Fixed error for vci parsing on diploid vci file

churchill-lab · Jun 6, 2018 · a7d69a5 · a7d69a5
1 parent 112be5e
commit a7d69a5
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Showing 4 changed files with 9 additions and 5 deletions.
diff --git a/g2gtools/__init__.py b/g2gtools/__init__.py
@@ -1,3 +1,3 @@
-__version__ = '0.2.5'
+__version__ = '0.2.6'
 __author__ = 'Matthew Vincent and Kwangbom \"KB\" Choi, The Jackson Laboratory'
 __email__ = 'matt.vincent@jax.org'
diff --git a/g2gtools/vci.py b/g2gtools/vci.py
@@ -294,8 +294,12 @@ def parse(self, reverse):
                     total_num_lines_processed += 1
 
 
-                interval = Interval(pos_from, self.contigs[contig],
-                                    IntervalInfo(contig, pos_to, pos_to + (self.contigs[contig] - pos_from), None, None, None, None))
+                if self.is_diploid():
+                    interval = Interval(pos_from, self.contigs[contig[:-2]],
+                                        IntervalInfo(contig, pos_to, pos_to + (self.contigs[contig[:-2]] - pos_from), None, None, None, None))
+                else:
+                    interval = Interval(pos_from, self.contigs[contig],
+                                        IntervalInfo(contig, pos_to, pos_to + (self.contigs[contig] - pos_from), None, None, None, None))
 
                 mapping_tree[contig].insert_interval(interval)
 

diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.5
+current_version = 0.2.6
 commit = True
 tag = True
 

diff --git a/setup.py b/setup.py
@@ -30,7 +30,7 @@
 
 setup(
     name='g2gtools',
-    version='0.2.5',
+    version='0.2.6',
     description="A suite of tools for the reconstruction of personal diploid genomes and better coordinate conversion",
     long_description=readme + '\n\n' + history,
     author='Matthew J. Vincent and Kwangbom "KB" Choi, The Jackson Laboratory',