Merge branch 'dysgu_dev' into master

kcleal · Sep 12, 2024 · 8960100 · 8960100
2 parents 4fe97e2 + 63b561b
commit 8960100
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Showing 3 changed files with 8 additions and 2 deletions.
diff --git a/dysgu/cluster.pyx b/dysgu/cluster.pyx
@@ -1100,6 +1100,10 @@ def pipe1(args, infile, kind, regions, ibam, ref_genome, sample_name, bam_iter=N
     cdef EventResult_t d
     for d in merged:
         d.type = args["pl"]
+        if d.posA > d.posB and d.chrA == d.chrB:
+            t = d.posA
+            d.posA = d.posB
+            d.posB = t
 
     coverage_analyser = post_call.CoverageAnalyser(tdir)
     preliminaries = coverage_analyser.process_events(merged)

diff --git a/dysgu/post_call.py b/dysgu/post_call.py
@@ -289,7 +289,9 @@ def ref_repetitiveness(events, ref_genome):
                 e.ref_rep = compute_rep(ref_seq)
             except (ValueError, KeyError, IndexError) as errors:
                 # Might be different reference genome version, compared to bam genome
-                logging.warning("Error fetching reference chromosome: {}".format(e.chrA), errors)
+                logging.warning(
+                    f"Error fetching reference chromosome: chrA={e.chrA}, posA={e.posA}, chrB={e.chrB}, posB={e.posB}. Error: {str(errors)}"
+                )
                 e.ref_seq = 0
     return events
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -10,7 +10,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "dysgu"
-version = "1.6.6"
+version = "1.6.7"
 description = "Structural variant calling"
 authors = [
     { name = "Kez Cleal", email = "clealk@cardiff.ac.uk" }