Commit c26ce5c0 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

benchmark-releases.py: test --filter-reads

parent 4b30c707
...@@ -16,6 +16,7 @@ CURRENT = 'HEAD' ...@@ -16,6 +16,7 @@ CURRENT = 'HEAD'
WARN_RATIO = 0.10 WARN_RATIO = 0.10
LIMIT2e5 = '-x 200000 '
LIMIT1e5 = '-x 100000 ' LIMIT1e5 = '-x 100000 '
LIMIT1e4 = '-x 10000 ' LIMIT1e4 = '-x 10000 '
LIMIT1e3 = '-x 1000 ' LIMIT1e3 = '-x 1000 '
...@@ -26,6 +27,7 @@ IGH = '-g ' + GERM_VAR + '/homo-sapiens.g:IGH ' ...@@ -26,6 +27,7 @@ IGH = '-g ' + GERM_VAR + '/homo-sapiens.g:IGH '
L4 = '../../demo/LIL-L4.fastq.gz ' L4 = '../../demo/LIL-L4.fastq.gz '
S22 = '../../demo/Stanford_S22.fasta ' S22 = '../../demo/Stanford_S22.fasta '
FILTER = '--filter-reads '
CONSENSUS_NO = '-y 0 -z 0 ' CONSENSUS_NO = '-y 0 -z 0 '
CONSENSUS_ALL = '-y all -z 0 ' CONSENSUS_ALL = '-y all -z 0 '
DESIGNATIONS = '-c designations ' DESIGNATIONS = '-c designations '
...@@ -36,6 +38,8 @@ BENCHS = OrderedDict([ ...@@ -36,6 +38,8 @@ BENCHS = OrderedDict([
('init', '-x 1 ' + MULTI + L4 + CONSENSUS_NO), ('init', '-x 1 ' + MULTI + L4 + CONSENSUS_NO),
('germ', LIMIT1e5 + MULTI + L4 + '-c germlines '), ('germ', LIMIT1e5 + MULTI + L4 + '-c germlines '),
('filter', LIMIT2e5 + FILTER + MULTI + L4),
('multi-0', LIMIT1e5 + MULTI + L4 + CONSENSUS_NO), ('multi-0', LIMIT1e5 + MULTI + L4 + CONSENSUS_NO),
('multi-1', LIMIT1e5 + MULTI + L4 + CONSENSUS_ALL), ('multi-1', LIMIT1e5 + MULTI + L4 + CONSENSUS_ALL),
('multi-a', LIMIT1e3 + MULTI + L4 + DESIGNATIONS + '-z 1000'), ('multi-a', LIMIT1e3 + MULTI + L4 + DESIGNATIONS + '-z 1000'),
......
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