Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
vidjil
vidjil
Commits
c26ce5c0
Commit
c26ce5c0
authored
Mar 18, 2021
by
Mathieu Giraud
Browse files
benchmark-releases.py: test --filter-reads
parent
4b30c707
Changes
1
Hide whitespace changes
Inline
Side-by-side
algo/tests/benchmark-releases.py
View file @
c26ce5c0
...
...
@@ -16,6 +16,7 @@ CURRENT = 'HEAD'
WARN_RATIO
=
0.10
LIMIT2e5
=
'-x 200000 '
LIMIT1e5
=
'-x 100000 '
LIMIT1e4
=
'-x 10000 '
LIMIT1e3
=
'-x 1000 '
...
...
@@ -26,6 +27,7 @@ IGH = '-g ' + GERM_VAR + '/homo-sapiens.g:IGH '
L4
=
'../../demo/LIL-L4.fastq.gz '
S22
=
'../../demo/Stanford_S22.fasta '
FILTER
=
'--filter-reads '
CONSENSUS_NO
=
'-y 0 -z 0 '
CONSENSUS_ALL
=
'-y all -z 0 '
DESIGNATIONS
=
'-c designations '
...
...
@@ -36,6 +38,8 @@ BENCHS = OrderedDict([
(
'init'
,
'-x 1 '
+
MULTI
+
L4
+
CONSENSUS_NO
),
(
'germ'
,
LIMIT1e5
+
MULTI
+
L4
+
'-c germlines '
),
(
'filter'
,
LIMIT2e5
+
FILTER
+
MULTI
+
L4
),
(
'multi-0'
,
LIMIT1e5
+
MULTI
+
L4
+
CONSENSUS_NO
),
(
'multi-1'
,
LIMIT1e5
+
MULTI
+
L4
+
CONSENSUS_ALL
),
(
'multi-a'
,
LIMIT1e3
+
MULTI
+
L4
+
DESIGNATIONS
+
'-z 1000'
),
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment