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blasr_cram_script = find_program('cram')
# third-party tools
blasr_samtools = find_program([
'samtools',
'/mnt/secondary/Smrtpipe/builds/Internal_Mainline_Nightly_LastSuccessfulBuild/analysis/bin/samtools'])
blasr_fast_test_list = [
['ecoli', 'FAST'],
['fastMaxInterval', 'FAST'],
['aggressiveIntervalCut', 'FAST'],
['multipart', 'FAST'],
['affineAlign', 'FAST'],
['bamOut', 'FAST'],
['ccsH5', 'FAST'],
['filtercriteria', 'FAST'],
['m0-5', 'FAST'],
['fofn', 'FAST'],
['alignScore', 'FAST'],
['hitpolicy', 'FAST'],
['noSplitSubreads', 'FAST'],
['bamIn', 'FAST'],
['open_fail', 'FAST'],
['verbose', 'FAST'],
['deterministic', 'FAST'],
['pgc-naive', 'FAST'],
['pgc-fasta', 'FAST'],
['pgc-concordant', 'FAST'],
['pgc-concordant-naive', 'FAST'],
# ['concordant', 'INTERMEDIATE'],
['bug25766', 'INTERMEDIATE'],
['holeNumbers', 'INTERMEDIATE'],
# ['bug25328', 'SLOW'],
# ['pgc-big', 'SLOW'],
# ['long-cigar', 'SLOW'],
]
blasr_test_remotedir = '/pbi/dept/secondary/siv/testdata/BlasrTestData/ctest'
blasr_test_testdir = meson.current_build_dir()
blasr_test_outdir = join_paths(blasr_test_testdir, 'out')
foreach i : blasr_fast_test_list
test(
'blasr cram test - ' + i[0],
blasr_cram_script,
args : [
'--xunit-file=' + join_paths(meson.build_root(), 'blasr-cram-' + i[0] + '.xml'),
'--verbose'] +
files(i[0] + '.t'),
env : [
'BLASR_EXE=' + blasr_main.full_path(),
'SAMTOOLS_EXE=' + blasr_samtools.path(),
'REMOTEDIR=' + blasr_test_remotedir,
'DATDIR=' + join_paths(blasr_test_remotedir, 'data'),
'STDDIR=' + join_paths(blasr_test_remotedir, 'stdout'),
'TMP1=' + join_paths(blasr_test_outdir, '$$.tmp.out'),
'TMP2=' + join_paths(blasr_test_outdir, '$$.tmp.stdout'),
'TESTDIR=' + blasr_test_testdir,
'OUTDIR=' + blasr_test_outdir,
'UPDATEDATE=2015_11_09'],
is_parallel : false,
timeout : 600)
endforeach
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