Fix regression on gapped consensus

nanoporetech · May 20, 2019 · f162a6f · f162a6f
1 parent 0530ff9
commit f162a6f
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Showing 3 changed files with 16 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,11 @@
 
+v0.7.1
+------
+Bug fix release
+
+* Fix regression in consensus stitching when chunks do not overlap
+
+
 v0.7.0
 ------
 Feature release

diff --git a/medaka/__init__.py b/medaka/__init__.py
@@ -3,7 +3,7 @@
 import os
 import subprocess
 
-__version__ = '0.7.0'
+__version__ = '0.7.1'
 
 
 def check_minimap2_version():

diff --git a/medaka/stitch.py b/medaka/stitch.py
@@ -62,8 +62,15 @@ def stitch_from_probs(probs_hdfs, regions=None, model_yml=None):
                         s2_name, s1_name
                     ))
                     continue
+                elif s2.first_pos >= s1.last_pos:
+                    # trigger a break
+                    end_1_ind, start_2_ind = None, None
                 else:
-                    end_1_ind, start_2_ind = medaka.common.Sample.overlap_indices(s1, s2)
+                    try:
+                        end_1_ind, start_2_ind = medaka.common.Sample.overlap_indices(s1, s2)
+                    except medaka.common.OverlapException as e:
+                        logger.info("Unhandled overlap type whilst stitching chunks.")
+                        raise(e)
 
             best = np.argmax(s1.label_probs[start_1_ind:end_1_ind], -1)
             seq += ''.join([label_decoding[x] for x in best]).replace(medaka.common._gap_, '')