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Fixed issue macs3-project#51. Set GCC flags to suppress all warning a…
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…nd set

optimization flag to -Ofast.
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@taoliu
taoliu committed Oct 23, 2014
1 parent 07d09ad commit 8b2ad81
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Showing 3 changed files with 52 additions and 56 deletions.
5 changes: 2 additions & 3 deletions MACS2/cPeakDetect.pyx
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@@ -1,4 +1,4 @@
# Time-stamp: <2014-08-22 13:49:38 Tao Liu>
# Time-stamp: <2014-10-23 15:18:38 Tao Liu>

"""Module Description
Expand Down Expand Up @@ -337,8 +337,7 @@ class PeakDetect:
save_SPMR = self.opt.do_SPMR,
cutoff_analysis_filename = self.opt.cutoff_analysis_file )

# calculate pvalue scores
if self.opt.trackline: self.scoretrack.enable_trackline()
if self.opt.trackline: scorecalculator.enable_trackline()

# call peaks
call_summits = self.opt.call_summits
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35 changes: 17 additions & 18 deletions setup.py
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@@ -1,5 +1,5 @@
#!/usr/bin/env python
# Time-stamp: <2014-10-23 15:06:57 Tao Liu>
# Time-stamp: <2014-10-23 15:48:18 Tao Liu>

"""Description
Expand Down Expand Up @@ -37,23 +37,22 @@ def main():
sys.stderr.write("CRITICAL: Python version must be 2.7!\n")
sys.exit(1)

ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir ),
Extension("MACS2.IO.cParser",["MACS2/IO/cParser.c"], include_dirs=numpy_include_dir),
Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir ),
Extension("MACS2.cArray", ["MACS2/cArray.c"]),
Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir),
Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.c"]),
Extension("MACS2.cSignal", ["MACS2/cSignal.c"], include_dirs=numpy_include_dir),
Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.c"],),
Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.c"],),
Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.c"], include_dirs=numpy_include_dir),
Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.c"], include_dirs=numpy_include_dir),
Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.c"], libraries=["m"]),
Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.c"], include_dirs=numpy_include_dir ),
#Extension("MACS2.IO.cDiffScore", ["MACS2/IO/cDiffScore.c"], include_dirs=numpy_include_dir ),
Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.c"], include_dirs=numpy_include_dir),
Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()]),
Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()]),
ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.cParser",["MACS2/IO/cParser.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.cArray", ["MACS2/cArray.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cSignal", ["MACS2/cSignal.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.c"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.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"]),
]

setup(name="MACS2",
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68 changes: 33 additions & 35 deletions setup_w_cython.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#!/usr/bin/env python
# Time-stamp: <2014-10-23 15:07:06 Tao Liu>
# Time-stamp: <2014-10-23 15:48:33 Tao Liu>

"""Description:
Expand Down Expand Up @@ -45,42 +45,40 @@ def main():
sys.exit(1)

if has_cython:
ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.pyx"], libraries=["m"], include_dirs=numpy_include_dir ),
Extension("MACS2.IO.cParser",["MACS2/IO/cParser.pyx"], include_dirs=numpy_include_dir),
Extension("MACS2.cPileup", ["MACS2/cPileup.pyx"], include_dirs=numpy_include_dir ),
Extension("MACS2.cArray", ["MACS2/cArray.pyx"]),
Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.pyx"], include_dirs=numpy_include_dir),
Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.pyx"]),
Extension("MACS2.cSignal", ["MACS2/cSignal.pyx"], include_dirs=numpy_include_dir),
Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.pyx"],),
Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.pyx"],),
Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.pyx"], include_dirs=numpy_include_dir),
Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.pyx"], include_dirs=numpy_include_dir),
Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.pyx"], libraries=["m"]),
Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.pyx"], include_dirs=numpy_include_dir ),
#Extension("MACS2.IO.cDiffScore", ["MACS2/IO/cDiffScore.pyx"], include_dirs=numpy_include_dir ),
Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.pyx"], include_dirs=numpy_include_dir),
Extension("MACS2.hashtable", ["MACS2/hashtable.pyx"], include_dirs=["MACS2/",numpy_get_include()]),
Extension("MACS2.Statistics", ["MACS2/Statistics.pyx", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()]),
ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.cParser",["MACS2/IO/cParser.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPileup", ["MACS2/cPileup.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.cArray", ["MACS2/cArray.pyx"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.pyx"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cSignal", ["MACS2/cSignal.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.pyx"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.pyx"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.pyx"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.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"]),
]
else:
ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir ),
Extension("MACS2.IO.cParser",["MACS2/IO/cParser.c"], include_dirs=numpy_include_dir),
Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir),
Extension("MACS2.cSignal", ["MACS2/cSignal.c"], include_dirs=numpy_include_dir),
Extension("MACS2.cArray", ["MACS2/cArray.c"]),
Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir),
Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.c"]),
Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.c"],),
Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.c"],),
Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.c"], include_dirs=numpy_include_dir),
Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.c"], include_dirs=numpy_include_dir),
Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.c"], libraries=["m"]),
Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.c"], include_dirs=numpy_include_dir),
#Extension("MACS2.IO.cDiffScore", ["MACS2/IO/cDiffScore.c"], include_dirs=numpy_include_dir ),
Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.c"], include_dirs=numpy_include_dir),
Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()]),
Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()]),
ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.cParser",["MACS2/IO/cParser.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.cArray", ["MACS2/cArray.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.cSignal", ["MACS2/cSignal.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.c"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.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"]),
]

setup(name="MACS2",
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