From 6c73a58a28a9c887d6ecf46f85b5290be2b7ce0e Mon Sep 17 00:00:00 2001
From: Chris Beaumont <cbeaumont@counsyl.com>
Date: Tue, 10 Mar 2015 17:34:24 -0700
Subject: [PATCH 1/3] Update setup.py for new pip

---
 setup.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index fb41e85..fbe149c 100644
--- a/setup.py
+++ b/setup.py
@@ -2,6 +2,7 @@
 
 from setuptools import setup
 from pip.req import parse_requirements
+from pip.download import PipSession
 import sys
 
 description = ("This library provides a simple to use Python API for parsing, "
@@ -32,7 +33,7 @@ def main():
         scripts=[],
         install_requires=['pip>=1.2'],
         tests_require=[str(line.req) for line in
-                       parse_requirements('requirements-dev.txt')],
+                       parse_requirements('requirements-dev.txt', session=PipSession())],
     )
 
 if __name__ == '__main__':

From 77015b8554293f8abf75608870f794541531f3bc Mon Sep 17 00:00:00 2001
From: Chris Beaumont <cbeaumont@counsyl.com>
Date: Wed, 11 Mar 2015 08:47:51 -0700
Subject: [PATCH 2/3] Raise error with nonincreasing coordinates in HGVS names.

Closes #17
---
 pyhgvs/__init__.py              |  9 ++++++++-
 pyhgvs/tests/test_hgvs_names.py | 14 ++++++++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/pyhgvs/__init__.py b/pyhgvs/__init__.py
index 0823e4e..c9b2c1b 100644
--- a/pyhgvs/__init__.py
+++ b/pyhgvs/__init__.py
@@ -92,7 +92,6 @@
 BASES = BASE+
 
 """
-
 import re
 
 from .variants import justify_indel
@@ -746,6 +745,7 @@ def parse(self, name):
         # Parse prefix and allele.
         self.parse_allele(allele)
         self.parse_prefix(prefix, self.kind)
+        self._validate()
 
     def parse_prefix(self, prefix, kind):
         """
@@ -970,6 +970,13 @@ def parse_genome(self, details):
 
         raise InvalidHGVSName(details, 'genomic allele')
 
+    def _validate(self):
+        """
+        Check for internal inconsistencies in representation
+        """
+        if self.start > self.end:
+            raise InvalidHGVSName(reason="Coordinates are nonincreasing")
+
     def __repr__(self):
         try:
             return "HGVSName('%s')" % self.format()
diff --git a/pyhgvs/tests/test_hgvs_names.py b/pyhgvs/tests/test_hgvs_names.py
index c947dd4..0f12cd8 100644
--- a/pyhgvs/tests/test_hgvs_names.py
+++ b/pyhgvs/tests/test_hgvs_names.py
@@ -11,6 +11,7 @@
 from .. import CDNACoord
 from .. import CDNA_STOP_CODON
 from .. import HGVSName
+from .. import InvalidHGVSName
 from .. import cdna_to_genomic_coord
 from .. import format_hgvs_name
 from .. import genomic_to_cdna_coord
@@ -177,6 +178,19 @@ def test_name_to_variant_refseqs():
             repr([hgvs_name, variant, hgvs_variant]))
 
 
+@nose.tools.raises(InvalidHGVSName)
+def test_invalid_coordinates():
+    """
+    Regression test for 17
+    """
+    if not SequenceFileDB:
+        raise nose.SkipTest
+
+    genome = SequenceFileDB('pyhgvs/tests/data/test_refseqs.fa')
+    hgvs_name = 'NC_000005.10:g.177421339_177421327delACTCGAGTGCTCC'
+    parse_hgvs_name(hgvs_name, genome, get_transcript=get_transcript)
+
+
 # Test examples of cDNA coordinates.
 _parse_cdna_coords = [
     ('1001', CDNACoord(1001)),

From cffd9c0c546ef379ae21fd383206720ce6ff8dc3 Mon Sep 17 00:00:00 2001
From: Chris Beaumont <cbeaumont@counsyl.com>
Date: Wed, 11 Mar 2015 15:34:51 -0700
Subject: [PATCH 3/3] version bump

---
 setup.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index fbe149c..ace27d1 100644
--- a/setup.py
+++ b/setup.py
@@ -20,7 +20,7 @@ def main():
 
     setup(
         name='pyhgvs',
-        version='0.9.3',
+        version='0.9.4',
         description='HGVS name parsing and formatting',
         long_description=description,
         author='Matt Rasmussen',
@@ -33,7 +33,8 @@ def main():
         scripts=[],
         install_requires=['pip>=1.2'],
         tests_require=[str(line.req) for line in
-                       parse_requirements('requirements-dev.txt', session=PipSession())],
+                       parse_requirements('requirements-dev.txt',
+                                          session=PipSession())],
     )
 
 if __name__ == '__main__':