def test35(self):
cur_dir = os.path.dirname(os.path.abspath(__file__))
in_bam1 = cur_dir + "/../data/5929_tumor_small.markdup.bam"
in_bam2 = None
sample1 = "5929_tumor"
sample2 = None
out_file = cur_dir + "/../data/5929_small_mutation_result_test35.txt"
ref_fa = cur_dir + "/../data/GRCh37.fa"
baseq_thres = 15
mismatch_rate_disease = 0.02
mismatch_rate_normal = None
post_10_q = 0.02
fisher_threshold = None
min_depth = 8
header_flag = False
min_variant_read = 4
samtools = self.samtools
samtools_params = "-q 20 -BQ0 -d 10000000 --ff UNMAP,SECONDARY,QCFAIL,DUP"
region = None
region_file = cur_dir + "/../data/GRCh37_2split.interval_list"
positions_bed = None
is_anno = False
fisher.Pileup_and_count(in_bam1, in_bam2, sample1, sample2, out_file, ref_fa,
baseq_thres, mismatch_rate_disease, mismatch_rate_normal, post_10_q,
fisher_threshold, min_depth, header_flag, min_variant_read, samtools,
samtools_params, region, region_file, positions_bed, is_anno
)
answer_file = cur_dir + "/../data/5929_small_mutation_result_answer_test35.txt"
self.assertTrue(filecmp.cmp(out_file, answer_file, shallow=False))
def test21(self):
cur_dir = os.path.dirname(os.path.abspath(__file__))
in_bam1 = cur_dir + "/../data/5929_tumor_small.markdup.bam"
in_bam2 = cur_dir + "/../data/5929_control_small.markdup.bam"
sample1 = "5929_tumor"
sample2 = "5929_control"
out_file = cur_dir + "/../data/5929_small_mutation_result_test21.txt"
ref_fa = cur_dir + "/../data/GRCh37.fa"
baseq_thres = 15
mismatch_rate_disease = 0.07
mismatch_rate_normal = 0.1
post_10_q = None
fisher_threshold = 0.05
min_depth = 10
header_flag = True
min_variant_read = 4
samtools = self.samtools
samtools_params = "-q 30 -BQ0 -d 10000000"
region = None
region_file = None
positions_bed = None
is_anno = False
fisher.Pileup_and_count(in_bam1, in_bam2, sample1, sample2, out_file, ref_fa,
baseq_thres, mismatch_rate_disease, mismatch_rate_normal, post_10_q,
fisher_threshold, min_depth, header_flag, min_variant_read, samtools,
samtools_params, region, region_file, positions_bed, is_anno
)
answer_file = cur_dir + "/../data/5929_small_mutation_result_answer_test21.txt"
self.assertTrue(filecmp.cmp(out_file, answer_file, shallow=False))
