Commitbf2010b

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

Release/v3.1.2

2 parents824dfa0 +5ceb3d6 commitbf2010bCopy full SHA for bf2010b

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+11

-5

lines changed

+11

-5

lines changed

Lines changed: 3 additions & 2 deletions

Original file line number	Diff line number	Diff line change
`@@ -11,7 +11,8 @@ from mavis_config import (`
`11`	`11`	`frommavis_config.constantsimportSUBCOMMAND`
`12`	`12`
`13`	`13`	`# env variable mainly for CI/CD`
`14`		`-CONTAINER=os.environ.get('SNAKEMAKE_CONTAINER','docker://bcgsc/mavis:v3.1.1')`
	`14`	`+CONTAINER=os.environ.get('SNAKEMAKE_CONTAINER','docker://bcgsc/mavis:v3.1.2')`
	`15`	`+`
`15`	`16`	`MAX_TIME=57600`
`16`	`17`	`DEFAULT_MEMORY_MB=16000`
`17`	`18`
`@@ -38,7 +39,7 @@ except Exception as err:`
`38`	`39`	`raiseWorkflowError(short_msg)`
`39`	`40`
`40`	`41`	`# ADD bindings for singularity`
`41`		`-workflow.singularity_args=f'-B{",".join(get_singularity_bindings(config))}'`
	`42`	`+workflow._singularity_args=f'-B{",".join(get_singularity_bindings(config))}'`
`42`	`43`
`43`	`44`	`libraries=sorted(list(config['libraries']))`
`44`	`45`	`VALIDATE_OUTPUT=output_dir('{library}/validate/batch-{job_id}/validation-passed.tab')`

Lines changed: 1 addition & 1 deletion

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`[metadata]`
`2`	`2`	`name = mavis`
`3`		`-version = 3.1.1`
	`3`	`+version = 3.1.2`
`4`	`4`	`url = https://github.com/bcgsc/mavis.git`
`5`	`5`	`download_url = https://github.com/bcgsc/mavis/archive/v2.2.10.tar.gz`
`6`	`6`	`description = A Structural Variant Post-Processing Package`

Lines changed: 3 additions & 1 deletion

Original file line number	Diff line number	Diff line change
`@@ -110,13 +110,15 @@ def main(inputs: List[str], output: str, config: Dict, start_time=int(time.time(`
`110`	`110`	`ifmatch:`
`111`	`111`	`netsize_min=abs(int(match.group(1)))`
`112`	`112`	`netsize_max=abs(int(match.group(2)))`
	`113`	`+ifpd.isnull(bpp.repeat_count):`
	`114`	`+bpp.data["repeat_count"]=0`
`113`	`115`
`114`	`116`	`ifall(`
`115`	`117`	`[`
`116`	`118`	`int(bpp.repeat_count)+1`
`117`	`119`	`>=HOMOPOLYMER_MIN_LENGTH,# repeat count is 1 less than the length of the repeat`
`118`	`120`	`netsize_min==netsize_maxandnetsize_min==1,`
`119`		`-PROTOCOL.GENOMEnotinbpp.data.get(COLUMNS.pairing,''),`
	`121`	`+PROTOCOL.GENOMEnotin(bpp.data.get(COLUMNS.pairing,'')or''),`
`120`	`122`	`]`
`121`	`123`	`):`
`122`	`124`	`bpp.data[COLUMNS.filter_comment]='homopolymer filter'`

Lines changed: 4 additions & 1 deletion

Original file line number	Diff line number	Diff line change
`@@ -563,7 +563,10 @@ def supports_primary_event(alignment):`
`563`	`563`	`std_reads=set()`
`564`	`564`	`alignments= []`
`565`	`565`	`forraw_readinreads_by_query.get(contig.seq, []):`
`566`		`-ifraw_read.reference_namenotin {evidence.break1.chr,evidence.break2.chr}:`
	`566`	`+if (`
	`567`	`+raw_read.reference_name!=evidence.break1.chr`
	`568`	`+andraw_read.reference_name!=evidence.break2.chr`
	`569`	`+ ):`
`567`	`570`	`continue`
`568`	`571`	`read=evidence.standardize_read(raw_read)`
`569`	`572`	`read.cigar=_cigar.merge_internal_events(`

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