INPUT_BAMS = ('NA06986.chromY.ILLUMINA.bwa.CEU.exon_targetted.20100311.bam',
'NA06986.chrom21.ILLUMINA.bwa.CEU.exon_targetted.20100311.bam',
'NA06986.chrom18.ILLUMINA.bwa.CEU.exon_targetted.20100311.bam')
RESULTS_EXPECTED = ('4afb9b8908959dbd4e2d5c54bf254c93',
'0dc006ed39ddad2790034ca497631234',
'36e37a0dab5926dbf5a1b8afc0cdac8b')
for i in range(len(INPUT_BAMS)):
INPUT_BAM = INPUT_BAMS[i]
RESULT_EXPECTED = RESULTS_EXPECTED[i]
OUTPUT_PATH = test_util.get_field_from_tsv(
test.TASKS_FILE, '--input INPUT_PATH', r'^.*/%s$' % INPUT_BAM,
'--output OUTPUT_PATH')
OUTPUT_FILE = '%s/%s.md5' % (OUTPUT_PATH[:-len('/*.md5')], INPUT_BAM)
RESULT = test_util.gsutil_cat(OUTPUT_FILE)
if not test_util.diff(RESULT_EXPECTED.strip(), RESULT.strip()):
print 'Output file does not match expected'
sys.exit(1)
print
print 'Output file matches expected:'
print '*****************************'
print 'RESULT'
print '*****************************'
print 'SUCCESS'
print >> sys.stderr, 'Launched job contains tasks.'
print >> sys.stderr, launched_job['task-id']
sys.exit(1)
print 'Launched job: %s' % launched_job['job-id']
print
print 'Checking output...'
# Check the results
RESULT_EXPECTED = """
VAR1=VAL1
VAR2=VAL2
VAR3=VAL3
VAR4=VAL4
VAR5=VAL5
""".lstrip()
RESULT = test_util.gsutil_cat(test.STDOUT_LOG)
if not test_util.diff(RESULT_EXPECTED, RESULT):
print 'Output file does not match expected'
sys.exit(1)
print
print 'Output file matches expected:'
print '*****************************'
print RESULT
print '*****************************'
print 'SUCCESS'