Merge pull request #125 from hammerlab/drop-read-evidence

Remove read_evidence and locus modules
openvax · Oct 1, 2015 · 9327dfc · 9327dfc
2 parents eb78621 + 8a5b0e3
commit 9327dfc
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Showing 14 changed files with 1 addition and 1,354 deletions.
diff --git a/setup.py b/setup.py
@@ -40,7 +40,7 @@
     setup(
         name='varcode',
         packages=find_packages(),
-        version="0.3.19",
+        version="0.4.0",
         description="Variant annotation in Python",
         long_description=readme,
         url="https://github.com/hammerlab/varcode",
@@ -62,6 +62,5 @@
             'biopython>=1.64',
             'pyvcf>=0.6.7',
             'memoized_property>=1.0.2',
-            'pysam>=0.8.3',
         ],
     )
diff --git a/test/data/reads/gatk_mini_bundle_extract.bam b/test/data/reads/gatk_mini_bundle_extract.bam
diff --git a/test/data/reads/gatk_mini_bundle_extract.bam.bai b/test/data/reads/gatk_mini_bundle_extract.bam.bai
diff --git a/test/data/reads/rna_chr17_41244936.bam b/test/data/reads/rna_chr17_41244936.bam
diff --git a/test/data/reads/rna_chr17_41244936.bam.bai b/test/data/reads/rna_chr17_41244936.bam.bai
diff --git a/test/read_evidence_performance.py b/test/read_evidence_performance.py
diff --git a/test/test_read_evidence.py b/test/test_read_evidence.py
diff --git a/varcode/__init__.py b/varcode/__init__.py
@@ -12,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .locus import Locus
 from .variant import Variant
 from .collection import Collection
 from .effect_collection import EffectCollection
@@ -52,7 +51,6 @@
 
 __all__ = [
     # basic classes
-    "Locus",
     "Variant",
     "Collection",
     "EffectCollection",

diff --git a/varcode/locus.py b/varcode/locus.py