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Alexis Mergez
PanGeTools
Commits
a4cb3075
Commit
a4cb3075
authored
10 months ago
by
Alexis Mergez
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Fixed bug with GFAstats
Forgot to remove '\n' when checking for header, preventing the script from running.
parent
939d0e70
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Pipeline
#199063
passed
10 months ago
Changes
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2 changed files
GFAstats.py
+3
-3
3 additions, 3 deletions
GFAstats.py
PanGeTools.def
+2
-2
2 additions, 2 deletions
PanGeTools.def
with
5 additions
and
5 deletions
GFAstats.py
+
3
−
3
View file @
a4cb3075
...
...
@@ -5,7 +5,7 @@ GFAstats: GFA statistics.
Compute general statistics of a GFA
@author: alexis.mergez@inrae.fr
@version: 0.3.
1
@version: 0.3.
2
"""
import
re
import
argparse
...
...
@@ -17,7 +17,7 @@ from functools import reduce
import
concurrent.futures
import
gzip
version
=
"
0.3.
1
"
version
=
"
0.3.
2
"
## Argument parser
arg_parser
=
argparse
.
ArgumentParser
(
description
=
'
GFAstats: GFA statistics
'
)
...
...
@@ -84,7 +84,7 @@ else :
gfaLines
=
[
line
.
decode
()
for
line
in
file
.
readlines
()]
## Checking Header for version number (not perfect)
if
gfaLines
[
0
].
split
(
'
\t
'
)[
1
]
!=
"
VN:Z:1.0
"
:
if
gfaLines
[
0
]
[:
-
1
]
.
split
(
'
\t
'
)[
1
]
!=
"
VN:Z:1.0
"
:
raise
ImportError
(
"
GFA v1 only are supported
"
)
## Initializing dictionnairies
...
...
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PanGeTools.def
+
2
−
2
View file @
a4cb3075
...
...
@@ -316,7 +316,7 @@ Stage: build
panacus.Version 0.2.3
gfatools.Version 0.5
GFAvc.Version 0.2
GFAstats.Version 0.3.
1
GFAstats.Version 0.3.
2
Samtools.Version 1.19
wfmash.Version 0.10.5
htslib.Version 1.19.1
...
...
@@ -340,7 +340,7 @@ Stage: build
- panacus v0.2.3
- gfatools v0.5
- GFAvc v0.2
- GFAstats v0.3.
1
- GFAstats v0.3.
2
- samtools v1.19
- bgzip v1.19.1
- wfmash v0.10.5
...
...
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