From 3a0ce5f0e6576bd28d92236ea91558c2e422965c Mon Sep 17 00:00:00 2001 From: Jeremy Fan Date: Wed, 26 Apr 2023 16:32:06 -0700 Subject: [PATCH 1/6] bump version to release 3.1.1 --- Snakefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Snakefile b/Snakefile index c361c753..1c20f397 100644 --- a/Snakefile +++ b/Snakefile @@ -11,7 +11,7 @@ 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:v3.0.0') +CONTAINER = os.environ.get('SNAKEMAKE_CONTAINER', 'docker://bcgsc/mavis:v3.1.1') MAX_TIME = 57600 DEFAULT_MEMORY_MB = 16000 From d7e7c0152f31829904f156a0bf437018c64f9056 Mon Sep 17 00:00:00 2001 From: Caleb Choo Date: Mon, 26 Jun 2023 10:34:26 -0700 Subject: [PATCH 2/6] fix errors on empty columns --- src/mavis/summary/main.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/mavis/summary/main.py b/src/mavis/summary/main.py index 1e43d398..de288d0e 100644 --- a/src/mavis/summary/main.py +++ b/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' From cf2395fc2bdd406f3ca3b3dc2b34cd83f09cb0ce Mon Sep 17 00:00:00 2001 From: Caleb Choo Date: Wed, 16 Aug 2023 10:40:14 -0700 Subject: [PATCH 3/6] #355 fix chromosome comparison check --- src/mavis/validate/align.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/mavis/validate/align.py b/src/mavis/validate/align.py index b4aafe6a..fe298c3f 100644 --- a/src/mavis/validate/align.py +++ b/src/mavis/validate/align.py @@ -563,7 +563,7 @@ 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( From 8343f1f67a15650d2bfa59e6ecc8f4ad39fae913 Mon Sep 17 00:00:00 2001 From: Caleb Choo Date: Wed, 16 Aug 2023 10:52:39 -0700 Subject: [PATCH 4/6] fix lint of chr check --- src/mavis/validate/align.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/mavis/validate/align.py b/src/mavis/validate/align.py index fe298c3f..037ff7f3 100644 --- a/src/mavis/validate/align.py +++ b/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 != evidence.break1.chr and raw_read.reference_name != 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( From 3bbe21978f1f71cb9fa36ba04f76eb55eb6bc289 Mon Sep 17 00:00:00 2001 From: Caleb Choo Date: Wed, 16 Aug 2023 15:37:43 -0700 Subject: [PATCH 5/6] update snakefile to work with updated Snakemake --- Snakefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Snakefile b/Snakefile index c361c753..5a57b56c 100644 --- a/Snakefile +++ b/Snakefile @@ -11,7 +11,7 @@ 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:v3.0.0') +CONTAINER = os.environ.get('SNAKEMAKE_CONTAINER', 'docker://bcgsc/mavis:v3.1.1') MAX_TIME = 57600 DEFAULT_MEMORY_MB = 16000 @@ -38,7 +38,7 @@ 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') From 42ae2f7072b537f8330feb013ae6543a1fba7479 Mon Sep 17 00:00:00 2001 From: Caleb Choo Date: Wed, 16 Aug 2023 16:07:28 -0700 Subject: [PATCH 6/6] bump version to v3.1.2 --- Snakefile | 2 +- setup.cfg | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Snakefile b/Snakefile index 5a57b56c..d76679bf 100644 --- a/Snakefile +++ b/Snakefile @@ -11,7 +11,7 @@ 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 diff --git a/setup.cfg b/setup.cfg index 8d50f33c..6807f3a4 100644 --- a/setup.cfg +++ b/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