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Feature/sniffle convert handling #300

Merged
merged 17 commits into from
Feb 3, 2022
Merged

Feature/sniffle convert handling #300

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7e07e2c
added handling of uncertain calls by sniffle
Jan 20, 2022
302d854
reformat file
Jan 20, 2022
e631170
Merge branch 'develop_v3' of https://github.com/bcgsc/mavis into feat…
Jan 22, 2022
b1b890a
adddressed Sniffles support
Jan 26, 2022
fda6213
re-lint files
Jan 26, 2022
a1849d5
changed unit test as sample Sniffles file changed
Jan 26, 2022
43cd309
add quick test to vcf module
Jan 29, 2022
d641270
Merge branch 'develop_v3' into feature/sniffle-convert-handling
Jan 29, 2022
db96aec
changed test case to include bp1
Jan 29, 2022
ec1e54b
update hooks.py to import from config
Jan 30, 2022
bb2cc16
Merge branch 'develop_v3' into feature/sniffle-convert-handling
creisle Jan 30, 2022
4e1c1e9
fixed checks
Jan 31, 2022
e80e013
Merge branch 'feature/sniffle-convert-handling' of https://github.com…
Jan 31, 2022
4c3365f
unfix deleted lines
Jan 31, 2022
1072534
re-lint vcf file
Jan 31, 2022
debbf27
change unit tests to accomodate changes
Jan 31, 2022
2987227
revert old changes
Feb 2, 2022
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2 changes: 2 additions & 0 deletions src/mavis/interval.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,8 @@ def __init__(self, start: int, end: Optional[int] = None, freq: int = 1, number_

self.start = self.number_type(self.start)
self.end = self.number_type(self.end)
if self.start == 0 and self.end == 1:
self.start = 1
if self.start > self.end:
raise AttributeError('interval start > end is not allowed', self.start, self.end)
self.freq = int(freq)
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4 changes: 4 additions & 0 deletions src/mavis/tools/constants.py
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Expand Up @@ -51,6 +51,10 @@ class SUPPORTED_TOOL(MavisNamespace):
'dup': [SVTYPE.DUP],
'ITD': [SVTYPE.DUP],
'IDP': [SVTYPE.INS],
'DEL/INV': [SVTYPE.DEL, SVTYPE.INV],
'DUP/INS': [SVTYPE.DUP, SVTYPE.INS],
'INVDUP': [SVTYPE.INV, SVTYPE.DUP, SVTYPE.INS],
'INV/INVDUP': [SVTYPE.INV, SVTYPE.DUP, SVTYPE.INS],
}
)

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4 changes: 2 additions & 2 deletions src/mavis/tools/vcf.py
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Expand Up @@ -275,7 +275,7 @@ def pandas_vcf(input_file) -> Tuple[List[str], pd.DataFrame]:
# read the data
df = pd.read_csv(
input_file,
sep='\t',
sep="\t",
skiprows=len(header_lines),
dtype={
'CHROM': str,
Expand All @@ -286,7 +286,7 @@ def pandas_vcf(input_file) -> Tuple[List[str], pd.DataFrame]:
'REF': str,
'ALT': str,
},
na_values=PANDAS_DEFAULT_NA_VALUES + ['.'],
na_values=PANDAS_DEFAULT_NA_VALUES + ["."],
)
df = df.rename(columns={df.columns[0]: df.columns[0].replace('#', '')})
required_columns = ['CHROM', 'INFO', 'POS', 'REF', 'ALT', 'ID']
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