Replace deletions with previous consensus, part of #393.

cfe-lab · Jul 27, 2017 · ed6966c · ed6966c
1 parent d9ccf04
commit ed6966c
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Showing 2 changed files with 32 additions and 1 deletion.
diff --git a/micall/core/remap.py b/micall/core/remap.py
@@ -372,7 +372,10 @@ def counts_to_conseqs(refmap, seeds=None):
                 else:
                     conseq += seed[pos-1]
             elif most_common == '-':
-                deletion += '-'
+                if seed is None:
+                    deletion += '-'
+                else:
+                    conseq += seed[pos-1]
             else:
                 if deletion:
                     if len(deletion) % 3 != 0:

diff --git a/micall/tests/remap_test.py b/micall/tests/remap_test.py
@@ -392,6 +392,34 @@ def testSeedsWithLowQuality(self):
 
         self.assertDictEqual(expected_conseqs, conseqs)
 
+    def testSeedsWithPartialDeletion(self):
+        samIO = StringIO(
+            "@SQ\tSN:test\n"
+            "test1\t99\ttest\t4\t44\t1M1D1M\t=\t10\t3\tTT\tJJ\n"
+        )
+        seeds = {'test': 'ACATTTGGGCAC'}
+        expected_conseqs = {'test': 'ACATTTGGGCAC'}
+
+        conseqs = remap.sam_to_conseqs(samIO,
+                                       seeds=seeds,
+                                       quality_cutoff=32)
+
+        self.assertDictEqual(expected_conseqs, conseqs)
+
+    def testSeedsWithCodonDeletion(self):
+        samIO = StringIO(
+            "@SQ\tSN:test\n"
+            "test1\t99\ttest\t1\t44\t3M3D3M\t=\t10\t6\tACAGGG\tJJJJJJ\n"
+        )
+        seeds = {'test': 'ACATTTGGGCAC'}
+        expected_conseqs = {'test': 'ACATTTGGGCAC'}
+
+        conseqs = remap.sam_to_conseqs(samIO,
+                                       seeds=seeds,
+                                       quality_cutoff=32)
+
+        self.assertDictEqual(expected_conseqs, conseqs)
+
     def testDebugReports(self):
         samIO = StringIO(
             "@SQ\tSN:test\n"