_2IO_6Parser_BEDParser.__pyx_base.__pyx___fw_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_9BEDParser___fw_parse_line;
__pyx_type_5MACS2_2IO_6Parser_BEDParser.tp_base = __pyx_ptype_5MACS2_2IO_6Parser_GenericParser;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BEDParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BEDParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6Parser_BEDParser.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_BEDParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_BEDParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "BEDParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BEDParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_BEDParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_BEDParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "BEDParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BEDParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6Parser_BEDParser = &__pyx_type_5MACS2_2IO_6Parser_BEDParser;
+ __pyx_vtabptr_5MACS2_2IO_6Parser_BEDPEParser = &__pyx_vtable_5MACS2_2IO_6Parser_BEDPEParser;
+ __pyx_vtable_5MACS2_2IO_6Parser_BEDPEParser.__pyx_base = *__pyx_vtabptr_5MACS2_2IO_6Parser_GenericParser;
+ __pyx_vtable_5MACS2_2IO_6Parser_BEDPEParser.__pyx___pe_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_11BEDPEParser___pe_parse_line;
+ __pyx_vtable_5MACS2_2IO_6Parser_BEDPEParser.build_petrack = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *, int __pyx_skip_dispatch))__pyx_f_5MACS2_2IO_6Parser_11BEDPEParser_build_petrack;
+ __pyx_vtable_5MACS2_2IO_6Parser_BEDPEParser.append_petrack = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BEDPEParser *, PyObject *, int __pyx_skip_dispatch))__pyx_f_5MACS2_2IO_6Parser_11BEDPEParser_append_petrack;
+ __pyx_type_5MACS2_2IO_6Parser_BEDPEParser.tp_base = __pyx_ptype_5MACS2_2IO_6Parser_GenericParser;
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BEDPEParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_type_5MACS2_2IO_6Parser_BEDPEParser.tp_print = 0;
+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_BEDPEParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_BEDPEParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "BEDPEParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BEDPEParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5MACS2_2IO_6Parser_BEDPEParser = &__pyx_type_5MACS2_2IO_6Parser_BEDPEParser;
__pyx_vtabptr_5MACS2_2IO_6Parser_ELANDResultParser = &__pyx_vtable_5MACS2_2IO_6Parser_ELANDResultParser;
__pyx_vtable_5MACS2_2IO_6Parser_ELANDResultParser.__pyx_base = *__pyx_vtabptr_5MACS2_2IO_6Parser_GenericParser;
__pyx_vtable_5MACS2_2IO_6Parser_ELANDResultParser.__pyx_base.__pyx___tlen_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_17ELANDResultParser___tlen_parse_line;
__pyx_vtable_5MACS2_2IO_6Parser_ELANDResultParser.__pyx_base.__pyx___fw_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_17ELANDResultParser___fw_parse_line;
__pyx_type_5MACS2_2IO_6Parser_ELANDResultParser.tp_base = __pyx_ptype_5MACS2_2IO_6Parser_GenericParser;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_ELANDResultParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_ELANDResultParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 459; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6Parser_ELANDResultParser.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_ELANDResultParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_ELANDResultParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "ELANDResultParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_ELANDResultParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_ELANDResultParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_ELANDResultParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 459; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "ELANDResultParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_ELANDResultParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 459; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6Parser_ELANDResultParser = &__pyx_type_5MACS2_2IO_6Parser_ELANDResultParser;
__pyx_vtabptr_5MACS2_2IO_6Parser_ELANDMultiParser = &__pyx_vtable_5MACS2_2IO_6Parser_ELANDMultiParser;
__pyx_vtable_5MACS2_2IO_6Parser_ELANDMultiParser.__pyx_base = *__pyx_vtabptr_5MACS2_2IO_6Parser_GenericParser;
__pyx_vtable_5MACS2_2IO_6Parser_ELANDMultiParser.__pyx_base.__pyx___tlen_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_16ELANDMultiParser___tlen_parse_line;
__pyx_vtable_5MACS2_2IO_6Parser_ELANDMultiParser.__pyx_base.__pyx___fw_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_16ELANDMultiParser___fw_parse_line;
__pyx_type_5MACS2_2IO_6Parser_ELANDMultiParser.tp_base = __pyx_ptype_5MACS2_2IO_6Parser_GenericParser;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_ELANDMultiParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 406; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_ELANDMultiParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6Parser_ELANDMultiParser.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_ELANDMultiParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_ELANDMultiParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 406; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "ELANDMultiParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_ELANDMultiParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 406; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_ELANDMultiParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_ELANDMultiParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "ELANDMultiParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_ELANDMultiParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6Parser_ELANDMultiParser = &__pyx_type_5MACS2_2IO_6Parser_ELANDMultiParser;
__pyx_vtabptr_5MACS2_2IO_6Parser_ELANDExportParser = &__pyx_vtable_5MACS2_2IO_6Parser_ELANDExportParser;
__pyx_vtable_5MACS2_2IO_6Parser_ELANDExportParser.__pyx_base = *__pyx_vtabptr_5MACS2_2IO_6Parser_GenericParser;
__pyx_vtable_5MACS2_2IO_6Parser_ELANDExportParser.__pyx_base.__pyx___tlen_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_17ELANDExportParser___tlen_parse_line;
__pyx_vtable_5MACS2_2IO_6Parser_ELANDExportParser.__pyx_base.__pyx___fw_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_17ELANDExportParser___fw_parse_line;
__pyx_type_5MACS2_2IO_6Parser_ELANDExportParser.tp_base = __pyx_ptype_5MACS2_2IO_6Parser_GenericParser;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_ELANDExportParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_ELANDExportParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6Parser_ELANDExportParser.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_ELANDExportParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_ELANDExportParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "ELANDExportParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_ELANDExportParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_ELANDExportParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_ELANDExportParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "ELANDExportParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_ELANDExportParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6Parser_ELANDExportParser = &__pyx_type_5MACS2_2IO_6Parser_ELANDExportParser;
__pyx_vtabptr_5MACS2_2IO_6Parser_SAMParser = &__pyx_vtable_5MACS2_2IO_6Parser_SAMParser;
__pyx_vtable_5MACS2_2IO_6Parser_SAMParser.__pyx_base = *__pyx_vtabptr_5MACS2_2IO_6Parser_GenericParser;
__pyx_vtable_5MACS2_2IO_6Parser_SAMParser.__pyx_base.__pyx___tlen_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_9SAMParser___tlen_parse_line;
__pyx_vtable_5MACS2_2IO_6Parser_SAMParser.__pyx_base.__pyx___fw_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_9SAMParser___fw_parse_line;
__pyx_type_5MACS2_2IO_6Parser_SAMParser.tp_base = __pyx_ptype_5MACS2_2IO_6Parser_GenericParser;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_SAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_SAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6Parser_SAMParser.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_SAMParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_SAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "SAMParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_SAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_SAMParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_SAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "SAMParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_SAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6Parser_SAMParser = &__pyx_type_5MACS2_2IO_6Parser_SAMParser;
__pyx_vtabptr_5MACS2_2IO_6Parser_BAMParser = &__pyx_vtable_5MACS2_2IO_6Parser_BAMParser;
__pyx_vtable_5MACS2_2IO_6Parser_BAMParser.__pyx_base = *__pyx_vtabptr_5MACS2_2IO_6Parser_GenericParser;
@@ -24300,19 +21641,13 @@ PyMODINIT_FUNC PyInit_Parser(void)
__pyx_vtable_5MACS2_2IO_6Parser_BAMParser.__pyx_base.append_fwtrack = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *, int __pyx_skip_dispatch))__pyx_f_5MACS2_2IO_6Parser_9BAMParser_append_fwtrack;
__pyx_vtable_5MACS2_2IO_6Parser_BAMParser.__pyx_base.sniff = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, int __pyx_skip_dispatch))__pyx_f_5MACS2_2IO_6Parser_9BAMParser_sniff;
__pyx_vtable_5MACS2_2IO_6Parser_BAMParser.get_references = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *, int __pyx_skip_dispatch))__pyx_f_5MACS2_2IO_6Parser_9BAMParser_get_references;
- __pyx_vtable_5MACS2_2IO_6Parser_BAMParser.__pyx___get_references_w_pysam = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *))__pyx_f_5MACS2_2IO_6Parser_9BAMParser___get_references_w_pysam;
- __pyx_vtable_5MACS2_2IO_6Parser_BAMParser.__pyx___get_references_wo_pysam = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *))__pyx_f_5MACS2_2IO_6Parser_9BAMParser___get_references_wo_pysam;
- __pyx_vtable_5MACS2_2IO_6Parser_BAMParser.__pyx___build_fwtrack_w_pysam = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *))__pyx_f_5MACS2_2IO_6Parser_9BAMParser___build_fwtrack_w_pysam;
- __pyx_vtable_5MACS2_2IO_6Parser_BAMParser.__pyx___build_fwtrack_wo_pysam = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *))__pyx_f_5MACS2_2IO_6Parser_9BAMParser___build_fwtrack_wo_pysam;
- __pyx_vtable_5MACS2_2IO_6Parser_BAMParser.__pyx___append_fwtrack_w_pysam = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_9BAMParser___append_fwtrack_w_pysam;
- __pyx_vtable_5MACS2_2IO_6Parser_BAMParser.__pyx___append_fwtrack_wo_pysam = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_9BAMParser___append_fwtrack_wo_pysam;
- __pyx_vtable_5MACS2_2IO_6Parser_BAMParser.__pyx___fw_binary_parse_wo_pysam = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_9BAMParser___fw_binary_parse_wo_pysam;
+ __pyx_vtable_5MACS2_2IO_6Parser_BAMParser.__pyx___fw_binary_parse = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_9BAMParser___fw_binary_parse;
__pyx_type_5MACS2_2IO_6Parser_BAMParser.tp_base = __pyx_ptype_5MACS2_2IO_6Parser_GenericParser;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6Parser_BAMParser.tp_print = 0;
#if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BAMParser, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BAMParser, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_5MACS2_2IO_6Parser_9BAMParser___init__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_5MACS2_2IO_6Parser_9BAMParser___init__.doc = __pyx_doc_5MACS2_2IO_6Parser_9BAMParser___init__;
@@ -24320,51 +21655,30 @@ PyMODINIT_FUNC PyInit_Parser(void)
}
}
#endif
- if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_BAMParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_BAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "BAMParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_BAMParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_BAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "BAMParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BAMParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6Parser_BAMParser = &__pyx_type_5MACS2_2IO_6Parser_BAMParser;
__pyx_vtabptr_5MACS2_2IO_6Parser_BAMPEParser = &__pyx_vtable_5MACS2_2IO_6Parser_BAMPEParser;
__pyx_vtable_5MACS2_2IO_6Parser_BAMPEParser.__pyx_base = *__pyx_vtabptr_5MACS2_2IO_6Parser_BAMParser;
__pyx_vtable_5MACS2_2IO_6Parser_BAMPEParser.build_petrack = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *, int __pyx_skip_dispatch))__pyx_f_5MACS2_2IO_6Parser_11BAMPEParser_build_petrack;
- __pyx_vtable_5MACS2_2IO_6Parser_BAMPEParser.__pyx___build_petrack_w_pysam = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *))__pyx_f_5MACS2_2IO_6Parser_11BAMPEParser___build_petrack_w_pysam;
- __pyx_vtable_5MACS2_2IO_6Parser_BAMPEParser.__pyx___build_petrack_wo_pysam = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *))__pyx_f_5MACS2_2IO_6Parser_11BAMPEParser___build_petrack_wo_pysam;
__pyx_vtable_5MACS2_2IO_6Parser_BAMPEParser.append_petrack = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *, PyObject *, int __pyx_skip_dispatch))__pyx_f_5MACS2_2IO_6Parser_11BAMPEParser_append_petrack;
__pyx_vtable_5MACS2_2IO_6Parser_BAMPEParser.__pyx___pe_binary_parse = (struct __pyx_t_5MACS2_2IO_6Parser__BAMPEParsed (*)(struct __pyx_obj_5MACS2_2IO_6Parser_BAMPEParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_11BAMPEParser___pe_binary_parse;
__pyx_type_5MACS2_2IO_6Parser_BAMPEParser.tp_base = __pyx_ptype_5MACS2_2IO_6Parser_BAMParser;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BAMPEParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1014; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BAMPEParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6Parser_BAMPEParser.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_BAMPEParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_BAMPEParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1014; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "BAMPEParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BAMPEParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1014; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_BAMPEParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_BAMPEParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "BAMPEParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BAMPEParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6Parser_BAMPEParser = &__pyx_type_5MACS2_2IO_6Parser_BAMPEParser;
__pyx_vtabptr_5MACS2_2IO_6Parser_BowtieParser = &__pyx_vtable_5MACS2_2IO_6Parser_BowtieParser;
__pyx_vtable_5MACS2_2IO_6Parser_BowtieParser.__pyx_base = *__pyx_vtabptr_5MACS2_2IO_6Parser_GenericParser;
__pyx_vtable_5MACS2_2IO_6Parser_BowtieParser.__pyx_base.__pyx___tlen_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_12BowtieParser___tlen_parse_line;
__pyx_vtable_5MACS2_2IO_6Parser_BowtieParser.__pyx_base.__pyx___fw_parse_line = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_6Parser_GenericParser *, PyObject *))__pyx_f_5MACS2_2IO_6Parser_12BowtieParser___fw_parse_line;
__pyx_type_5MACS2_2IO_6Parser_BowtieParser.tp_base = __pyx_ptype_5MACS2_2IO_6Parser_GenericParser;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BowtieParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6Parser_BowtieParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6Parser_BowtieParser.tp_print = 0;
- if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_BowtieParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_BowtieParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "BowtieParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BowtieParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6Parser_BowtieParser.tp_dict, __pyx_vtabptr_5MACS2_2IO_6Parser_BowtieParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "BowtieParser", (PyObject *)&__pyx_type_5MACS2_2IO_6Parser_BowtieParser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6Parser_BowtieParser = &__pyx_type_5MACS2_2IO_6Parser_BowtieParser;
- __pyx_vtabptr_5MACS2_2IO_6Parser_PySAMParser = &__pyx_vtable_5MACS2_2IO_6Parser_PySAMParser;
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+ __Pyx_GOTREF(__pyx_t_2);
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+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "numpy.pxd":975
* arr.base = baseptr
@@ -24746,8 +21967,8 @@ PyMODINIT_FUNC PyInit_Parser(void)
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_4);
if (__pyx_m) {
if (__pyx_d) {
__Pyx_AddTraceback("init MACS2.IO.Parser", __pyx_clineno, __pyx_lineno, __pyx_filename);
@@ -25628,6 +22849,12 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
+static CYTHON_INLINE long __Pyx_mod_long(long a, long b) {
+ long r = a % b;
+ r += ((r != 0) & ((r ^ b) < 0)) * b;
+ return r;
+}
+
static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
diff --git a/MACS2/IO/Parser.pyx b/MACS2/IO/Parser.pyx
index 9ebf665..bd0b5f7 100644
--- a/MACS2/IO/Parser.pyx
+++ b/MACS2/IO/Parser.pyx
@@ -1,4 +1,4 @@
-# Time-stamp: <2015-08-14 14:29:30 Tao Liu>
+# Time-stamp: <2016-02-15 16:02:11 Tao Liu>
"""Module for all MACS Parser classes for input.
@@ -27,16 +27,6 @@ from MACS2.Constants import *
from MACS2.IO.FixWidthTrack import FWTrack
from MACS2.IO.PairedEndTrack import PETrackI
-cdef public bint HAS_PYSAM
-
-try:
- import pysam
- HAS_PYSAM = True
-except:
- HAS_PYSAM = False
-
-HAS_PYSAM=False
-
from cpython cimport bool
import numpy as np
@@ -66,6 +56,7 @@ __doc__ = "All Parser classes"
# ------------------------------------
cpdef guess_parser ( fhd, long buffer_size = 100000 ):
+ # Note: BAMPE and BEDPE can't be automatically detected.
order_list = ("BAM",
"BED",
"ELAND",
@@ -298,11 +289,11 @@ cdef class GenericParser:
self.fhd.close()
cdef class BEDParser( GenericParser ):
- """File Parser Class for tabular File.
+ """File Parser Class for BED File.
"""
cdef __tlen_parse_line ( self, str thisline ):
- """Parse 5' and 3' position, then calculate tag length.
+ """Parse 5' and 3' position, then calculate frag length.
"""
thisline = thisline.rstrip()
@@ -350,6 +341,120 @@ cdef class BEDParser( GenericParser ):
return ( chromname,
atoi( thisfields[ 1 ] ),
0 )
+
+cdef class BEDPEParser(GenericParser):
+ """Parser for BED format file containing PE information, and also
+ can be used for the cases when users predefine the fragment
+ locations by shifting/extending by themselves.
+
+ Format:
+
+ chromosome_name frag_leftend frag_rightend
+
+
+ Note: Only the first columns are used!
+ """
+
+ cdef public int n
+ cdef public int d
+
+ cdef __pe_parse_line ( self, str thisline ):
+ """ Parse each line, and return chromosome, left and right positions
+
+ """
+ thisline = thisline.rstrip()
+
+ # skip track/browser/comment lines
+ if not thisline or thisline[ :5 ] == "track" \
+ or thisline[ :7 ] == "browser" \
+ or thisline[ 0 ] == "#":
+ return ( "", -1, -1 )
+
+ # still only support tabular as delimiter.
+ thisfields = thisline.split( '\t' )
+ try:
+ return ( thisfields[ 0 ],
+ atoi( thisfields[ 1 ] ),
+ atoi( thisfields[ 2 ] ) )
+ except IndexError:
+ raise Exception("Less than 3 columns found at this line: %s\n" % thisline)
+
+ cpdef build_petrack ( self ):
+ """Build PETrackI from all lines.
+
+ """
+ cdef:
+ str chromname
+ int left_pos
+ int right_pos
+ long i = 0
+ long m = 0
+ float d = 0 # the average fragment size
+
+ petrack = PETrackI( buffer_size = self.buffer_size )
+ add_loc = petrack.add_loc
+
+ for thisline in self.fhd:
+ ( chromosome, left_pos, right_pos ) = self.__pe_parse_line( thisline )
+ if left_pos < 0 or not chromosome:
+ continue
+
+ assert right_pos > left_pos, "Right position must be larger than left position, check your BED file at line: %s" % thisline
+ d = ( d * i + right_pos-left_pos ) / ( i + 1 ) # keep track of avg fragment size
+ i += 1
+
+ if i % 1000000 == 0:
+ m += 1
+ logging.info( " %d" % ( m*1000000 ) )
+
+ add_loc( chromosome, left_pos, right_pos )
+
+ self.n = i
+ self.d = int( d )
+
+ assert d >= 0, "Something went wrong (mean fragment size was negative)"
+
+ self.close()
+ petrack.set_rlengths( {"DUMMYCHROM":0} )
+ return petrack
+
+ cpdef append_petrack (self, petrack):
+ """Build PETrackI from all lines, return a PETrackI object.
+ """
+ cdef:
+ str chromname
+ int left_pos
+ int right_pos
+ long i = 0
+ long m = 0
+ float d = 0 # the average fragment size
+
+ add_loc = petrack.add_loc
+
+ for thisline in self.fhd:
+ ( chromosome, left_pos, right_pos ) = self.__pe_parse_line( thisline )
+
+ if left_pos < 0 or not chromosome:
+ continue
+
+ assert right_pos > left_pos, "Right position must be larger than left position, check your BED file at line: %s" % thisline
+ d = ( d * i + right_pos-left_pos ) / ( i + 1 ) # keep track of avg fragment size
+ i += 1
+
+ if i % 1000000 == 0:
+ m += 1
+ logging.info( " %d" % ( m*1000000 ) )
+
+ add_loc( chromosome, left_pos, righ_pos )
+
+ self.d = int( self.d * self.n + d * i )/( self.n + i )
+ self.n += i
+
+ assert d >= 0, "Something went wrong (mean fragment size was negative)"
+
+ self.close()
+ petrack.set_rlengths( {"DUMMYCHROM":0} )
+ return petrack
cdef class ELANDResultParser( GenericParser ):
"""File Parser Class for tabular File.
@@ -663,48 +768,37 @@ cdef class BAMParser( GenericParser ):
self.gzipped = True
self.tag_size = -1
self.buffer_size = buffer_size
- if HAS_PYSAM:
- self.fhd = pysam.Samfile(filename)
+ # try gzip first
+ f = gzip.open( filename )
+ try:
+ f.read( 10 )
+ except IOError:
+ # not a gzipped file
+ self.gzipped = False
+ f.close()
+ if self.gzipped:
+ # open with gzip.open, then wrap it with BufferedReader!
+ self.fhd = io.BufferedReader( gzip.open( filename, mode='rb' ) )
else:
- # try gzip first
- f = gzip.open( filename )
- try:
- f.read( 10 )
- except IOError:
- # not a gzipped file
- self.gzipped = False
- f.close()
- if self.gzipped:
- # open with gzip.open, then wrap it with BufferedReader!
- self.fhd = io.BufferedReader( gzip.open( filename, mode='rb' ) )
- else:
- self.fhd = io.open( filename, mode='rb' ) # binary mode! I don't expect unicode here!
+ self.fhd = io.open( filename, mode='rb' ) # binary mode! I don't expect unicode here!
cpdef sniff( self ):
"""Check the first 3 bytes of BAM file. If it's 'BAM', check
is success.
"""
- if HAS_PYSAM:
- try:
- self.fhd.tell()
- except:
- return False
- else:
+ magic_header = self.fhd.read( 3 )
+ if magic_header == "BAM":
+ tsize = self.tsize()
+ if tsize > 0:
+ self.fhd.seek( 0 )
return True
- else:
- magic_header = self.fhd.read( 3 )
- if magic_header == "BAM":
- tsize = self.tsize()
- if tsize > 0:
- self.fhd.seek( 0 )
- return True
- else:
- self.fhd.seek( 0 )
- raise Exception( "File is not of a valid BAM format! %d" % tsize )
else:
self.fhd.seek( 0 )
- return False
+ raise Exception( "File is not of a valid BAM format! %d" % tsize )
+ else:
+ self.fhd.seek( 0 )
+ return False
cpdef int tsize ( self ):
"""Get tag size from BAM file -- read l_seq field.
@@ -750,27 +844,6 @@ cdef class BAMParser( GenericParser ):
return self.tag_size
cpdef tuple get_references( self ):
- if HAS_PYSAM:
- return self.__get_references_w_pysam()
- else:
- return self.__get_references_wo_pysam()
-
- cdef tuple __get_references_w_pysam( self ):
- """
- read in references from BAM header
-
- return a tuple (references (list of names),
- rlengths (dict of lengths)
- """
- cdef:
- list references = []
- dict rlengths = {}
-
- references = list(self.fhd.references)
- rlengths = dict( zip( references, self.fhd.lengths ) )
- return (references, rlengths)
-
- cdef tuple __get_references_wo_pysam( self ):
"""
read in references from BAM header
@@ -803,55 +876,6 @@ cdef class BAMParser( GenericParser ):
return (references, rlengths)
cpdef build_fwtrack ( self ):
- try:
- if HAS_PYSAM:
- return self.__build_fwtrack_w_pysam()
- else:
- return self.__build_fwtrack_wo_pysam()
- except IOError:
- logging.error( "BAM files might be corrupted!" )
- sys.exit(0)
-
-
- cdef __build_fwtrack_w_pysam ( self ): # obsolete function
- cdef:
- int i = 0
- int m = 0
- int fpos, strand, chrid
- list references
- dict rlengths
-
- fwtrack = FWTrack( buffer_size = self.buffer_size )
- self.fhd.reset()
- references, rlengths = self.get_references()
- while True:
- try:
- a = self.fhd.next()
- except StopIteration:
- break
- chrid = a.tid
- if a.is_unmapped or (a.is_paired and (not a.is_proper_pair or a.is_read2)):
- fpos = -1
- else:
- if a.is_reverse:
- strand = 1 # minus strand
- fpos = a.aend # rightmost position
- else:
- strand = 0 # plus strand
- fpos = a.pos
- i+=1
- if i == 1000000:
- m += 1
- logging.info( " %d" % ( m*1000000 ) )
- i = 0
- if fpos >= 0:
- fwtrack.add_loc( references[ chrid ], fpos, strand )
- self.fhd.close()
- fwtrack.finalize()
- fwtrack.set_rlengths( rlengths )
- return fwtrack
-
- cdef __build_fwtrack_wo_pysam ( self ):
"""Build FWTrack from all lines, return a FWTrack object.
Note only the unique match for a tag is kept.
@@ -874,7 +898,7 @@ cdef class BAMParser( GenericParser ):
entrylength = unpack( '<i', fread( 4 ) )[ 0 ]
except struct.error:
break
- ( chrid, fpos, strand ) = self.__fw_binary_parse_wo_pysam( fread( entrylength ) )
+ ( chrid, fpos, strand ) = self.__fw_binary_parse( fread( entrylength ) )
i+=1
if i == 1000000:
m += 1
@@ -889,50 +913,6 @@ cdef class BAMParser( GenericParser ):
return fwtrack
cpdef append_fwtrack ( self, fwtrack ):
- if HAS_PYSAM:
- return self.__append_fwtrack_w_pysam( fwtrack )
- else:
- return self.__append_fwtrack_wo_pysam( fwtrack )
-
- cdef __append_fwtrack_w_pysam ( self, fwtrack ): # obsolete function
- cdef:
- int i = 0
- int m = 0
- int fpos, strand, chrid
- list references
- dict rlengths
-
- self.fhd.reset()
- references, rlengths = self.get_references()
- while True:
- try:
- a = self.fhd.next()
- except StopIteration:
- break
- chrid = a.tid
- if a.is_unmapped or (a.is_paired and (not a.is_proper_pair or a.is_read2)):
- fpos = -1
- else:
- if a.is_reverse:
- strand = 1 # minus strand
- fpos = a.aend # rightmost position
- else:
- strand = 0 # plus strand
- fpos = a.pos
- i+=1
- if i == 1000000:
- m += 1
- logging.info( " %d" % ( m*1000000 ) )
- i = 0
- if fpos >= 0:
- fwtrack.add_loc( references[ chrid ], fpos, strand )
- self.fhd.close()
- fwtrack.finalize()
- if isinstance( fwtrack.rlengths, dict ):
- fwtrack.set_rlengths(rlengths)
- return fwtrack
-
- cdef __append_fwtrack_wo_pysam ( self, fwtrack ):
"""Build FWTrack from all lines, return a FWTrack object.
Note only the unique match for a tag is kept.
@@ -954,7 +934,7 @@ cdef class BAMParser( GenericParser ):
entrylength = unpack( '<i', fread( 4 ) )[ 0 ]
except struct.error:
break
- ( chrid, fpos, strand ) = self.__fw_binary_parse_wo_pysam( fread( entrylength ) )
+ ( chrid, fpos, strand ) = self.__fw_binary_parse( fread( entrylength ) )
i+=1
if i == 1000000:
m += 1
@@ -968,7 +948,7 @@ cdef class BAMParser( GenericParser ):
fwtrack.set_rlengths( rlengths )
return fwtrack
- cdef tuple __fw_binary_parse_wo_pysam (self, data ):
+ cdef tuple __fw_binary_parse (self, data ):
cdef:
int thisref, thisstart, thisstrand, i
short bwflag, l_read_name, n_cigar_op
@@ -1035,97 +1015,14 @@ cdef class BAMPEParser(BAMParser):
512 does not pass quality check
1024 PCR or optical duplicate
"""
- cdef public int n
- cdef public int d
+ cdef public int n # total number of fragments
+ cdef public int d # the average length of fragments in integar
cpdef build_petrack ( self ):
- if HAS_PYSAM:
- return self.__build_petrack_w_pysam()
- else:
- return self.__build_petrack_wo_pysam()
-
- cdef __build_petrack_w_pysam ( self ):
- return
-# cdef:
-# int i = 0
-# int m = 0
-# int entrylength, fpos, chrid, tlen
-# int *asint
-# list references
-# dict rlengths
-# float d = 0.0
-# char *rawread, *rawentrylength
-# _BAMPEParsed read
-
-# petrack = PETrackI()
-# self.fhd.reset()
-
-# references, rlengths = self.get_references()
-# while True:
-# try:
-# a = self.fhd.next()
-# except StopIteration:
-# break
-# chrid = a.tid
-# if a.is_paired:
-# # not from paired-end sequencing? Pass
-
-# if a.is_unmapped or (a.is_paired and (not a.is_proper_pair or a.is_read2)):
-# fpos = -1
-# else:
-# if a.is_reverse:
-# strand = 1 # minus strand
-# fpos = a.pos + a.rlen # rightmost position
-# else:
-# strand = 0 # plus strand
-# fpos = a.pos
-# i+=1
-# if i == 1000000:
-# m += 1
-# logging.info( " %d" % ( m*1000000 ) )
-# i = 0
-# if fpos >= 0:
-# fwtrack.add_loc( references[ chrid ], fpos, strand )
-# self.fhd.close()
-# fwtrack.finalize()
-# fwtrack.set_rlengths( rlengths )
-# return fwtrack
-
-
-# # for convenience, only count valid pairs
-# add_loc = petrack.add_loc
-# info = logging.info
-# err = struct.error
-# while True:
-# try: entrylength = unpack('<i', fread(4))[0]
-# except err: break
-# rawread = <bytes>fread(32)
-# # rawread = <bytes>fread(entrylength)
-# read = self.__pe_binary_parse(rawread)
-# fseek(entrylength - 32, 1)
-# if read.ref == -1: continue
-# d = (d * i + abs(read.tlen)) / (i + 1) # keep track of avg fragment size
-# i+=1
-
-# if i == 1000000:
-# m += 1
-# info(" %d" % (m*1000000))
-# i=0
-# petrack.add_loc(references[read.ref], read.start, read.start + read.tlen)
-# self.n = m * 1000000 + i
-# self.d = int(d)
-# assert d >= 0, "Something went wrong (mean fragment size was negative)"
-# self.fhd.close()
-# petrack.finalize()
-# petrack.set_rlengths( rlengths )
-# return petrack
-
-
- cdef __build_petrack_wo_pysam ( self ):
"""Build PETrackI from all lines, return a FWTrack object.
"""
cdef:
- int i = 0
+ long i = 0
int m = 0
int entrylength, fpos, chrid, tlen
int *asint
@@ -1156,19 +1053,16 @@ cdef class BAMPEParser(BAMParser):
fseek(entrylength - 32, 1)
if read.ref == -1: continue
d = (d * i + abs(read.tlen)) / (i + 1) # keep track of avg fragment size
- i+=1
+ i += 1
- if i == 1000000:
+ if i % 1000000 == 0:
m += 1
info(" %d" % (m*1000000))
- i=0
add_loc(references[read.ref], read.start, read.start + read.tlen)
- self.n = m * 1000000 + i
+ self.n = i
self.d = int(d)
assert d >= 0, "Something went wrong (mean fragment size was negative)"
self.fhd.close()
- # this is the problematic part. If fwtrack is finalized, then it's impossible to increase the length of it in a step of buffer_size for multiple input files.
- # petrack.finalize()
petrack.set_rlengths( rlengths )
return petrack
@@ -1176,7 +1070,7 @@ cdef class BAMPEParser(BAMParser):
"""Build PETrackI from all lines, return a PETrackI object.
"""
cdef:
- int i = 0
+ long i = 0
int m = 0
int entrylength, fpos, chrid, tlen
int *asint
@@ -1211,8 +1105,8 @@ cdef class BAMPEParser(BAMParser):
info(" %d" % (m*1000000))
i=0
add_loc(references[read.ref], read.start, read.start + read.tlen)
- self.n = m * 1000000 + i
- self.d = int(d)
+ self.d = int( self.d * self.n + d * i )/( self.n + i )
+ self.n += i
assert d >= 0, "Something went wrong (mean fragment size was negative)"
self.fhd.close()
# this is the problematic part. If fwtrack is finalized, then it's impossible to increase the length of it in a step of buffer_size for multiple input files.
@@ -1362,179 +1256,3 @@ cdef class BowtieParser( GenericParser ):
else:
raise StrandFormatError( thisline, thisfields[ 1 ] )
-cdef class PySAMParser:
- """Parser using PySAM to parse SAM or BAM
-
- """
- cdef str filename
- cdef bool gzipped
- cdef int tag_size
- cdef object fhd
-
- def __init__ ( self, str filename, long buffer_size = 100000 ):
- """Open input file. Determine whether it's a gzipped file.
-
- 'filename' must be a string object.
-
- This function initialize the following attributes:
-
- 1. self.filename: the filename for input file.
- 2. self.gzipped: a boolean indicating whether input file is gzipped.
- 3. self.fhd: buffered I/O stream of input file
- """
- self.filename = filename
- self.gzipped = True
- self.tag_size = -1
- self.buffer_size = buffer_size
- # try gzip first
- f = gzip.open( filename )
- try:
- f.read( 10 )
- except IOError:
- # not a gzipped file
- self.gzipped = False
- f.close()
- if self.gzipped:
- # open with gzip.open, then wrap it with BufferedReader!
- self.fhd = io.BufferedReader( gzip.open( filename, mode='rb' ) )
- else:
- self.fhd = io.open( filename, mode='rb' ) # binary mode! I don't expect unicode here!
-
- def tsize( self ):
- """General function to detect tag size.
-
- * Although it can be used by most parsers, it must be
- rewritten by BAMParser!
- """
- cdef:
- int s = 0
- int n = 0 # number of successful/valid read alignments
- int m = 0 # number of trials
- int this_taglength
-
- if self.tag_size != -1:
- # if we have already calculated tag size (!= -1), return it.
- return self.tag_size
-
- # try 10k times or retrieve 10 successfule alignments
- while n < 10 and m < 10000:
- m += 1
- thisline = self.fhd.readline()
- this_taglength = self.__tlen_parse_line( thisline )
- if this_taglength > 0:
- # this_taglength == 0 means this line doesn't contain
- # successful alignment.
- s += this_taglength
- n += 1
- # done
- self.fhd.seek( 0 )
- self.tag_size = s/n
- return self.tag_size
-
- cdef __tlen_parse_line ( self, str thisline ):
- """Abstract function to detect tag length.
-
- """
- raise NotImplemented
-
- def build_fwtrack ( self ):
- """Generic function to build FWTrack object. Create a new
- FWTrack object. If you want to append new records to an
- existing FWTrack object, try append_fwtrack function.
-
- * BAMParser for binary BAM format should have a different one.
- """
- cdef:
- long i, m, fpos, strand
- str chromosome
-
- fwtrack = FWTrack( buffer_size = self.buffer_size )
- i = 0
- m = 0
- for thisline in self.fhd:
- ( chromosome, fpos, strand ) = self.__fw_parse_line( thisline )
- i+=1
- if fpos < 0 or not chromosome:
- # normally __fw_parse_line will return -1 if the line
- # contains no successful alignment.
- continue
- if i == 1000000:
- m += 1
- logging.info( " %d" % ( m*1000000 ) )
- i=0
- fwtrack.add_loc( chromosome, fpos, strand )
-
- # close fwtrack and sort
- # fwtrack.finalize()
- # this is the problematic part. If fwtrack is finalized, then it's impossible to increase the length of it in a step of buffer_size for multiple input files.
- # close file stream.
- self.close()
- return fwtrack
-
- def append_fwtrack ( self, fwtrack ):
- """Add more records to an existing FWTrack object.
-
- """
- i = 0
- m = 0
- for thisline in self.fhd:
- ( chromosome, fpos, strand ) = self.__fw_parse_line( thisline )
- i+=1
- if fpos < 0 or not chromosome:
- # normally __fw_parse_line will return -1 if the line
- # contains no successful alignment.
- continue
- if i == 1000000:
- m += 1
- logging.info( " %d" % ( m*1000000 ) )
- i=0
- fwtrack.add_loc( chromosome, fpos, strand )
-
- # close fwtrack and sort
- # fwtrack.finalize()
- # this is the problematic part. If fwtrack is finalized, then it's impossible to increase the length of it in a step of buffer_size for multiple input files.
- self.close()
- return fwtrack
-
-
-
- cdef __fw_parse_line ( self, str thisline ):
- """Abstract function to parse chromosome, 5' end position and
- strand.
-
- """
- cdef str chromosome = ""
- cdef int fpos = -1
- cdef int strand = -1
- return ( chromosome, fpos, strand )
-
- cpdef sniff ( self ):
- """Detect whether this parser is the correct parser for input
- file.
-
- Rule: try to find the tag size using this parser, if error
- occurs or tag size is too small or too big, check is failed.
-
- * BAMParser has a different sniff function.
- """
- cdef int t
-
- try:
- t = self.tsize()
- except:
- self.fhd.seek( 0 )
- return False
- else:
- if t <= 10 or t >= 10000:
- self.fhd.seek( 0 )
- return False
- else:
- self.fhd.seek( 0 )
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diff --git a/MACS2/IO/PeakIO.c b/MACS2/IO/PeakIO.c
index 44f07ff..df66691 100644
--- a/MACS2/IO/PeakIO.c
+++ b/MACS2/IO/PeakIO.c
@@ -491,7 +491,7 @@ struct __pyx_obj_5MACS2_2IO_6PeakIO_PeakIO {
};
-/* "MACS2/IO/PeakIO.pyx":647
+/* "MACS2/IO/PeakIO.pyx":649
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*
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@@ -503,7 +503,7 @@ struct __pyx_obj_5MACS2_2IO_6PeakIO_Region {
};
-/* "MACS2/IO/PeakIO.pyx":716
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*
*
* cdef class BroadPeakContent: # <<<<<<<<<<<<<<
@@ -529,7 +529,7 @@ struct __pyx_obj_5MACS2_2IO_6PeakIO_BroadPeakContent {
};
-/* "MACS2/IO/PeakIO.pyx":789
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*
* cdef class BroadPeakIO: # <<<<<<<<<<<<<<
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* self.peaks[chromosome].append(peakcontent)
*
* def get_data_from_chrom (self, str chrom): # <<<<<<<<<<<<<<
- * return self.peaks[chrom]
- *
+ * if not self.peaks.has_key( chrom ):
+ * self.peaks[chrom]= []
*/
/* Python wrapper */
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static PyObject *__pyx_pf_5MACS2_2IO_6PeakIO_6PeakIO_6get_data_from_chrom(struct __pyx_obj_5MACS2_2IO_6PeakIO_PeakIO *__pyx_v_self, PyObject *__pyx_v_chrom) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
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const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
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/* "MACS2/IO/PeakIO.pyx":158
*
* def get_data_from_chrom (self, str chrom):
+ * if not self.peaks.has_key( chrom ): # <<<<<<<<<<<<<<
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+ * return self.peaks[chrom]
+ */
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}
/*else*/ {
- /* "MACS2/IO/PeakIO.pyx":230
+ /* "MACS2/IO/PeakIO.pyx":232
* print_func("\t".join(("chr","start", "end", "length", "abs_summit", "pileup", "-log10(pvalue)", "fold_enrichment", "-log10(qvalue)", "name"))+"\n")
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@@ -5125,7 +5161,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_6PeakIO_6PeakIO_22_to_xls(struct __pyx_obj_
}
__pyx_L3:;
- /* "MACS2/IO/PeakIO.pyx":232
+ /* "MACS2/IO/PeakIO.pyx":234
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__Pyx_XGOTREF(__pyx_t_9);
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__Pyx_GOTREF(__pyx_t_2);
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__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
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+ if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_3, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
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__Pyx_GOTREF(__pyx_t_3);
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__pyx_L11_try_end:;
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__pyx_v_peaks = ((PyObject*)__pyx_t_6);
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PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "keys");
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+ __pyx_t_6 = __Pyx_PyDict_Keys(__pyx_v_peaks); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 238; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_chrs, __pyx_n_s_sort); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -5293,7 +5329,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_6PeakIO_6PeakIO_22_to_xls(struct __pyx_obj_
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__pyx_t_3 = 0;
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
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__Pyx_XDECREF_SET(__pyx_v_chrom, __pyx_t_2);
__pyx_t_2 = 0;
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return __pyx_r;
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}
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- /* "MACS2/IO/PeakIO.pyx":315
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}
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return __pyx_r;
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__Pyx_RefNannySetupContext("tobed", 0);
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__pyx_t_3 = 0;
goto __pyx_L0;
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return __pyx_r;
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return __pyx_r;
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goto __pyx_L0;
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return __pyx_r;
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+ /* "MACS2/IO/PeakIO.pyx":469
* write = fhd.write
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@@ -9102,17 +9138,17 @@ static PyObject *__pyx_pf_5MACS2_2IO_6PeakIO_6PeakIO_36write_to_narrowPeak(struc
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@@ -9160,46 +9196,46 @@ static PyObject *__pyx_pf_5MACS2_2IO_6PeakIO_6PeakIO_36write_to_narrowPeak(struc
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__Pyx_XDECREF_SET(__pyx_v_chrom, ((PyObject*)__pyx_t_2));
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* write("track type=narrowPeak name=\"%s\" description=\"%s\" nextItemButton=on\n" % (name, name))
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
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+ __Pyx_RaiseArgtupleInvalid("__init__", 0, 12, 13, 8); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ __Pyx_RaiseArgtupleInvalid("__init__", 0, 12, 13, 9); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ __Pyx_RaiseArgtupleInvalid("__init__", 0, 12, 13, 10); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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else {
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+ __Pyx_RaiseArgtupleInvalid("__init__", 0, 12, 13, 11); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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__pyx_v_self->peaks = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "MACS2/IO/PeakIO.pyx":796
+ /* "MACS2/IO/PeakIO.pyx":798
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@@ -15397,7 +15433,7 @@ static int __pyx_pf_5MACS2_2IO_6PeakIO_11BroadPeakIO___init__(struct __pyx_obj_5
return __pyx_r;
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-/* "MACS2/IO/PeakIO.pyx":799
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* self.peaks = {}
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case 1:
if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_start)) != 0)) kw_args--;
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+ __Pyx_RaiseArgtupleInvalid("add", 0, 3, 14, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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- __Pyx_RaiseArgtupleInvalid("add", 0, 3, 14, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("add", 0, 3, 14, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -15530,7 +15566,7 @@ static PyObject *__pyx_pw_5MACS2_2IO_6PeakIO_11BroadPeakIO_3add(PyObject *__pyx_
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__Pyx_AddTraceback("MACS2.IO.PeakIO.BroadPeakIO.add", __pyx_clineno, __pyx_lineno, __pyx_filename);
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return __pyx_r;
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__pyx_L10_try_end:;
}
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* except: peakprefix = name_prefix
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PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_name);
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__Pyx_INCREF(__pyx_v_desc);
PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_desc);
__Pyx_GIVEREF(__pyx_v_desc);
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PyTuple_SET_ITEM(__pyx_t_9, 0+1, __pyx_t_8);
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}
__pyx_L23:;
- /* "MACS2/IO/PeakIO.pyx":956
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@@ -17448,7 +17484,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_6PeakIO_11BroadPeakIO_12write_to_gappedPeak
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if (exc_type) {
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- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 956; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_XDECREF_SET(__pyx_v_chrom, __pyx_t_2);
__pyx_t_2 = 0;
- /* "MACS2/IO/PeakIO.pyx":957
+ /* "MACS2/IO/PeakIO.pyx":959
* fhd.write("track name=\"%s\" description=\"%s\" type=gappedPeak nextItemButton=on\n" % (name, desc) )
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_XDECREF_SET(__pyx_v_peak, __pyx_t_2);
__pyx_t_2 = 0;
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* (chrom,peak["start"],peak["end"],peakprefix,n_peak,int(10*peak["qscore"]),
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* fhd.write( "%s\t%d\t%d\t%s%d\t%d\t.\t%s\t%s\t0\t%d\t%s\t%s\t%.5f\t%.5f\t%.5f\n"
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__pyx_t_15 = 0;
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* fhd.write( "%s\t%d\t%d\t%s%d\t%d\t.\t%s\t%s\t0\t%d\t%s\t%s\n"
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if (exc_type) {
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__Pyx_GOTREF(__pyx_t_2);
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+ __pyx_t_12 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_1, __pyx_t_9); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_12 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_13); __Pyx_INCREF(__pyx_t_12); __pyx_t_13++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_12 = PySequence_ITEM(__pyx_t_9, __pyx_t_13); __pyx_t_13++; if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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* peak = these_peaks[0]
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* peakname = "%s%d" % (peakprefix, n_peak)
* fhd.write( "%s\t%d\t%d\t%s\t%d\t.\t%.5f\t%.5f\t%.5f\n" %
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__Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
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* fhd.write( "%s\t%d\t%d\t%s\t%d\t.\t%.5f\t%.5f\t%.5f\n" %
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+ __pyx_t_17 = PyObject_GetItem(__pyx_v_peak, __pyx_n_s_fc); if (unlikely(__pyx_t_17 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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* peakname = "%s%d" % (peakprefix, n_peak)
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@@ -19626,7 +19662,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_6PeakIO_11BroadPeakIO_18write_to_xls(struct
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*/
- __pyx_tuple__22 = PyTuple_Pack(1, __pyx_n_s_end); if (unlikely(!__pyx_tuple__22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__22 = PyTuple_Pack(1, __pyx_n_s_end); if (unlikely(!__pyx_tuple__22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 519; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__22);
__Pyx_GIVEREF(__pyx_tuple__22);
- /* "MACS2/IO/PeakIO.pyx":531
+ /* "MACS2/IO/PeakIO.pyx":533
* write("\t%.5f" % (peak['qscore'])) # -log10qvalue at summit
* write("\t%s" % peakname)
* write("\n") # <<<<<<<<<<<<<<
* else:
* peak = these_peaks[0]
*/
- __pyx_tuple__23 = PyTuple_Pack(1, __pyx_kp_s__4); if (unlikely(!__pyx_tuple__23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__23 = PyTuple_Pack(1, __pyx_kp_s__4); if (unlikely(!__pyx_tuple__23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__23);
__Pyx_GIVEREF(__pyx_tuple__23);
- /* "MACS2/IO/PeakIO.pyx":543
+ /* "MACS2/IO/PeakIO.pyx":545
* write("\t%.5f" % (peak['qscore'])) # -log10qvalue at summit
* write("\t%s" % peakname)
* write("\n") # <<<<<<<<<<<<<<
* return
*
*/
- __pyx_tuple__24 = PyTuple_Pack(1, __pyx_kp_s__4); if (unlikely(!__pyx_tuple__24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__24 = PyTuple_Pack(1, __pyx_kp_s__4); if (unlikely(!__pyx_tuple__24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__24);
__Pyx_GIVEREF(__pyx_tuple__24);
- /* "MACS2/IO/PeakIO.pyx":606
+ /* "MACS2/IO/PeakIO.pyx":608
*
* # sanity check
* columns = line.rstrip().split('\t') # <<<<<<<<<<<<<<
* for a,b in zip(columns, ("chr","start", "end", "length", "abs_summit",
* "pileup", "-log10(pvalue)", "fold_enrichment",
*/
- __pyx_tuple__27 = PyTuple_Pack(1, __pyx_kp_s__2); if (unlikely(!__pyx_tuple__27)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__27 = PyTuple_Pack(1, __pyx_kp_s__2); if (unlikely(!__pyx_tuple__27)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__27);
__Pyx_GIVEREF(__pyx_tuple__27);
- /* "MACS2/IO/PeakIO.pyx":607
+ /* "MACS2/IO/PeakIO.pyx":609
* # sanity check
* columns = line.rstrip().split('\t')
* for a,b in zip(columns, ("chr","start", "end", "length", "abs_summit", # <<<<<<<<<<<<<<
* "pileup", "-log10(pvalue)", "fold_enrichment",
* "-log10(qvalue)", "name")):
*/
- __pyx_tuple__28 = PyTuple_Pack(10, __pyx_n_s_chr, __pyx_n_s_start, __pyx_n_s_end, __pyx_n_s_length, __pyx_n_s_abs_summit, __pyx_n_s_pileup, __pyx_kp_s_log10_pvalue, __pyx_n_s_fold_enrichment, __pyx_kp_s_log10_qvalue, __pyx_n_s_name); if (unlikely(!__pyx_tuple__28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 607; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__28 = PyTuple_Pack(10, __pyx_n_s_chr, __pyx_n_s_start, __pyx_n_s_end, __pyx_n_s_length, __pyx_n_s_abs_summit, __pyx_n_s_pileup, __pyx_kp_s_log10_pvalue, __pyx_n_s_fold_enrichment, __pyx_kp_s_log10_qvalue, __pyx_n_s_name); if (unlikely(!__pyx_tuple__28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__28);
__Pyx_GIVEREF(__pyx_tuple__28);
- /* "MACS2/IO/PeakIO.pyx":638
+ /* "MACS2/IO/PeakIO.pyx":640
* cdef:
* str peak_id, peaknumber, subpeak
* peak_id = peakname.split('_')[-1] # <<<<<<<<<<<<<<
* x = re.split('(\D.*)', peak_id)
* peaknumber = int(x[0])
*/
- __pyx_tuple__30 = PyTuple_Pack(1, __pyx_n_s__29); if (unlikely(!__pyx_tuple__30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__30 = PyTuple_Pack(1, __pyx_n_s__29); if (unlikely(!__pyx_tuple__30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__30);
__Pyx_GIVEREF(__pyx_tuple__30);
- /* "MACS2/IO/PeakIO.pyx":1109
+ /* "MACS2/IO/PeakIO.pyx":1111
* write("track type=broadPeak name=\"%s\" description=\"%s\" nextItemButton=on\n" % (name, name))
* for chrom in chrs:
* for end, group in groupby(self.peaks[chrom], key=itemgetter("end")): # <<<<<<<<<<<<<<
* n_peak += 1
* these_peaks = list(group)
*/
- __pyx_tuple__32 = PyTuple_Pack(1, __pyx_n_s_end); if (unlikely(!__pyx_tuple__32)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__32 = PyTuple_Pack(1, __pyx_n_s_end); if (unlikely(!__pyx_tuple__32)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__32);
__Pyx_GIVEREF(__pyx_tuple__32);
- /* "MACS2/IO/PeakIO.pyx":1129
+ /* "MACS2/IO/PeakIO.pyx":1131
* """
* write = ofhd.write
* write("\t".join(("chr","start", "end", "length", "pileup", "-log10(pvalue)", "fold_enrichment", "-log10(qvalue)", "name"))+"\n") # <<<<<<<<<<<<<<
*
* try: peakprefix = name_prefix % name
*/
- __pyx_tuple__33 = PyTuple_Pack(9, __pyx_n_s_chr, __pyx_n_s_start, __pyx_n_s_end, __pyx_n_s_length, __pyx_n_s_pileup, __pyx_kp_s_log10_pvalue, __pyx_n_s_fold_enrichment, __pyx_kp_s_log10_qvalue, __pyx_n_s_name); if (unlikely(!__pyx_tuple__33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1129; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__33 = PyTuple_Pack(9, __pyx_n_s_chr, __pyx_n_s_start, __pyx_n_s_end, __pyx_n_s_length, __pyx_n_s_pileup, __pyx_kp_s_log10_pvalue, __pyx_n_s_fold_enrichment, __pyx_kp_s_log10_qvalue, __pyx_n_s_name); if (unlikely(!__pyx_tuple__33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__33);
__Pyx_GIVEREF(__pyx_tuple__33);
- /* "MACS2/IO/PeakIO.pyx":1139
+ /* "MACS2/IO/PeakIO.pyx":1141
* n_peak = 0
* for chrom in chrs:
* for end, group in groupby(peaks[chrom], key=itemgetter("end")): # <<<<<<<<<<<<<<
* n_peak += 1
* these_peaks = list(group)
*/
- __pyx_tuple__34 = PyTuple_Pack(1, __pyx_n_s_end); if (unlikely(!__pyx_tuple__34)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__34 = PyTuple_Pack(1, __pyx_n_s_end); if (unlikely(!__pyx_tuple__34)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__34);
__Pyx_GIVEREF(__pyx_tuple__34);
- /* "MACS2/IO/PeakIO.pyx":1150
+ /* "MACS2/IO/PeakIO.pyx":1152
* write("\t%.5f" % (peak['qscore'])) # -log10qvalue at summit
* write("\t%s" % peakname)
* write("\n") # <<<<<<<<<<<<<<
* return
*/
- __pyx_tuple__35 = PyTuple_Pack(1, __pyx_kp_s__4); if (unlikely(!__pyx_tuple__35)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_tuple__35 = PyTuple_Pack(1, __pyx_kp_s__4); if (unlikely(!__pyx_tuple__35)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__35);
__Pyx_GIVEREF(__pyx_tuple__35);
__Pyx_RefNannyFinishContext();
@@ -21425,17 +21461,17 @@ PyMODINIT_FUNC PyInit_PeakIO(void)
if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_6PeakIO_PeakIO.tp_dict, __pyx_vtabptr_5MACS2_2IO_6PeakIO_PeakIO) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (PyObject_SetAttrString(__pyx_m, "PeakIO", (PyObject *)&__pyx_type_5MACS2_2IO_6PeakIO_PeakIO) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6PeakIO_PeakIO = &__pyx_type_5MACS2_2IO_6PeakIO_PeakIO;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6PeakIO_Region) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6PeakIO_Region) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6PeakIO_Region.tp_print = 0;
- if (PyObject_SetAttrString(__pyx_m, "Region", (PyObject *)&__pyx_type_5MACS2_2IO_6PeakIO_Region) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "Region", (PyObject *)&__pyx_type_5MACS2_2IO_6PeakIO_Region) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6PeakIO_Region = &__pyx_type_5MACS2_2IO_6PeakIO_Region;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6PeakIO_BroadPeakContent) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6PeakIO_BroadPeakContent) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6PeakIO_BroadPeakContent.tp_print = 0;
- if (PyObject_SetAttrString(__pyx_m, "BroadPeakContent", (PyObject *)&__pyx_type_5MACS2_2IO_6PeakIO_BroadPeakContent) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "BroadPeakContent", (PyObject *)&__pyx_type_5MACS2_2IO_6PeakIO_BroadPeakContent) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6PeakIO_BroadPeakContent = &__pyx_type_5MACS2_2IO_6PeakIO_BroadPeakContent;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_6PeakIO_BroadPeakIO) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_6PeakIO_BroadPeakIO) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_6PeakIO_BroadPeakIO.tp_print = 0;
- if (PyObject_SetAttrString(__pyx_m, "BroadPeakIO", (PyObject *)&__pyx_type_5MACS2_2IO_6PeakIO_BroadPeakIO) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "BroadPeakIO", (PyObject *)&__pyx_type_5MACS2_2IO_6PeakIO_BroadPeakIO) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_6PeakIO_BroadPeakIO = &__pyx_type_5MACS2_2IO_6PeakIO_BroadPeakIO;
/*--- Type import code ---*/
/*--- Variable import code ---*/
@@ -21541,7 +21577,7 @@ PyMODINIT_FUNC PyInit_PeakIO(void)
*/
if (PyDict_SetItem(__pyx_d, __pyx_n_s_doc, __pyx_kp_s_PeakIO_class) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "MACS2/IO/PeakIO.pyx":225
+ /* "MACS2/IO/PeakIO.pyx":227
* print_func=fhd.write)
*
* def _to_xls (self, name_prefix="%s_peak_", name="MACS", print_func=print): # <<<<<<<<<<<<<<
@@ -21552,7 +21588,7 @@ PyMODINIT_FUNC PyInit_PeakIO(void)
__pyx_k_ = __pyx_builtin_print;
__Pyx_GIVEREF(__pyx_builtin_print);
- /* "MACS2/IO/PeakIO.pyx":271
+ /* "MACS2/IO/PeakIO.pyx":273
* def _to_bed(self, name_prefix="%s_peak_", name="MACS",
* description="%s", score_column="score",
* print_func=print, trackline=False): # <<<<<<<<<<<<<<
@@ -21563,7 +21599,7 @@ PyMODINIT_FUNC PyInit_PeakIO(void)
__pyx_k__8 = __pyx_builtin_print;
__Pyx_GIVEREF(__pyx_builtin_print);
- /* "MACS2/IO/PeakIO.pyx":299
+ /* "MACS2/IO/PeakIO.pyx":301
* def _to_summits_bed(self, name_prefix="%s_peak_", name="MACS",
* description = "%s", score_column="score",
* print_func=print, trackline=False): # <<<<<<<<<<<<<<
@@ -21575,7 +21611,7 @@ PyMODINIT_FUNC PyInit_PeakIO(void)
__Pyx_GIVEREF(__pyx_builtin_print);
/* "MACS2/IO/PeakIO.pyx":1
- * # Time-stamp: <2014-08-22 15:41:27 Tao Liu> # <<<<<<<<<<<<<<
+ * # Time-stamp: <2016-02-26 10:12:50 Tao Liu> # <<<<<<<<<<<<<<
*
* """Module for PeakIO IO classes.
*/
diff --git a/MACS2/IO/PeakIO.pyx b/MACS2/IO/PeakIO.pyx
index 2c5a09b..c0ee684 100644
--- a/MACS2/IO/PeakIO.pyx
+++ b/MACS2/IO/PeakIO.pyx
@@ -1,4 +1,4 @@
-# Time-stamp: <2014-08-22 15:41:27 Tao Liu>
+# Time-stamp: <2016-02-26 10:12:50 Tao Liu>
"""Module for PeakIO IO classes.
@@ -155,6 +155,8 @@ cdef class PeakIO:
self.peaks[chromosome].append(peakcontent)
def get_data_from_chrom (self, str chrom):
+ if not self.peaks.has_key( chrom ):
+ self.peaks[chrom]= []
return self.peaks[chrom]
def get_chr_names (self):
diff --git a/MACS2/IO/ScoreTrack.c b/MACS2/IO/ScoreTrack.c
index 9e75a56..69b5571 100644
--- a/MACS2/IO/ScoreTrack.c
+++ b/MACS2/IO/ScoreTrack.c
@@ -456,7 +456,7 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
"MACS2/IO/ScoreTrack.pyx",
- "numpy.pxd",
+ "__init__.pxd",
"type.pxd",
"bool.pxd",
"complex.pxd",
@@ -497,7 +497,7 @@ typedef struct {
} __Pyx_BufFmt_Context;
-/* "numpy.pxd":723
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726
* # in Cython to enable them only on the right systems.
*
* ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
@@ -506,7 +506,7 @@ typedef struct {
*/
typedef npy_int8 __pyx_t_5numpy_int8_t;
-/* "numpy.pxd":724
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":727
*
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
@@ -515,7 +515,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t;
*/
typedef npy_int16 __pyx_t_5numpy_int16_t;
-/* "numpy.pxd":725
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":728
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
@@ -524,7 +524,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t;
*/
typedef npy_int32 __pyx_t_5numpy_int32_t;
-/* "numpy.pxd":726
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":729
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
@@ -533,7 +533,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t;
*/
typedef npy_int64 __pyx_t_5numpy_int64_t;
-/* "numpy.pxd":730
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733
* #ctypedef npy_int128 int128_t
*
* ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
@@ -542,7 +542,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t;
*/
typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-/* "numpy.pxd":731
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":734
*
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
@@ -551,7 +551,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t;
*/
typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-/* "numpy.pxd":732
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":735
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
@@ -560,7 +560,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t;
*/
typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-/* "numpy.pxd":733
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":736
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
@@ -569,7 +569,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t;
*/
typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-/* "numpy.pxd":737
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":740
* #ctypedef npy_uint128 uint128_t
*
* ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
@@ -578,7 +578,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t;
*/
typedef npy_float32 __pyx_t_5numpy_float32_t;
-/* "numpy.pxd":738
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":741
*
* ctypedef npy_float32 float32_t
* ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
@@ -587,7 +587,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t;
*/
typedef npy_float64 __pyx_t_5numpy_float64_t;
-/* "numpy.pxd":747
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":750
* # The int types are mapped a bit surprising --
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t # <<<<<<<<<<<<<<
@@ -596,7 +596,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t;
*/
typedef npy_long __pyx_t_5numpy_int_t;
-/* "numpy.pxd":748
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
@@ -605,7 +605,7 @@ typedef npy_long __pyx_t_5numpy_int_t;
*/
typedef npy_longlong __pyx_t_5numpy_long_t;
-/* "numpy.pxd":749
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
@@ -614,7 +614,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t;
*/
typedef npy_longlong __pyx_t_5numpy_longlong_t;
-/* "numpy.pxd":751
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":754
* ctypedef npy_longlong longlong_t
*
* ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
@@ -623,7 +623,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t;
*/
typedef npy_ulong __pyx_t_5numpy_uint_t;
-/* "numpy.pxd":752
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755
*
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
@@ -632,7 +632,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-/* "numpy.pxd":753
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
@@ -641,7 +641,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-/* "numpy.pxd":755
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758
* ctypedef npy_ulonglong ulonglong_t
*
* ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
@@ -650,7 +650,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
*/
typedef npy_intp __pyx_t_5numpy_intp_t;
-/* "numpy.pxd":756
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759
*
* ctypedef npy_intp intp_t
* ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
@@ -659,7 +659,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t;
*/
typedef npy_uintp __pyx_t_5numpy_uintp_t;
-/* "numpy.pxd":758
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":761
* ctypedef npy_uintp uintp_t
*
* ctypedef npy_double float_t # <<<<<<<<<<<<<<
@@ -668,7 +668,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t;
*/
typedef npy_double __pyx_t_5numpy_float_t;
-/* "numpy.pxd":759
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762
*
* ctypedef npy_double float_t
* ctypedef npy_double double_t # <<<<<<<<<<<<<<
@@ -677,7 +677,7 @@ typedef npy_double __pyx_t_5numpy_float_t;
*/
typedef npy_double __pyx_t_5numpy_double_t;
-/* "numpy.pxd":760
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763
* ctypedef npy_double float_t
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
@@ -711,7 +711,7 @@ struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII;
struct __pyx_obj_5MACS2_2IO_10ScoreTrack_TwoConditionScores;
struct __pyx_obj_5MACS2_2IO_10ScoreTrack___pyx_scope_struct____add_broadpeak;
-/* "numpy.pxd":762
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":765
* ctypedef npy_longdouble longdouble_t
*
* ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
@@ -720,7 +720,7 @@ struct __pyx_obj_5MACS2_2IO_10ScoreTrack___pyx_scope_struct____add_broadpeak;
*/
typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-/* "numpy.pxd":763
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766
*
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
@@ -729,7 +729,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
*/
typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-/* "numpy.pxd":764
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":767
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
@@ -738,7 +738,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
*/
typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-/* "numpy.pxd":766
+/* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":769
* ctypedef npy_clongdouble clongdouble_t
*
* ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
@@ -755,7 +755,7 @@ struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_18TwoConditionScores_write_bedGrap
struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_18TwoConditionScores_write_matrix;
struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_18TwoConditionScores_call_peaks;
-/* "MACS2/IO/ScoreTrack.pyx":962
+/* "MACS2/IO/ScoreTrack.pyx":980
* return
*
* cpdef write_bedGraph ( self, fhd, str name, str description, short column = 3): # <<<<<<<<<<<<<<
@@ -767,7 +767,7 @@ struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII_write_bedGraph {
short column;
};
-/* "MACS2/IO/ScoreTrack.pyx":1068
+/* "MACS2/IO/ScoreTrack.pyx":1086
* # return ret_peaks
*
* cpdef call_peaks (self, float cutoff=5.0, int min_length=200, int max_gap=50, bool call_summits=False): # <<<<<<<<<<<<<<
@@ -782,7 +782,7 @@ struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_peaks {
PyBoolObject *call_summits;
};
-/* "MACS2/IO/ScoreTrack.pyx":1141
+/* "MACS2/IO/ScoreTrack.pyx":1159
* return peaks
*
* cdef bool __close_peak (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<<
@@ -794,7 +794,7 @@ struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak {
int smoothlen;
};
-/* "MACS2/IO/ScoreTrack.pyx":1192
+/* "MACS2/IO/ScoreTrack.pyx":1210
* return True
*
* cdef bool __close_peak2 (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<<
@@ -807,7 +807,7 @@ struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak2 {
float min_valley;
};
-/* "MACS2/IO/ScoreTrack.pyx":1281
+/* "MACS2/IO/ScoreTrack.pyx":1299
* return t
*
* cpdef tuple call_broadpeaks (self, float lvl1_cutoff=5.0, float lvl2_cutoff=1.0, int min_length=200, int lvl1_max_gap=50, int lvl2_max_gap=400): # <<<<<<<<<<<<<<
@@ -823,7 +823,7 @@ struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_broadpeaks {
int lvl2_max_gap;
};
-/* "MACS2/IO/ScoreTrack.pyx":1621
+/* "MACS2/IO/ScoreTrack.pyx":1639
* return l
*
* cpdef write_bedGraph ( self, fhd, str name, str description, short column = 3): # <<<<<<<<<<<<<<
@@ -835,7 +835,7 @@ struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_18TwoConditionScores_write_bedGrap
short column;
};
-/* "MACS2/IO/ScoreTrack.pyx":1666
+/* "MACS2/IO/ScoreTrack.pyx":1684
* return True
*
* cpdef write_matrix ( self, fhd, str name, str description, short column = 3 ): # <<<<<<<<<<<<<<
@@ -847,7 +847,7 @@ struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_18TwoConditionScores_write_matrix
short column;
};
-/* "MACS2/IO/ScoreTrack.pyx":1704
+/* "MACS2/IO/ScoreTrack.pyx":1722
* return True
*
* cpdef call_peaks (self, float cutoff=3, int min_length=200, int max_gap = 100, # <<<<<<<<<<<<<<
@@ -887,7 +887,7 @@ struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII {
};
-/* "MACS2/IO/ScoreTrack.pyx":1367
+/* "MACS2/IO/ScoreTrack.pyx":1385
* return bpeaks
*
* cdef class TwoConditionScores: # <<<<<<<<<<<<<<
@@ -913,7 +913,7 @@ struct __pyx_obj_5MACS2_2IO_10ScoreTrack_TwoConditionScores {
};
-/* "MACS2/IO/ScoreTrack.pyx":1336
+/* "MACS2/IO/ScoreTrack.pyx":1354
* return lvl1_peaks, broadpeaks
*
* def __add_broadpeak (self, bpeaks, str chrom, dict lvl2peak, list lvl1peakset): # <<<<<<<<<<<<<<
@@ -955,6 +955,7 @@ struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII {
PyObject *(*compute_foldenrichment)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *);
PyObject *(*compute_subtraction)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *);
PyObject *(*compute_SPMR)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *);
+ PyObject *(*compute_max)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *);
PyObject *(*write_bedGraph)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *, PyObject *, PyObject *, PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII_write_bedGraph *__pyx_optional_args);
PyObject *(*call_peaks)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *, int __pyx_skip_dispatch, struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_peaks *__pyx_optional_args);
PyBoolObject *(*__pyx___close_peak)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *, PyObject *, PyObject *, int, PyObject *, struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak *__pyx_optional_args);
@@ -965,7 +966,7 @@ struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII {
static struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *__pyx_vtabptr_5MACS2_2IO_10ScoreTrack_scoreTrackII;
-/* "MACS2/IO/ScoreTrack.pyx":1367
+/* "MACS2/IO/ScoreTrack.pyx":1385
* return bpeaks
*
* cdef class TwoConditionScores: # <<<<<<<<<<<<<<
@@ -1525,8 +1526,6 @@ 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 int __Pyx_check_binary_version(void);
#if !defined(__Pyx_PyIdentifier_FromString)
@@ -1562,6 +1561,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_logFE(st
static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_foldenrichment(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *__pyx_v_self); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_subtraction(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *__pyx_v_self); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_SPMR(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *__pyx_v_self); /* proto*/
+static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_max(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *__pyx_v_self); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_write_bedGraph(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *__pyx_v_self, PyObject *__pyx_v_fhd, PyObject *__pyx_v_name, PyObject *__pyx_v_description, int __pyx_skip_dispatch, struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII_write_bedGraph *__pyx_optional_args); /* proto*/
static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_peaks(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_peaks *__pyx_optional_args); /* proto*/
static PyBoolObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *__pyx_v_self, PyObject *__pyx_v_peak_content, PyObject *__pyx_v_peaks, int __pyx_v_min_length, PyObject *__pyx_v_chrom, struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak *__pyx_optional_args); /* proto*/
@@ -1985,7 +1985,7 @@ static char __pyx_k_CombinedTwoTrack_get_chr_names[] = "CombinedTwoTrack.get_chr
static char __pyx_k_Tao_Liu_vladimir_liu_gmail_com[] = "Tao Liu <vladimir.liu at gmail.com>";
static char __pyx_k_CombinedTwoTrack_add_chromosome[] = "CombinedTwoTrack.add_chromosome";
static char __pyx_k_CombinedTwoTrack_write_bedGraph[] = "CombinedTwoTrack.write_bedGraph";
-static char __pyx_k_Users_taoliu_Dropbox_projects_m[] = "/Users/taoliu/Dropbox/projects/macs2/MACS/MACS2/IO/ScoreTrack.pyx";
+static char __pyx_k_Users_taoliu_Dropbox_Projects_M[] = "/Users/taoliu/Dropbox/Projects/MACS2/MACS/MACS2/IO/ScoreTrack.pyx";
static char __pyx_k_column_should_be_between_1_2_or[] = "column should be between 1, 2 or 3.";
static char __pyx_k_level_1_cutoff_should_be_larger[] = "level 1 cutoff should be larger than level 2.";
static char __pyx_k_proportion_background_empirical[] = "proportion_background_empirical_distribution";
@@ -2037,7 +2037,7 @@ static PyObject *__pyx_n_s_PeakIO;
static PyObject *__pyx_n_s_RuntimeError;
static PyObject *__pyx_n_s_StopIteration;
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_V1;
static PyObject *__pyx_n_s_V2;
static PyObject *__pyx_n_s_ValueError;
@@ -2235,7 +2235,6 @@ static PyObject *__pyx_int_1;
static PyObject *__pyx_int_2;
static PyObject *__pyx_int_4;
static PyObject *__pyx_int_10;
-static PyObject *__pyx_int_15;
static PyObject *__pyx_int_neg_1;
static PyObject *__pyx_tuple_;
static PyObject *__pyx_tuple__2;
@@ -12360,16 +12359,16 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_change_score_met
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
- /* "MACS2/IO/ScoreTrack.pyx":710
- * elif scoring_method == 'd':
- * self.compute_subtraction()
- * elif scoring_method == 'm': # <<<<<<<<<<<<<<
+ /* "MACS2/IO/ScoreTrack.pyx":713
+ * elif scoring_method == 'm':
* self.compute_SPMR()
+ * elif scoring_method == 'M': # <<<<<<<<<<<<<<
+ * self.compute_max()
* else:
*/
switch (__pyx_v_scoring_method) {
- /* "MACS2/IO/ScoreTrack.pyx":693
+ /* "MACS2/IO/ScoreTrack.pyx":694
* m: fragment pileup per million reads
* """
* if scoring_method == 'p': # <<<<<<<<<<<<<<
@@ -12378,19 +12377,19 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_change_score_met
*/
case 'p':
- /* "MACS2/IO/ScoreTrack.pyx":694
+ /* "MACS2/IO/ScoreTrack.pyx":695
* """
* if scoring_method == 'p':
* self.compute_pvalue() # <<<<<<<<<<<<<<
* elif scoring_method == 'q':
* #if not already calculated p, compute pvalue first
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_pvalue(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_pvalue(__pyx_v_self); 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_DECREF(__pyx_t_1); __pyx_t_1 = 0;
break;
- /* "MACS2/IO/ScoreTrack.pyx":695
+ /* "MACS2/IO/ScoreTrack.pyx":696
* if scoring_method == 'p':
* self.compute_pvalue()
* elif scoring_method == 'q': # <<<<<<<<<<<<<<
@@ -12399,7 +12398,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_change_score_met
*/
case 'q':
- /* "MACS2/IO/ScoreTrack.pyx":697
+ /* "MACS2/IO/ScoreTrack.pyx":698
* elif scoring_method == 'q':
* #if not already calculated p, compute pvalue first
* if self.scoring_method != 'p': # <<<<<<<<<<<<<<
@@ -12409,33 +12408,33 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_change_score_met
__pyx_t_7 = ((__pyx_v_self->scoring_method != 'p') != 0);
if (__pyx_t_7) {
- /* "MACS2/IO/ScoreTrack.pyx":698
+ /* "MACS2/IO/ScoreTrack.pyx":699
* #if not already calculated p, compute pvalue first
* if self.scoring_method != 'p':
* self.compute_pvalue() # <<<<<<<<<<<<<<
* self.compute_qvalue()
* elif scoring_method == 'l':
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_pvalue(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_pvalue(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L3;
}
__pyx_L3:;
- /* "MACS2/IO/ScoreTrack.pyx":699
+ /* "MACS2/IO/ScoreTrack.pyx":700
* if self.scoring_method != 'p':
* self.compute_pvalue()
* self.compute_qvalue() # <<<<<<<<<<<<<<
* elif scoring_method == 'l':
* self.compute_likelihood()
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_qvalue(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_qvalue(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
break;
- /* "MACS2/IO/ScoreTrack.pyx":700
+ /* "MACS2/IO/ScoreTrack.pyx":701
* self.compute_pvalue()
* self.compute_qvalue()
* elif scoring_method == 'l': # <<<<<<<<<<<<<<
@@ -12444,19 +12443,19 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_change_score_met
*/
case 'l':
- /* "MACS2/IO/ScoreTrack.pyx":701
+ /* "MACS2/IO/ScoreTrack.pyx":702
* self.compute_qvalue()
* elif scoring_method == 'l':
* self.compute_likelihood() # <<<<<<<<<<<<<<
* elif scoring_method == 's':
* self.compute_sym_likelihood()
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_likelihood(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_likelihood(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
break;
- /* "MACS2/IO/ScoreTrack.pyx":702
+ /* "MACS2/IO/ScoreTrack.pyx":703
* elif scoring_method == 'l':
* self.compute_likelihood()
* elif scoring_method == 's': # <<<<<<<<<<<<<<
@@ -12465,19 +12464,19 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_change_score_met
*/
case 's':
- /* "MACS2/IO/ScoreTrack.pyx":703
+ /* "MACS2/IO/ScoreTrack.pyx":704
* self.compute_likelihood()
* elif scoring_method == 's':
* self.compute_sym_likelihood() # <<<<<<<<<<<<<<
* elif scoring_method == 'f':
* self.compute_logFE()
*/
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+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_sym_likelihood(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
break;
- /* "MACS2/IO/ScoreTrack.pyx":704
+ /* "MACS2/IO/ScoreTrack.pyx":705
* elif scoring_method == 's':
* self.compute_sym_likelihood()
* elif scoring_method == 'f': # <<<<<<<<<<<<<<
@@ -12486,19 +12485,19 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_change_score_met
*/
case 'f':
- /* "MACS2/IO/ScoreTrack.pyx":705
+ /* "MACS2/IO/ScoreTrack.pyx":706
* self.compute_sym_likelihood()
* elif scoring_method == 'f':
* self.compute_logFE() # <<<<<<<<<<<<<<
* elif scoring_method == 'F':
* self.compute_foldenrichment()
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_logFE(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_logFE(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
break;
- /* "MACS2/IO/ScoreTrack.pyx":706
+ /* "MACS2/IO/ScoreTrack.pyx":707
* elif scoring_method == 'f':
* self.compute_logFE()
* elif scoring_method == 'F': # <<<<<<<<<<<<<<
@@ -12507,19 +12506,19 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_change_score_met
*/
case 'F':
- /* "MACS2/IO/ScoreTrack.pyx":707
+ /* "MACS2/IO/ScoreTrack.pyx":708
* self.compute_logFE()
* elif scoring_method == 'F':
* self.compute_foldenrichment() # <<<<<<<<<<<<<<
* elif scoring_method == 'd':
* self.compute_subtraction()
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_foldenrichment(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_foldenrichment(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
break;
- /* "MACS2/IO/ScoreTrack.pyx":708
+ /* "MACS2/IO/ScoreTrack.pyx":709
* elif scoring_method == 'F':
* self.compute_foldenrichment()
* elif scoring_method == 'd': # <<<<<<<<<<<<<<
@@ -12528,49 +12527,70 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_change_score_met
*/
case 'd':
- /* "MACS2/IO/ScoreTrack.pyx":709
+ /* "MACS2/IO/ScoreTrack.pyx":710
* self.compute_foldenrichment()
* elif scoring_method == 'd':
* self.compute_subtraction() # <<<<<<<<<<<<<<
* elif scoring_method == 'm':
* self.compute_SPMR()
*/
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+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_subtraction(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
break;
- /* "MACS2/IO/ScoreTrack.pyx":710
+ /* "MACS2/IO/ScoreTrack.pyx":711
* elif scoring_method == 'd':
* self.compute_subtraction()
* elif scoring_method == 'm': # <<<<<<<<<<<<<<
* self.compute_SPMR()
- * else:
+ * elif scoring_method == 'M':
*/
case 'm':
- /* "MACS2/IO/ScoreTrack.pyx":711
+ /* "MACS2/IO/ScoreTrack.pyx":712
* self.compute_subtraction()
* elif scoring_method == 'm':
* self.compute_SPMR() # <<<<<<<<<<<<<<
+ * elif scoring_method == 'M':
+ * self.compute_max()
+ */
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_SPMR(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ break;
+
+ /* "MACS2/IO/ScoreTrack.pyx":713
+ * elif scoring_method == 'm':
+ * self.compute_SPMR()
+ * elif scoring_method == 'M': # <<<<<<<<<<<<<<
+ * self.compute_max()
+ * else:
+ */
+ case 'M':
+
+ /* "MACS2/IO/ScoreTrack.pyx":714
+ * self.compute_SPMR()
+ * elif scoring_method == 'M':
+ * self.compute_max() # <<<<<<<<<<<<<<
* else:
* raise NotImplemented
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_SPMR(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->compute_max(__pyx_v_self); 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_DECREF(__pyx_t_1); __pyx_t_1 = 0;
break;
default:
- /* "MACS2/IO/ScoreTrack.pyx":713
- * self.compute_SPMR()
+ /* "MACS2/IO/ScoreTrack.pyx":716
+ * self.compute_max()
* else:
* raise NotImplemented # <<<<<<<<<<<<<<
*
* cdef compute_pvalue ( self ):
*/
__Pyx_Raise(__pyx_builtin_NotImplemented, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
break;
}
@@ -12602,7 +12622,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_change_score_met
/* Python wrapper */
static PyObject *__pyx_pw_5MACS2_2IO_10ScoreTrack_12scoreTrackII_19change_score_method(PyObject *__pyx_v_self, PyObject *__pyx_arg_scoring_method); /*proto*/
-static char __pyx_doc_5MACS2_2IO_10ScoreTrack_12scoreTrackII_18change_score_method[] = "\n scoring_method: p: -log10 pvalue;\n q: -log10 qvalue;\n l: log10 likelihood ratio ( minus for depletion )\n\t\t\t s: symmetric log10 likelihood ratio ( for comparing two ChIPs )\n f: log10 fold enrichment\n F: linear fold enrichment\n d: subtraction\n [...]
+static char __pyx_doc_5MACS2_2IO_10ScoreTrack_12scoreTrackII_18change_score_method[] = "\n scoring_method: p: -log10 pvalue;\n q: -log10 qvalue;\n l: log10 likelihood ratio ( minus for depletion )\n\t\t\t s: symmetric log10 likelihood ratio ( for comparing two ChIPs )\n f: log10 fold enrichment\n F: linear fold enrichment\n d: subtraction\n [...]
static PyObject *__pyx_pw_5MACS2_2IO_10ScoreTrack_12scoreTrackII_19change_score_method(PyObject *__pyx_v_self, PyObject *__pyx_arg_scoring_method) {
char __pyx_v_scoring_method;
int __pyx_lineno = 0;
@@ -12653,7 +12673,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_10ScoreTrack_12scoreTrackII_18change_score_
return __pyx_r;
}
-/* "MACS2/IO/ScoreTrack.pyx":715
+/* "MACS2/IO/ScoreTrack.pyx":718
* raise NotImplemented
*
* cdef compute_pvalue ( self ): # <<<<<<<<<<<<<<
@@ -12726,7 +12746,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_pvalue(s
__pyx_pybuffernd_pos.data = NULL;
__pyx_pybuffernd_pos.rcbuffer = &__pyx_pybuffer_pos;
- /* "MACS2/IO/ScoreTrack.pyx":724
+ /* "MACS2/IO/ScoreTrack.pyx":727
* str chrom
*
* for chrom in self.data.keys(): # <<<<<<<<<<<<<<
@@ -12735,17 +12755,17 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_pvalue(s
*/
if (unlikely(__pyx_v_self->data == Py_None)) {
PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "keys");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
__pyx_t_4 = NULL;
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+ __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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for (;;) {
@@ -12753,16 +12773,16 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_pvalue(s
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+ __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
- __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -12771,17 +12791,17 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_pvalue(s
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 = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
__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 = 724; __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 = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF_SET(__pyx_v_chrom, ((PyObject*)__pyx_t_1));
__pyx_t_1 = 0;
- /* "MACS2/IO/ScoreTrack.pyx":725
+ /* "MACS2/IO/ScoreTrack.pyx":728
*
* for chrom in self.data.keys():
* prev_pos = 0 # <<<<<<<<<<<<<<
@@ -12790,7 +12810,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_pvalue(s
*/
__pyx_v_prev_pos = 0;
- /* "MACS2/IO/ScoreTrack.pyx":726
+ /* "MACS2/IO/ScoreTrack.pyx":729
* for chrom in self.data.keys():
* prev_pos = 0
* pos = self.data[chrom][0] # <<<<<<<<<<<<<<
@@ -12799,14 +12819,14 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_pvalue(s
*/
if (unlikely(__pyx_v_self->data == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_1, 0, long, 1, __Pyx_PyInt_From_long, 0, 0, 1); if (unlikely(__pyx_t_5 == NULL)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+ if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -12822,13 +12842,13 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_pvalue(s
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+ if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_XDECREF_SET(__pyx_v_pos, ((PyArrayObject *)__pyx_t_5));
__pyx_t_5 = 0;
- /* "MACS2/IO/ScoreTrack.pyx":727
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* pos = self.data[chrom][0]
* p = self.data[chrom][1] # <<<<<<<<<<<<<<
@@ -12837,14 +12857,14 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_pvalue(s
*/
if (unlikely(__pyx_v_self->data == Py_None)) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*/
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*
* self.scoring_method = 'q'
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@@ -13648,7 +13668,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_qvalue(s
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
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return __pyx_r;
}
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/* Check if overridden in Python */
else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) {
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+ if (!(likely(PyDict_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "dict", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -13753,7 +13773,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_make_pq_table(st
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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* assert self.scoring_method == 'p' # <<<<<<<<<<<<<<
@@ -13764,12 +13784,12 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_make_pq_table(st
if (unlikely(!Py_OptimizeFlag)) {
if (unlikely(!((__pyx_v_self->scoring_method == 'p') != 0))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
}
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+ /* "MACS2/IO/ScoreTrack.pyx":801
* assert self.scoring_method == 'p'
*
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@@ -13781,7 +13801,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_make_pq_table(st
__pyx_v_value_dict = ((PyObject*)__pyx_t_1);
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PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "values");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 804; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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+ __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 = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ /* "MACS2/IO/ScoreTrack.pyx":810
* #for i in range(len(unique_values)):
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@@ -13815,7 +13835,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_make_pq_table(st
*/
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- /* "MACS2/IO/ScoreTrack.pyx":808
+ /* "MACS2/IO/ScoreTrack.pyx":811
* #N += value_dict.get_item(unique_values[i])
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@@ -13824,7 +13844,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_make_pq_table(st
*/
__pyx_v_f = (-log10(__pyx_v_N));
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+ /* "MACS2/IO/ScoreTrack.pyx":812
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@@ -13833,7 +13853,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_make_pq_table(st
*/
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- /* "MACS2/IO/ScoreTrack.pyx":810
+ /* "MACS2/IO/ScoreTrack.pyx":813
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@@ -13842,7 +13862,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_make_pq_table(st
*/
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+ /* "MACS2/IO/ScoreTrack.pyx":814
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@@ -13851,19 +13871,19 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_make_pq_table(st
*/
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- /* "MACS2/IO/ScoreTrack.pyx":813
+ /* "MACS2/IO/ScoreTrack.pyx":816
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* pvalue2qvalue = {}#Float64HashTable() # <<<<<<<<<<<<<<
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+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_1 = 0;
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* pvalue2qvalue = {}#Float64HashTable()
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PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "keys");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ 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 = 817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_6; __pyx_t_5+=1) {
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ /* "MACS2/IO/ScoreTrack.pyx":855
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- /* "MACS2/IO/ScoreTrack.pyx":842
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@@ -14393,7 +14413,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_likeliho
}
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- /* "MACS2/IO/ScoreTrack.pyx":854
+ /* "MACS2/IO/ScoreTrack.pyx":857
* v[ i ] = logLR_asym( v1 + pseudocount, v2 + pseudocount ) #logLR( d[ i, 1]/100.0, d[ i, 2]/100.0 )
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* self.scoring_method = 'l' # <<<<<<<<<<<<<<
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*/
__pyx_v_self->scoring_method = 'l';
- /* "MACS2/IO/ScoreTrack.pyx":855
+ /* "MACS2/IO/ScoreTrack.pyx":858
* #print v1, v2, v[i]
* self.scoring_method = 'l'
* return # <<<<<<<<<<<<<<
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__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
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* return pvalue2qvalue
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return __pyx_r;
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* return
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__pyx_t_1 = __pyx_v_self->pseudocount;
__pyx_v_pseudocount = __pyx_t_1;
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+ /* "MACS2/IO/ScoreTrack.pyx":873
* pseudocount = self.pseudocount
*
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PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "keys");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 870; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -14528,17 +14548,17 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_sym_like
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+ 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 = 873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
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return __pyx_r;
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case 'T':
case 'N':
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+ __pyx_t_5 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak2(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, &__pyx_t_15)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- /* "MACS2/IO/ScoreTrack.pyx":1137
+ /* "MACS2/IO/ScoreTrack.pyx":1155
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+ __pyx_t_5 = ((PyObject *)((struct __pyx_vtabstruct_5MACS2_2IO_10ScoreTrack_scoreTrackII *)__pyx_v_self->__pyx_vtab)->__pyx___close_peak(__pyx_v_self, __pyx_v_peak_content, __pyx_v_peaks, __pyx_v_min_length, __pyx_v_chrom, &__pyx_t_16)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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__pyx_L12:;
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- /* "MACS2/IO/ScoreTrack.pyx":1093
+ /* "MACS2/IO/ScoreTrack.pyx":1111
*
* self.cutoff = cutoff
* for chrom in chrs: # <<<<<<<<<<<<<<
@@ -17320,7 +17601,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_peaks(struc
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "MACS2/IO/ScoreTrack.pyx":1139
+ /* "MACS2/IO/ScoreTrack.pyx":1157
* self.__close_peak(peak_content, peaks, min_length, chrom, max_gap/2 )
*
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@@ -17332,7 +17613,7 @@ static PyObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_peaks(struc
__pyx_r = __pyx_v_peaks;
goto __pyx_L0;
- /* "MACS2/IO/ScoreTrack.pyx":1068
+ /* "MACS2/IO/ScoreTrack.pyx":1086
* # return ret_peaks
*
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@@ -17424,7 +17705,7 @@ static PyObject *__pyx_pw_5MACS2_2IO_10ScoreTrack_12scoreTrackII_25call_peaks(Py
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}
if (unlikely(kw_args > 0)) {
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+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "call_peaks") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1086; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -17437,17 +17718,17 @@ static PyObject *__pyx_pw_5MACS2_2IO_10ScoreTrack_12scoreTrackII_25call_peaks(Py
}
}
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+ __pyx_v_cutoff = __pyx_PyFloat_AsFloat(values[0]); if (unlikely((__pyx_v_cutoff == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1086; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_cutoff = ((float)5.0);
}
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- __pyx_v_min_length = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_min_length == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1068; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_min_length = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_min_length == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1086; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_min_length = ((int)200);
}
if (values[2]) {
- __pyx_v_max_gap = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_max_gap == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1068; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_max_gap = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_max_gap == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1086; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_max_gap = ((int)50);
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@@ -17455,13 +17736,13 @@ static PyObject *__pyx_pw_5MACS2_2IO_10ScoreTrack_12scoreTrackII_25call_peaks(Py
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goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("call_peaks", 0, 0, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1068; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("call_peaks", 0, 0, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1086; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("MACS2.IO.ScoreTrack.scoreTrackII.call_peaks", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
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+ 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 = 1086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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/* function exit code */
@@ -17488,7 +17769,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_10ScoreTrack_12scoreTrackII_24call_peaks(st
__pyx_t_2.min_length = __pyx_v_min_length;
__pyx_t_2.max_gap = __pyx_v_max_gap;
__pyx_t_2.call_summits = __pyx_v_call_summits;
- __pyx_t_1 = __pyx_vtabptr_5MACS2_2IO_10ScoreTrack_scoreTrackII->call_peaks(__pyx_v_self, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1068; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_vtabptr_5MACS2_2IO_10ScoreTrack_scoreTrackII->call_peaks(__pyx_v_self, 1, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
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@@ -17505,7 +17786,7 @@ static PyObject *__pyx_pf_5MACS2_2IO_10ScoreTrack_12scoreTrackII_24call_peaks(st
return __pyx_r;
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+/* "MACS2/IO/ScoreTrack.pyx":1159
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if (__pyx_optional_args) {
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+ /* "MACS2/IO/ScoreTrack.pyx":1171
* double summit_value, tvalue, tsummitvalue
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@@ -17563,57 +17844,57 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_1);
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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__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;
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+ __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 = 1172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_4) {
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+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_tsummit = ((PyObject*)__pyx_t_3);
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@@ -17622,7 +17903,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak
*/
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PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -17669,7 +17950,7 @@ static PyBoolObject *__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak
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+ /* "MACS2/IO/ScoreTrack.pyx":1295
*
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}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "MACS2/IO/ScoreTrack.pyx":1279
+ /* "MACS2/IO/ScoreTrack.pyx":1297
* for chrom in self.data.keys():
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__pyx_r = __pyx_v_t;
goto __pyx_L0;
- /* "MACS2/IO/ScoreTrack.pyx":1268
+ /* "MACS2/IO/ScoreTrack.pyx":1286
* return True
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return __pyx_r;
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+ if (!(likely(PyTuple_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected %.16s, got %.200s", "tuple", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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- /* "MACS2/IO/ScoreTrack.pyx":1300
+ /* "MACS2/IO/ScoreTrack.pyx":1318
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1300; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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+ /* "MACS2/IO/ScoreTrack.pyx":1320
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* assert lvl1_max_gap < lvl2_max_gap, "level 2 maximum gap should be larger than level 1."
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__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
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+ if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_8, &__pyx_t_11) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1333; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
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__Pyx_GOTREF(__pyx_t_8);
__Pyx_GOTREF(__pyx_t_11);
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__pyx_L12_try_end:;
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__pyx_v_i = __pyx_t_17;
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__Pyx_XDECREF_SET(__pyx_v_lvl2, __pyx_t_11);
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__Pyx_XGOTREF(__pyx_t_14);
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*/
while (1) {
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goto __pyx_L0;
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return __pyx_r;
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+/* "MACS2/IO/ScoreTrack.pyx":1398
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else {
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case 2:
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+ __Pyx_RaiseArgtupleInvalid("__init__", 0, 4, 8, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1398; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -21452,17 +21733,17 @@ static int __pyx_pw_5MACS2_2IO_10ScoreTrack_18TwoConditionScores_1__init__(PyObj
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int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("total", 0);
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PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "keys");
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return __pyx_r;
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__pyx_v_ndim = PyArray_NDIM(__pyx_v_self);
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__Pyx_GOTREF(__pyx_t_3);
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
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- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_info->buf = PyArray_DATA(__pyx_v_self);
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__pyx_v_info->ndim = __pyx_v_ndim;
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__pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2)));
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+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":230
* # 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 # <<<<<<<<<<<<<<
@@ -28393,7 +28674,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim);
- /* "numpy.pxd":228
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":231
* 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): # <<<<<<<<<<<<<<
@@ -28404,7 +28685,7 @@ 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;
- /* "numpy.pxd":229
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":232
* info.shape = info.strides + ndim
* for i in range(ndim):
* info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<<
@@ -28413,7 +28694,7 @@ 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]);
- /* "numpy.pxd":230
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":233
* for i in range(ndim):
* info.strides[i] = PyArray_STRIDES(self)[i]
* info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<<
@@ -28426,7 +28707,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
/*else*/ {
- /* "numpy.pxd":232
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":235
* info.shape[i] = PyArray_DIMS(self)[i]
* else:
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self) # <<<<<<<<<<<<<<
@@ -28435,7 +28716,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self));
- /* "numpy.pxd":233
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":236
* else:
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self)
* info.shape = <Py_ssize_t*>PyArray_DIMS(self) # <<<<<<<<<<<<<<
@@ -28446,7 +28727,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
__pyx_L11:;
- /* "numpy.pxd":234
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":237
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self)
* info.shape = <Py_ssize_t*>PyArray_DIMS(self)
* info.suboffsets = NULL # <<<<<<<<<<<<<<
@@ -28455,7 +28736,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->suboffsets = NULL;
- /* "numpy.pxd":235
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":238
* info.shape = <Py_ssize_t*>PyArray_DIMS(self)
* info.suboffsets = NULL
* info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<<
@@ -28464,7 +28745,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self);
- /* "numpy.pxd":236
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":239
* info.suboffsets = NULL
* info.itemsize = PyArray_ITEMSIZE(self)
* info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<<
@@ -28473,7 +28754,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0));
- /* "numpy.pxd":239
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":242
*
* cdef int t
* cdef char* f = NULL # <<<<<<<<<<<<<<
@@ -28482,7 +28763,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_f = NULL;
- /* "numpy.pxd":240
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":243
* cdef int t
* cdef char* f = NULL
* cdef dtype descr = self.descr # <<<<<<<<<<<<<<
@@ -28494,7 +28775,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_descr = ((PyArray_Descr *)__pyx_t_3);
__pyx_t_3 = 0;
- /* "numpy.pxd":244
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":247
* cdef int offset
*
* cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<<
@@ -28503,7 +28784,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
__pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr);
- /* "numpy.pxd":246
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":249
* cdef bint hasfields = PyDataType_HASFIELDS(descr)
*
* if not hasfields and not copy_shape: # <<<<<<<<<<<<<<
@@ -28521,7 +28802,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_L15_bool_binop_done:;
if (__pyx_t_1) {
- /* "numpy.pxd":248
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":251
* if not hasfields and not copy_shape:
* # do not call releasebuffer
* info.obj = None # <<<<<<<<<<<<<<
@@ -28537,7 +28818,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
/*else*/ {
- /* "numpy.pxd":251
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":254
* else:
* # need to call releasebuffer
* info.obj = self # <<<<<<<<<<<<<<
@@ -28552,7 +28833,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
__pyx_L14:;
- /* "numpy.pxd":253
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":256
* info.obj = self
*
* if not hasfields: # <<<<<<<<<<<<<<
@@ -28562,7 +28843,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0);
if (__pyx_t_1) {
- /* "numpy.pxd":254
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257
*
* if not hasfields:
* t = descr.type_num # <<<<<<<<<<<<<<
@@ -28572,7 +28853,7 @@ 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;
- /* "numpy.pxd":255
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258
* if not hasfields:
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* if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<<
@@ -28592,7 +28873,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
}
__pyx_L20_next_or:;
- /* "numpy.pxd":256
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259
* t = descr.type_num
* if ((descr.byteorder == c'>' and little_endian) or
* (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<<
@@ -28610,21 +28891,21 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_L19_bool_binop_done:;
if (__pyx_t_1) {
- /* "numpy.pxd":257
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260
* if ((descr.byteorder == c'>' and little_endian) or
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- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- /* "numpy.pxd":274
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":277
* elif t == NPY_CDOUBLE: f = "Zd"
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* elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<<
@@ -28633,7 +28914,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
*/
switch (__pyx_v_t) {
- /* "numpy.pxd":258
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":261
* (descr.byteorder == c'<' and not little_endian)):
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* if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<<
@@ -28644,7 +28925,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_b;
break;
- /* "numpy.pxd":259
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":262
* raise ValueError(u"Non-native byte order not supported")
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* elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<<
@@ -28655,7 +28936,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_B;
break;
- /* "numpy.pxd":260
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":263
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B"
* elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<<
@@ -28666,7 +28947,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_h;
break;
- /* "numpy.pxd":261
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":264
* elif t == NPY_UBYTE: f = "B"
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@@ -28677,7 +28958,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_H;
break;
- /* "numpy.pxd":262
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265
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@@ -28688,7 +28969,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_i;
break;
- /* "numpy.pxd":263
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266
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@@ -28699,7 +28980,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_I;
break;
- /* "numpy.pxd":264
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":267
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@@ -28710,7 +28991,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_l;
break;
- /* "numpy.pxd":265
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268
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@@ -28721,7 +29002,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P
__pyx_v_f = __pyx_k_L;
break;
- /* "numpy.pxd":266
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":269
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__pyx_v_f = __pyx_k_q;
break;
- /* "numpy.pxd":267
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270
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__pyx_v_f = __pyx_k_Q;
break;
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__pyx_v_f = __pyx_k_f;
break;
- /* "numpy.pxd":269
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272
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__pyx_v_f = __pyx_k_d;
break;
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__pyx_v_f = __pyx_k_g;
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__pyx_v_f = __pyx_k_Zf;
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+ __pyx_tuple__15 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__15)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__15);
__Pyx_GIVEREF(__pyx_tuple__15);
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__Pyx_GOTREF(__pyx_tuple__16);
__Pyx_GIVEREF(__pyx_tuple__16);
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+ __pyx_codeobj__17 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__16, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_init, 183, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MACS2/IO/ScoreTrack.pyx":191
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@@ -31014,7 +31291,7 @@ static int __Pyx_InitCachedConstants(void) {
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__Pyx_GOTREF(__pyx_tuple__18);
__Pyx_GIVEREF(__pyx_tuple__18);
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+ __pyx_codeobj__19 = (PyObject*)__Pyx_PyCode_New(3, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__18, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_add_chromosome, 191, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MACS2/IO/ScoreTrack.pyx":199
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@@ -31026,7 +31303,7 @@ static int __Pyx_InitCachedConstants(void) {
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__Pyx_GOTREF(__pyx_tuple__20);
__Pyx_GIVEREF(__pyx_tuple__20);
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+ __pyx_codeobj__21 = (PyObject*)__Pyx_PyCode_New(5, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__20, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_add, 199, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MACS2/IO/ScoreTrack.pyx":214
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@@ -31038,7 +31315,7 @@ static int __Pyx_InitCachedConstants(void) {
__pyx_tuple__22 = PyTuple_Pack(4, __pyx_n_s_self, __pyx_n_s_chrom, __pyx_n_s_d, __pyx_n_s_l); if (unlikely(!__pyx_tuple__22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__22);
__Pyx_GIVEREF(__pyx_tuple__22);
- __pyx_codeobj__23 = (PyObject*)__Pyx_PyCode_New(1, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__22, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_projects_m, __pyx_n_s_finalize, 214, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__23 = (PyObject*)__Pyx_PyCode_New(1, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__22, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_finalize, 214, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MACS2/IO/ScoreTrack.pyx":222
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@@ -31050,7 +31327,7 @@ static int __Pyx_InitCachedConstants(void) {
__pyx_tuple__24 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_chromosome); if (unlikely(!__pyx_tuple__24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__24);
__Pyx_GIVEREF(__pyx_tuple__24);
- __pyx_codeobj__25 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__24, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_projects_m, __pyx_n_s_get_data_by_chr, 222, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__25 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__24, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_get_data_by_chr, 222, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MACS2/IO/ScoreTrack.pyx":233
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@@ -31062,7 +31339,7 @@ static int __Pyx_InitCachedConstants(void) {
__pyx_tuple__26 = PyTuple_Pack(2, __pyx_n_s_self, __pyx_n_s_l); if (unlikely(!__pyx_tuple__26)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__26);
__Pyx_GIVEREF(__pyx_tuple__26);
- __pyx_codeobj__27 = (PyObject*)__Pyx_PyCode_New(1, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__26, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_projects_m, __pyx_n_s_get_chr_names, 233, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__27)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__27 = (PyObject*)__Pyx_PyCode_New(1, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__26, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_get_chr_names, 233, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__27)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MACS2/IO/ScoreTrack.pyx":242
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@@ -31074,7 +31351,7 @@ static int __Pyx_InitCachedConstants(void) {
__pyx_tuple__28 = PyTuple_Pack(14, __pyx_n_s_self, __pyx_n_s_fhd, __pyx_n_s_name, __pyx_n_s_description, __pyx_n_s_colname, __pyx_n_s_chrom, __pyx_n_s_chrs, __pyx_n_s_pre, __pyx_n_s_i, __pyx_n_s_l, __pyx_n_s_pos, __pyx_n_s_value, __pyx_n_s_write, __pyx_n_s_d); if (unlikely(!__pyx_tuple__28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_tuple__28);
__Pyx_GIVEREF(__pyx_tuple__28);
- __pyx_codeobj__29 = (PyObject*)__Pyx_PyCode_New(5, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__28, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_projects_m, __pyx_n_s_write_bedGraph, 242, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__29)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__29 = (PyObject*)__Pyx_PyCode_New(5, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__28, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_write_bedGraph, 242, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__29)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MACS2/IO/ScoreTrack.pyx":274
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@@ -31086,7 +31363,7 @@ static int __Pyx_InitCachedConstants(void) {
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__Pyx_GOTREF(__pyx_tuple__30);
__Pyx_GIVEREF(__pyx_tuple__30);
- __pyx_codeobj__31 = (PyObject*)__Pyx_PyCode_New(1, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__30, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_projects_m, __pyx_n_s_total, 274, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 274; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__31 = (PyObject*)__Pyx_PyCode_New(1, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__30, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_total, 274, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 274; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MACS2/IO/ScoreTrack.pyx":287
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@@ -31098,7 +31375,7 @@ static int __Pyx_InitCachedConstants(void) {
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__Pyx_GOTREF(__pyx_tuple__32);
__Pyx_GIVEREF(__pyx_tuple__32);
- __pyx_codeobj__33 = (PyObject*)__Pyx_PyCode_New(2, 0, 25, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__32, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_projects_m, __pyx_n_s_extract_value, 287, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__33 = (PyObject*)__Pyx_PyCode_New(2, 0, 25, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__32, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_extract_value, 287, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MACS2/IO/ScoreTrack.pyx":378
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@@ -31110,7 +31387,7 @@ static int __Pyx_InitCachedConstants(void) {
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__Pyx_GOTREF(__pyx_tuple__34);
__Pyx_GIVEREF(__pyx_tuple__34);
- __pyx_codeobj__35 = (PyObject*)__Pyx_PyCode_New(2, 0, 16, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__34, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_projects_m, __pyx_n_s_extract_average, 378, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__35)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_codeobj__35 = (PyObject*)__Pyx_PyCode_New(2, 0, 16, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__34, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_extract_average, 378, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__35)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MACS2/IO/ScoreTrack.pyx":408
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@@ -31122,7 +31399,7 @@ static int __Pyx_InitCachedConstants(void) {
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__Pyx_GOTREF(__pyx_tuple__36);
__Pyx_GIVEREF(__pyx_tuple__36);
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+ __pyx_codeobj__37 = (PyObject*)__Pyx_PyCode_New(2, 0, 15, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__36, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_taoliu_Dropbox_Projects_M, __pyx_n_s_extract_sum, 408, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__37)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_RefNannyFinishContext();
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__pyx_L1_error:;
@@ -31139,7 +31416,6 @@ static int __Pyx_InitGlobals(void) {
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__pyx_int_4 = PyInt_FromLong(4); if (unlikely(!__pyx_int_4)) {__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;}
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__pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
@@ -31248,6 +31524,7 @@ PyMODINIT_FUNC PyInit_ScoreTrack(void)
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__pyx_vtable_5MACS2_2IO_10ScoreTrack_scoreTrackII.compute_subtraction = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *))__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_subtraction;
__pyx_vtable_5MACS2_2IO_10ScoreTrack_scoreTrackII.compute_SPMR = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *))__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_SPMR;
+ __pyx_vtable_5MACS2_2IO_10ScoreTrack_scoreTrackII.compute_max = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *))__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_compute_max;
__pyx_vtable_5MACS2_2IO_10ScoreTrack_scoreTrackII.write_bedGraph = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *, PyObject *, PyObject *, PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII_write_bedGraph *__pyx_optional_args))__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_write_bedGraph;
__pyx_vtable_5MACS2_2IO_10ScoreTrack_scoreTrackII.call_peaks = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *, int __pyx_skip_dispatch, struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_peaks *__pyx_optional_args))__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII_call_peaks;
__pyx_vtable_5MACS2_2IO_10ScoreTrack_scoreTrackII.__pyx___close_peak = (PyBoolObject *(*)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_scoreTrackII *, PyObject *, PyObject *, int, PyObject *, struct __pyx_opt_args_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak *__pyx_optional_args))__pyx_f_5MACS2_2IO_10ScoreTrack_12scoreTrackII___close_peak;
@@ -31284,11 +31561,11 @@ PyMODINIT_FUNC PyInit_ScoreTrack(void)
__pyx_vtable_5MACS2_2IO_10ScoreTrack_TwoConditionScores.__pyx___add_a_peak = (PyObject *(*)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_TwoConditionScores *, PyObject *, PyObject *, PyArrayObject *, PyArrayObject *, PyArrayObject *, PyArrayObject *, int, int))__pyx_f_5MACS2_2IO_10ScoreTrack_18TwoConditionScores___add_a_peak;
__pyx_vtable_5MACS2_2IO_10ScoreTrack_TwoConditionScores.mean_from_peakcontent = (float (*)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_TwoConditionScores *, PyObject *))__pyx_f_5MACS2_2IO_10ScoreTrack_18TwoConditionScores_mean_from_peakcontent;
__pyx_vtable_5MACS2_2IO_10ScoreTrack_TwoConditionScores.total = (long (*)(struct __pyx_obj_5MACS2_2IO_10ScoreTrack_TwoConditionScores *))__pyx_f_5MACS2_2IO_10ScoreTrack_18TwoConditionScores_total;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_10ScoreTrack_TwoConditionScores) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_10ScoreTrack_TwoConditionScores) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_10ScoreTrack_TwoConditionScores.tp_print = 0;
#if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_5MACS2_2IO_10ScoreTrack_TwoConditionScores, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_5MACS2_2IO_10ScoreTrack_TwoConditionScores, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_5MACS2_2IO_10ScoreTrack_18TwoConditionScores___init__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_5MACS2_2IO_10ScoreTrack_18TwoConditionScores___init__.doc = __pyx_doc_5MACS2_2IO_10ScoreTrack_18TwoConditionScores___init__;
@@ -31296,10 +31573,10 @@ PyMODINIT_FUNC PyInit_ScoreTrack(void)
}
}
#endif
- if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_10ScoreTrack_TwoConditionScores.tp_dict, __pyx_vtabptr_5MACS2_2IO_10ScoreTrack_TwoConditionScores) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttrString(__pyx_m, "TwoConditionScores", (PyObject *)&__pyx_type_5MACS2_2IO_10ScoreTrack_TwoConditionScores) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5MACS2_2IO_10ScoreTrack_TwoConditionScores.tp_dict, __pyx_vtabptr_5MACS2_2IO_10ScoreTrack_TwoConditionScores) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttrString(__pyx_m, "TwoConditionScores", (PyObject *)&__pyx_type_5MACS2_2IO_10ScoreTrack_TwoConditionScores) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5MACS2_2IO_10ScoreTrack_TwoConditionScores = &__pyx_type_5MACS2_2IO_10ScoreTrack_TwoConditionScores;
- if (PyType_Ready(&__pyx_type_5MACS2_2IO_10ScoreTrack___pyx_scope_struct____add_broadpeak) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5MACS2_2IO_10ScoreTrack___pyx_scope_struct____add_broadpeak) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5MACS2_2IO_10ScoreTrack___pyx_scope_struct____add_broadpeak.tp_print = 0;
__pyx_ptype_5MACS2_2IO_10ScoreTrack___pyx_scope_struct____add_broadpeak = &__pyx_type_5MACS2_2IO_10ScoreTrack___pyx_scope_struct____add_broadpeak;
/*--- Type import code ---*/
@@ -31311,10 +31588,10 @@ PyMODINIT_FUNC PyInit_ScoreTrack(void)
#endif
0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __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 = 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;}
+ __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_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;}
/*--- Variable import code ---*/
@@ -31802,7 +32079,7 @@ PyMODINIT_FUNC PyInit_ScoreTrack(void)
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
/* "MACS2/IO/ScoreTrack.pyx":1
- * # Time-stamp: <2015-03-05 14:21:33 Tao Liu> # <<<<<<<<<<<<<<
+ * # Time-stamp: <2016-02-12 00:12:45 Tao Liu> # <<<<<<<<<<<<<<
*
* """Module for Feature IO classes.
*/
@@ -31811,7 +32088,7 @@ PyMODINIT_FUNC PyInit_ScoreTrack(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;
- /* "numpy.pxd":975
+ /* "../../../../../../Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979
* arr.base = baseptr
*
* cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<<
@@ -35489,32 +35766,6 @@ 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 int __Pyx_check_binary_version(void) {
char ctversion[4], rtversion[4];
PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
diff --git a/MACS2/IO/ScoreTrack.pyx b/MACS2/IO/ScoreTrack.pyx
index 91a4d72..1800666 100644
--- a/MACS2/IO/ScoreTrack.pyx
+++ b/MACS2/IO/ScoreTrack.pyx
@@ -1,4 +1,4 @@
-# Time-stamp: <2015-03-05 14:21:33 Tao Liu>
+# Time-stamp: <2016-02-12 00:12:45 Tao Liu>
"""Module for Feature IO classes.
@@ -688,6 +688,7 @@ cdef class scoreTrackII:
f: log10 fold enrichment
F: linear fold enrichment
d: subtraction
+ M: maximum
m: fragment pileup per million reads
"""
if scoring_method == 'p':
@@ -709,6 +710,8 @@ cdef class scoreTrackII:
self.compute_subtraction()
elif scoring_method == 'm':
self.compute_SPMR()
+ elif scoring_method == 'M':
+ self.compute_max()
else:
raise NotImplemented
@@ -959,6 +962,21 @@ cdef class scoreTrackII:
self.scoring_method = 'm'
return
+ cdef compute_max ( self ):
+ cdef:
+ np.ndarray p, c, v
+ long l, i
+
+ for chrom in self.data.keys():
+ p = self.data[chrom][1]
+ c = self.data[chrom][2]
+ v = self.data[chrom][3]
+ l = self.datalength[chrom]
+ for i in range(l):
+ v[ i ] = max(p[ i ],c[ i ])
+ self.scoring_method = 'M'
+ return
+
cpdef write_bedGraph ( self, fhd, str name, str description, short column = 3):
"""Write all data to fhd in bedGraph Format.
diff --git a/MACS2/OptValidator.py b/MACS2/OptValidator.py
index 02d3bc4..4c72412 100644
--- a/MACS2/OptValidator.py
+++ b/MACS2/OptValidator.py
@@ -1,4 +1,4 @@
-# Time-stamp: <2015-05-19 13:42:30 Tao Liu>
+# Time-stamp: <2016-02-15 14:57:27 Tao Liu>
"""Module Description
@@ -25,8 +25,8 @@ from argparse import ArgumentError
from subprocess import Popen, PIPE
from math import log
from MACS2.IO.Parser import BEDParser, ELANDResultParser, ELANDMultiParser, \
- ELANDExportParser, SAMParser, BAMParser, \
- BAMPEParser, BowtieParser, guess_parser
+ ELANDExportParser, SAMParser, BAMParser, BAMPEParser,\
+ BEDPEParser, BowtieParser, guess_parser
# ------------------------------------
# constants
# ------------------------------------
@@ -76,6 +76,9 @@ def opt_validate ( options ):
options.parser = BAMPEParser
options.gzip_flag = True
options.nomodel = True
+ elif options.format == "BEDPE":
+ options.parser = BEDPEParser
+ options.nomodel = True
elif options.format == "BOWTIE":
options.parser = BowtieParser
elif options.format == "AUTO":
@@ -213,9 +216,12 @@ def opt_validate ( options ):
if options.fecutoff != 1.0:
options.argtxt += "# Additional cutoff on fold-enrichment is: %.2f\n" % (options.fecutoff)
- if options.format == "BAMPE":
+ if options.format in ["BAMPE", "BEDPE"]:
# neutralize SHIFT
options.shift = 0
+ options.argtxt += "# Paired-End mode is on\n"
+ else:
+ options.argtxt += "# Paired-End mode is off\n"
#if options.refine_peaks:
# options.argtxt += "# Refining peak for read balance is on\n"
@@ -542,6 +548,9 @@ def opt_validate_predictd ( options ):
options.parser = BAMPEParser
options.gzip_flag = True
options.nomodel = True
+ elif options.format == "BEDPE":
+ options.parser = BEDPEParser
+ options.nomodel = True
elif options.format == "BOWTIE":
options.parser = BowtieParser
elif options.format == "AUTO":
@@ -653,7 +662,7 @@ def opt_validate_bdgcmp ( options ):
# methods should be valid:
for method in set(options.method):
- if method not in [ 'ppois', 'qpois', 'subtract', 'logFE', 'FE', 'logLR', 'slogLR' ]:
+ if method not in [ 'ppois', 'qpois', 'subtract', 'logFE', 'FE', 'logLR', 'slogLR', 'max' ]:
logging.error( "Invalid method: %s" % method )
sys.exit( 1 )
@@ -732,7 +741,7 @@ def opt_validate_bdgopt ( options ):
# methods should be valid:
- if options.method.lower() not in [ 'multiply', 'add', 'p2q']:
+ if options.method.lower() not in [ 'multiply', 'add', 'p2q', 'max', 'min']:
logging.error( "Invalid method: %s" % options.method )
sys.exit( 1 )
diff --git a/MACS2/Pileup.c b/MACS2/Pileup.c
index 138a145..318997c 100644
--- a/MACS2/Pileup.c
+++ b/MACS2/Pileup.c
@@ -13345,7 +13345,7 @@ PyMODINIT_FUNC PyInit_Pileup(void)
__pyx_t_2 = 0;
/* "MACS2/Pileup.pyx":1
- * # Time-stamp: <2015-04-20 14:26:53 Tao Liu> # <<<<<<<<<<<<<<
+ * # Time-stamp: <2016-02-15 16:18:10 Tao Liu> # <<<<<<<<<<<<<<
*
* """Module Description: For pileup functions.
*/
diff --git a/MACS2/Pileup.pyx b/MACS2/Pileup.pyx
index fc85d1c..cd26f0a 100644
--- a/MACS2/Pileup.pyx
+++ b/MACS2/Pileup.pyx
@@ -1,4 +1,4 @@
-# Time-stamp: <2015-04-20 14:26:53 Tao Liu>
+# Time-stamp: <2016-02-15 16:18:10 Tao Liu>
"""Module Description: For pileup functions.
diff --git a/MACS2/bdgcmp_cmd.py b/MACS2/bdgcmp_cmd.py
index 9cd3946..30dfa5e 100644
--- a/MACS2/bdgcmp_cmd.py
+++ b/MACS2/bdgcmp_cmd.py
@@ -1,4 +1,4 @@
-# Time-stamp: <2015-03-05 13:40:31 Tao Liu>
+# Time-stamp: <2016-02-12 00:11:11 Tao Liu>
import sys
import os
@@ -78,6 +78,8 @@ def run( options ):
sbtrack.change_score_method( ord('l') )
elif method == 'slogLR': # log likelihood
sbtrack.change_score_method( ord('s') )
+ elif method == 'max':
+ sbtrack.change_score_method( ord('M') )
else:
raise Exception("Can't reach here!")
diff --git a/MACS2/bdgopt_cmd.py b/MACS2/bdgopt_cmd.py
index 3cd9535..796fe9e 100644
--- a/MACS2/bdgopt_cmd.py
+++ b/MACS2/bdgopt_cmd.py
@@ -1,4 +1,4 @@
-# Time-stamp: <2015-03-05 13:41:20 Tao Liu>
+# Time-stamp: <2016-02-12 00:43:42 Tao Liu>
"""Description: Modify bedGraph file
@@ -54,14 +54,20 @@ def run( options ):
btrack = bio.build_bdgtrack(baseline_value=0)
info("Modify bedGraph...")
- if options.method.lower() == "multiply":
- btrack.apply_func( lambda x: x * options.extraparam)
- elif options.method.lower() == "add":
- btrack.apply_func( lambda x: x + options.extraparam)
- elif options.method.lower() == "p2q":
+ if options.method.lower() == "p2q":
btrack.p2q()
elif options.method.lower() == "analen":
btrack.analen()
+ else:
+ extraparam = float(options.extraparam[0])
+ if options.method.lower() == "multiply":
+ btrack.apply_func( lambda x: x * extraparam)
+ elif options.method.lower() == "add":
+ btrack.apply_func( lambda x: x + extraparam)
+ elif options.method.lower() == "max":
+ btrack.apply_func( lambda x: x if x> extraparam else extraparam )
+ elif options.method.lower() == "min":
+ btrack.apply_func( lambda x: x if x< extraparam else extraparam )
ofile = os.path.join( options.outdir, options.ofile )
info("Write bedGraph of modified scores...")
diff --git a/MACS2/callpeak_cmd.py b/MACS2/callpeak_cmd.py
index 00462cd..4cf5c8a 100644
--- a/MACS2/callpeak_cmd.py
+++ b/MACS2/callpeak_cmd.py
@@ -1,4 +1,4 @@
-# Time-stamp: <2015-12-22 11:55:15 Tao Liu>
+# Time-stamp: <2016-02-15 16:12:30 Tao Liu>
"""Description: MACS 2 main executable
@@ -23,6 +23,7 @@ import os
import sys
import logging
from time import strftime
+import tempfile
# ------------------------------------
# own python modules
@@ -60,16 +61,18 @@ def run( args ):
error = options.error
#0 output arguments
info("\n"+options.argtxt)
- options.PE_MODE = options.format in ('BAMPE',)
+ options.PE_MODE = options.format in ('BAMPE','BEDPE')
if options.PE_MODE: tag = 'fragment' # call things fragments not tags
else: tag = 'tag'
-
+
+ tempfile.tempdir = options.tempdir
+
#1 Read tag files
info("#1 read %s files...", tag)
if options.PE_MODE: (treat, control) = load_frag_files_options (options)
else: (treat, control) = load_tag_files_options (options)
if control is not None: check_names(treat, control, error)
-
+
info("#1 %s size = %d", tag, options.tsize)
tagsinfo = "# %s size is determined as %d bps\n" % (tag, options.tsize)
diff --git a/PKG-INFO b/PKG-INFO
index af49a01..cf74d85 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: MACS2
-Version: 2.1.0.20151222
+Version: 2.1.1.20160226
Summary: Model Based Analysis for ChIP-Seq data
Home-page: http://github.com/taoliu/MACS/
Author: Tao Liu
diff --git a/README.rst b/README.rst
index 520f5d3..18039c4 100644
--- a/README.rst
+++ b/README.rst
@@ -1,7 +1,7 @@
========================
README for MACS (2.1.0)
========================
-Time-stamp: <2015-04-20 15:37:09 Tao Liu>
+Time-stamp: <2016-02-15 15:31:42 Tao Liu>
Introduction
============
@@ -103,9 +103,11 @@ option.
Format of tag file, can be "ELAND", "BED", "ELANDMULTI",
"ELANDEXPORT", "ELANDMULTIPET" (for pair-end tags), "SAM", "BAM",
-"BOWTIE" or "BAMPE". Default is "AUTO" which will allow MACS to decide
-the format automatically. "AUTO" is also usefule when you combine
-different formats of files.
+"BOWTIE", "BAMPE" or "BEDPE". Default is "AUTO" which will allow MACS
+to decide the format automatically. "AUTO" is also usefule when you
+combine different formats of files. Note that MACS can't detect
+"BAMPE" or "BEDPE" format with "AUTO", and you have to implicitly
+specify the format for "BAMPE" and "BEDPE".
The BED format can be found at `UCSC genome browser website <http://genome.ucsc.edu/FAQ/FAQformat#format1>`_.
@@ -142,6 +144,12 @@ each line MUST represents only ONE tag, with fields of:
was A, not whatever is was in read).
12. Position and type of first substitution error, as above.
+The BEDPE format is a simplified and more flexible BED format, which
+only contains the first three columns defining the chromosome name,
+left and right position of the fragment from Paired-end
+sequencing. Note, this is NOT the same format used by BEDTOOLS, and
+BEDTOOLS version of BEDPE is actually not in a standard BED format.
+
If the format is ELANDMULTI, the file must be ELAND output file from
multiple-match mode, each line MUST represents only ONE tag, with
fields of:
@@ -161,8 +169,8 @@ If the format is BAM/SAM, please check the definition in
(http://samtools.sourceforge.net/samtools.shtml). Pair-end mapping
results can be saved in a single BAM file, if so, MACS will
automatically keep the left mate(5' end) tag. However, when format
-BAMPE is specified, MACS will use the real fragments inferred from
-alignment results for reads pileup.
+BAMPE is specified, MACS will use the real fragments inferred
+from alignment results for reads pileup.
If the format is BOWTIE, you need to provide the ASCII bowtie output
file with the suffix '.map'. Please note that, you need to make sure
@@ -225,10 +233,10 @@ uses 11th column as the sequence name which should be the chromosome
names.
5) A special mode will be triggered while format is specified as
-'BAMPE'. In this way, MACS2 will process the BAM files as paired-end
-data. Instead of building bimodal distribution of plus and minus
-strand reads to predict fragment size, MACS2 now will use actual
-insert sizes of pairs of reads to build fragment pileup.
+'BAMPE' or 'BEDPE'. In this way, MACS2 will process the BAM or BED
+files as paired-end data. Instead of building bimodal distribution of
+plus and minus strand reads to predict fragment size, MACS2 now will
+use actual insert sizes of pairs of reads to build fragment pileup.
-g/--gsize
@@ -347,7 +355,7 @@ fragments. When this value is negative, ends will be moved toward
as default 0 for ChIP-Seq datasets, or -1 * half of EXTSIZE together
with --extsize option for detecting enriched cutting loci such as
certain DNAseI-Seq datasets. Note, you can't set values other than 0
-if format is BAMPE for paired-end data. Default is 0.
+if format is BAMPE or BEDPE for paired-end data. Default is 0.
Here are some examples for combining --shift and --extsize:
diff --git a/bin/macs2 b/bin/macs2
index 615a074..d11db9e 100644
--- a/bin/macs2
+++ b/bin/macs2
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-# Time-stamp: <2015-06-03 00:07:13 Tao Liu>
+# Time-stamp: <2016-02-15 14:56:39 Tao Liu>
"""Description: MACS v2 main executable.
@@ -23,6 +23,7 @@ the distribution).
import os
import sys
import argparse as ap
+import tempfile
# ------------------------------------
# own python modules
@@ -183,8 +184,8 @@ def add_callpeak_parser( subparsers ):
group_input.add_argument( "-f", "--format", dest = "format", type = str,
choices = ("AUTO", "BAM", "SAM", "BED", "ELAND",
"ELANDMULTI", "ELANDEXPORT", "BOWTIE",
- "BAMPE"),
- help = "Format of tag file, \"AUTO\", \"BED\" or \"ELAND\" or \"ELANDMULTI\" or \"ELANDEXPORT\" or \"SAM\" or \"BAM\" or \"BOWTIE\" or \"BAMPE\". The default AUTO option will let MACS decide which format the file is. Please check the definition in README file if you choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT: \"AUTO\"",
+ "BAMPE", "BEDPE"),
+ help = "Format of tag file, \"AUTO\", \"BED\" or \"ELAND\" or \"ELANDMULTI\" or \"ELANDEXPORT\" or \"SAM\" or \"BAM\" or \"BOWTIE\" or \"BAMPE\" or \"BEDPE\". The default AUTO option will let MACS decide which format (except for BAMPE and BEDPE which should be implicitly set) the file is. Please check the definition in README. Please note that if the format is set as BAMPE or BEDPE, MACS2 will call its special Paired-end mode to call peaks by piling up the a [...]
default = "AUTO" )
group_input.add_argument( "-g", "--gsize", dest = "gsize", type = str, default = "hs",
help = "Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs" )
@@ -225,7 +226,7 @@ def add_callpeak_parser( subparsers ):
help = "Whether or not to build the shifting model. If True, MACS will not build model. by default it means shifting size = 100, try to set extsize to change it. DEFAULT: False",
default = False )
group_bimodal.add_argument( "--shift", dest = "shift", type = int, default = 0,
- help = "(NOT the legacy --shiftsize option!) The arbitrary shift in bp. Use discretion while setting it other than default value. When NOMODEL is set, MACS will use this value to move cutting ends (5') towards 5'->3' direction then apply EXTSIZE to extend them to fragments. When this value is negative, ends will be moved toward 3'->5' direction. Recommended to keep it as default 0 for ChIP-Seq datasets, or -1 * half of EXTSIZE together with EXTSIZE option f [...]
+ help = "(NOT the legacy --shiftsize option!) The arbitrary shift in bp. Use discretion while setting it other than default value. When NOMODEL is set, MACS will use this value to move cutting ends (5') towards 5'->3' direction then apply EXTSIZE to extend them to fragments. When this value is negative, ends will be moved toward 3'->5' direction. Recommended to keep it as default 0 for ChIP-Seq datasets, or -1 * half of EXTSIZE together with EXTSIZE option f [...]
group_bimodal.add_argument( "--extsize", dest = "extsize", type = int, default = 200,
help = "The arbitrary extension size in bp. When nomodel is true, MACS will use this value as fragment size to extend each read towards 3' end, then pile them up. It's exactly twice the number of obsolete SHIFTSIZE. In previous language, each read is moved 5'->3' direction to middle of fragment by 1/2 d, then extended to both direction with 1/2 d. This is equivalent to say each read is extended towards 5'->3' into a d size fragment. DEFAULT: 200. EXTSIZE a [...]
# The next two options are obsolete. To compare two conditions, using bdgcmp.
@@ -252,6 +253,8 @@ def add_callpeak_parser( subparsers ):
help = "When set, random sampling method will scale down the bigger sample. By default, MACS uses linear scaling. Warning: This option will make your result unstable and irreproducible since each time, random reads would be selected. Consider to use 'randsample' script instead. <not implmented>If used together with --SPMR, 1 million unique reads will be randomly picked.</not implemented> Caution: due to the implementation, the final number of selected rea [...]
group_callpeak.add_argument( "--seed", dest = "seed", type = int, default = -1,
help = "Set the random seed while down sampling data. Must be a non-negative integer in order to be effective. DEFAULT: not set" )
+ group_callpeak.add_argument( "--tempdir", dest="tempdir", default=tempfile.gettempdir(),
+ help = "Optional directory to store temp files. DEFAULT: %(default)s")
group_callpeak.add_argument( "--nolambda", dest = "nolambda", action = "store_true",
help = "If True, MACS will use fixed background lambda as local lambda for every peak region. Normally, MACS calculates a dynamic local lambda to reflect the local bias due to potential chromatin structure. ",
default = False )
@@ -429,8 +432,8 @@ def add_bdgcmp_parser( subparsers ):
help = "The pseudocount used for calculating logLR, logFE or FE. The count will be applied after normalization of sequencing depth. DEFAULT: 0.0, no pseudocount is applied.")
argparser_bdgcmp.add_argument( "-m", "--method", dest = "method", type = str, nargs = "+",
- choices = ( "ppois", "qpois", "subtract", "logFE", "FE", "logLR", "slogLR" ),
- help = "Method to use while calculating a score in any bin by comparing treatment value and control value. Available choices are: ppois, qpois, subtract, logFE, logLR, and slogLR. They represent Poisson Pvalue (-log10(pvalue) form) using control as lambda and treatment as observation, q-value through a BH process for poisson pvalues, subtraction from treatment, linear scale fold enrichment, log10 fold enrichment(need to set pseudocount), log10 likelihoo [...]
+ choices = ( "ppois", "qpois", "subtract", "logFE", "FE", "logLR", "slogLR", "max" ),
+ help = "Method to use while calculating a score in any bin by comparing treatment value and control value. Available choices are: ppois, qpois, subtract, logFE, logLR, and slogLR. They represent Poisson Pvalue (-log10(pvalue) form) using control as lambda and treatment as observation, q-value through a BH process for poisson pvalues, subtraction from treatment, linear scale fold enrichment, log10 fold enrichment(need to set pseudocount), log10 likelihoo [...]
add_outdir_option( argparser_bdgcmp )
output_group = argparser_bdgcmp.add_mutually_exclusive_group( required = True )
@@ -448,8 +451,8 @@ def add_bdgopt_parser( subparsers ):
argparser_bdgopt.add_argument( "-i", "--ifile", dest = "ifile", type = str, required = True,
help = "MACS score in bedGraph. Note: this must be a bedGraph file covering the ENTIRE genome. REQUIRED" )
argparser_bdgopt.add_argument( "-m", "--method", dest = "method", type = str,
- choices = ( "multiply", "add", "p2q" ),
- help = "Method to modify the score column of bedGraph file. Available choices are: multiply, add or p2q. 1) multiply, the EXTRAPARAM is required and will be multiplied to the score column. If you intend to divide the score column by X, use value of 1/X as EXTRAPARAM. 2) add, the EXTRAPARAM is required and will be added to the score column. If you intend to subtract the score column by X, use value of -X as EXTRAPARAM. 3) p2q, this will convert p-value s [...]
+ choices = ( "multiply", "add", "p2q", "max", "min" ),
+ help = "Method to modify the score column of bedGraph file. Available choices are: multiply, add, max, min, or p2q. 1) multiply, the EXTRAPARAM is required and will be multiplied to the score column. If you intend to divide the score column by X, use value of 1/X as EXTRAPARAM. 2) add, the EXTRAPARAM is required and will be added to the score column. If you intend to subtract the score column by X, use value of -X as EXTRAPARAM. 3) max, the EXTRAPARAM i [...]
argparser_bdgopt.add_argument( "-p", "--extra-param", dest = "extraparam", type = float, nargs = "*",
help = "The extra parameter for METHOD. Check the detail of -m option.")
add_outdir_option( argparser_bdgopt )
@@ -566,8 +569,8 @@ def add_predictd_parser( subparsers ):
argparser_predictd.add_argument( "-f", "--format", dest = "format", type = str,
choices = ("AUTO", "BAM", "SAM", "BED", "ELAND",
"ELANDMULTI", "ELANDEXPORT", "BOWTIE",
- "BAMPE"),
- help = "Format of tag file, \"AUTO\", \"BED\" or \"ELAND\" or \"ELANDMULTI\" or \"ELANDEXPORT\" or \"SAM\" or \"BAM\" or \"BOWTIE\". The default AUTO option will let MACS decide which format the file is. Please check the definition in README file if you choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT: \"AUTO\"",
+ "BAMPE", "BEDPE"),
+ help = "Format of tag file, \"AUTO\", \"BED\" or \"ELAND\" or \"ELANDMULTI\" or \"ELANDEXPORT\" or \"SAM\" or \"BAM\" or \"BOWTIE\" or \"BAMPE\" or \"BEDPE\". The default AUTO option will let MACS decide which format the file is. Please check the definition in README file if you choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT: \"AUTO\"",
default = "AUTO" )
argparser_predictd.add_argument( "-g", "--gsize", dest = "gsize", type = str, default = "hs",
help = "Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs" )
diff --git a/setup.py b/setup.py
index 733d87b..f1da836 100644
--- a/setup.py
+++ b/setup.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-# Time-stamp: <2015-12-22 16:21:04 Tao Liu>
+# Time-stamp: <2016-02-26 10:41:57 Tao Liu>
"""Description
@@ -37,27 +37,28 @@ def main():
sys.stderr.write("CRITICAL: Python version must be 2.7!\n")
sys.exit(1)
- # User must check GCC, if >= 4.6, use -Ofast, otherwise -O3.
+ # I intend to use -Ofast, however if gcc version < 4.6, this option is unavailable so...
+ extra_c_args = ["-w","-O3","-ffast-math"] # for C, -Ofast implies -O3 and -ffast-math
- ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
- Extension("MACS2.IO.Parser",["MACS2/IO/Parser.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.Pileup", ["MACS2/Pileup.c","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
- Extension("MACS2.PeakModel", ["MACS2/PeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.c"], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.Signal", ["MACS2/Signal.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.c"], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.c"], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.c"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
- Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
+ ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
+ Extension("MACS2.IO.Parser",["MACS2/IO/Parser.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.Pileup", ["MACS2/Pileup.c","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
+ Extension("MACS2.PeakModel", ["MACS2/PeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.c"], extra_compile_args=extra_c_args),
+ Extension("MACS2.Signal", ["MACS2/Signal.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.c"], extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.c"], extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.c"], libraries=["m"], extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
+ Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),
+ Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),
]
setup(name="MACS2",
- version="2.1.0.20151222",
+ version="2.1.1.20160226",
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 f9898b6..5154664 100644
--- a/setup_w_cython.py
+++ b/setup_w_cython.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-# Time-stamp: <2015-12-22 16:21:12 Tao Liu>
+# Time-stamp: <2016-02-26 10:42:04 Tao Liu>
"""Description:
@@ -44,43 +44,46 @@ def main():
sys.stderr.write("CRITICAL: Python version must be 2.7!\n")
sys.exit(1)
+ # I intend to use -Ofast, however if gcc version < 4.6, this option is unavailable so...
+ extra_c_args = ["-w","-O3","-ffast-math"] # for C, -Ofast implies -O3 and -ffast-math
+
if has_cython:
- ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
- Extension("MACS2.IO.Parser",["MACS2/IO/Parser.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.Pileup", ["MACS2/Pileup.pyx","MACS2/cPosValCalculation.pxd","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
- Extension("MACS2.PeakModel", ["MACS2/PeakModel.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.pyx"], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.Signal", ["MACS2/Signal.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.pyx"], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.pyx"], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.pyx"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
- Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.hashtable", ["MACS2/hashtable.pyx"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.Statistics", ["MACS2/Statistics.pyx", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
+ ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
+ Extension("MACS2.IO.Parser",["MACS2/IO/Parser.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.Pileup", ["MACS2/Pileup.pyx","MACS2/cPosValCalculation.pxd","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
+ Extension("MACS2.PeakModel", ["MACS2/PeakModel.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.pyx"], extra_compile_args=extra_c_args),
+ Extension("MACS2.Signal", ["MACS2/Signal.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.pyx"], extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.pyx"], extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.pyx"], libraries=["m"], extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
+ Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.hashtable", ["MACS2/hashtable.pyx"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),
+ Extension("MACS2.Statistics", ["MACS2/Statistics.pyx", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),
]
else:
- ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
- Extension("MACS2.IO.Parser",["MACS2/IO/Parser.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.Pileup", ["MACS2/Pileup.c","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
- Extension("MACS2.PeakModel", ["MACS2/PeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.c"], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.Signal", ["MACS2/Signal.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.c"], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.c"], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.c"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
- Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
- Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
+ ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
+ Extension("MACS2.IO.Parser",["MACS2/IO/Parser.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.Pileup", ["MACS2/Pileup.c","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
+ Extension("MACS2.PeakModel", ["MACS2/PeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.c"], extra_compile_args=extra_c_args),
+ Extension("MACS2.Signal", ["MACS2/Signal.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.c"], extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.c"], extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.c"], libraries=["m"], extra_compile_args=extra_c_args),
+ Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
+ Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+ Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),
+ Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),
]
setup(name="MACS2",
- version="2.1.0.20151222",
+ version="2.1.1.20160226",
description="Model Based Analysis for ChIP-Seq data",
author='Tao Liu',
author_email='vladimir.liu at gmail.com',
--
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