Merge pull request #357 from bcgsc/release/v3.1.2

Release/v3.1.2

Snakefile

@@ -11,7 +11,8 @@ from mavis_config import (
 from mavis_config.constants import SUBCOMMAND
 
 # env variable mainly for CI/CD
-CONTAINER = os.environ.get('SNAKEMAKE_CONTAINER', 'docker://bcgsc/mavis:v3.1.1')
+CONTAINER = os.environ.get('SNAKEMAKE_CONTAINER', 'docker://bcgsc/mavis:v3.1.2')
+
 MAX_TIME = 57600
 DEFAULT_MEMORY_MB = 16000
 
@@ -38,7 +39,7 @@ except Exception as err:
     raise WorkflowError(short_msg)
 
 # ADD bindings for singularity
-workflow.singularity_args = f'-B {",".join(get_singularity_bindings(config))}'
+workflow._singularity_args = f'-B {",".join(get_singularity_bindings(config))}'
 
 libraries = sorted(list(config['libraries']))
 VALIDATE_OUTPUT = output_dir('{library}/validate/batch-{job_id}/validation-passed.tab')

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = mavis
-version = 3.1.1
+version = 3.1.2
 url = https://github.com/bcgsc/mavis.git
 download_url = https://github.com/bcgsc/mavis/archive/v2.2.10.tar.gz
 description = A Structural Variant Post-Processing Package

src/mavis/summary/main.py

@@ -110,13 +110,15 @@ def main(inputs: List[str], output: str, config: Dict, start_time=int(time.time(
             if match:
                 netsize_min = abs(int(match.group(1)))
                 netsize_max = abs(int(match.group(2)))
+                if pd.isnull(bpp.repeat_count):
+                    bpp.data["repeat_count"] = 0
 
                 if all(
                     [
                         int(bpp.repeat_count) + 1
                         >= HOMOPOLYMER_MIN_LENGTH,  # repeat count is 1 less than the length of the repeat
                         netsize_min == netsize_max and netsize_min == 1,
-                        PROTOCOL.GENOME not in bpp.data.get(COLUMNS.pairing, ''),
+                        PROTOCOL.GENOME not in (bpp.data.get(COLUMNS.pairing, '') or ''),
                     ]
                 ):
                     bpp.data[COLUMNS.filter_comment] = 'homopolymer filter'

src/mavis/validate/align.py

@@ -563,7 +563,10 @@ def supports_primary_event(alignment):
         std_reads = set()
         alignments = []
         for raw_read in reads_by_query.get(contig.seq, []):
-            if raw_read.reference_name not in {evidence.break1.chr, evidence.break2.chr}:
+            if (
+                raw_read.reference_name != evidence.break1.chr
+                and raw_read.reference_name != evidence.break2.chr
+            ):
                 continue
             read = evidence.standardize_read(raw_read)
             read.cigar = _cigar.merge_internal_events(