🔥 small but great performance improvements

papaemmelab · Dec 12, 2018 · 429cdea · 429cdea
1 parent 629ef50
commit 429cdea
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Showing 5 changed files with 3 additions and 1 deletion.
diff --git a/mergesvvcf/locations.py → mergesvvcf/locations.pyx b/mergesvvcf/locations.py → mergesvvcf/locations.pyx
@@ -130,6 +130,7 @@ def __find__(self, locn):
             if super(locationdict, self).__contains__(locn+off):
                 present = True
                 foundoff = off
+                break
         return present, foundoff
 
     def __contains__(self, locn):

diff --git a/mergesvvcf/mergedfile.py b/mergesvvcf/mergedfile.py
@@ -1,4 +1,5 @@
 from __future__ import print_function
+import pyximport; pyximport.install()
 import os
 import operator
 import pysam

diff --git a/mergesvvcf/variantdict.py → mergesvvcf/variantdict.pyx b/mergesvvcf/variantdict.py → mergesvvcf/variantdict.pyx
diff --git a/mergesvvcf/vcftobreakpoints.py → mergesvvcf/vcftobreakpoints.pyx b/mergesvvcf/vcftobreakpoints.py → mergesvvcf/vcftobreakpoints.pyx
diff --git a/setup.py b/setup.py
@@ -52,7 +52,7 @@
 
     packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
 
-    install_requires=['pysam'],
+    install_requires=['pysam','Cython'],
 
     test_suite='tests',