def test_get_num_kept_reads():
"""
Test the scale factor functinos
"""
args = "--bam {} -o /tmp/test".format(BAMFILE_A, BAMFILE_B).split()
args = bam_cov.process_args(args)
num_kept_reads, total_reads = gs.get_num_kept_reads(args)
# bam file 1 has 2 reads in 3R and 2 read in chr_cigar
assert num_kept_reads == 3, "num_kept_reads is wrong"
assert total_reads == 3, "num total reads is wrong"
# ignore chr_cigar to count the total number of reads
args = "--bam {} --ignoreForNormalization chr_cigar -o /tmp/test".format(
BAMFILE_A, BAMFILE_B).split()
args = bam_cov.process_args(args)
num_kept_reads, total_reads = gs.get_num_kept_reads(args)
# the number of kept reads should be 2 as the read on chr_cigar is skipped
assert num_kept_reads == 2, "num_kept_reads is wrong ({})".format(
num_kept_reads)
# test filtering by read direction. Only forward reads are kept
args = "--bam {} -o /tmp/test --samFlagExclude 16 --ignoreForNormalization chr_cigar ".format(
BAMFILE_A, BAMFILE_B).split()
args = bam_cov.process_args(args)
num_kept_reads, total_reads = gs.get_num_kept_reads(args)
# only one forward read is expected in
assert num_kept_reads == 1, "num_kept_reads is wrong"
def test_get_num_kept_reads():
"""
Test the scale factor functinos
"""
args = "--bam {} -o /tmp/test".format(BAMFILE_A, BAMFILE_B).split()
args = bam_cov.process_args(args)
num_kept_reads, total_reads = gs.get_num_kept_reads(args)
# bam file 1 has 2 reads in 3R and 2 read in chr_cigar
assert num_kept_reads == 3, "num_kept_reads is wrong"
assert total_reads == 3, "num total reads is wrong"
# ignore chr_cigar to count the total number of reads
args = "--bam {} --ignoreForNormalization chr_cigar -o /tmp/test".format(BAMFILE_A, BAMFILE_B).split()
args = bam_cov.process_args(args)
num_kept_reads, total_reads = gs.get_num_kept_reads(args)
# the number of kept reads should be 2 as the read on chr_cigar is skipped
assert num_kept_reads == 2, "num_kept_reads is wrong ({})".format(num_kept_reads)
# test filtering by read direction. Only forward reads are kept
args = "--bam {} -o /tmp/test --samFlagExclude 16 --ignoreForNormalization chr_cigar ".format(BAMFILE_A, BAMFILE_B).split()
args = bam_cov.process_args(args)
num_kept_reads, total_reads = gs.get_num_kept_reads(args)
# only one forward read is expected in
assert num_kept_reads == 1, "num_kept_reads is wrong"