def main(bam, config):
actg = set("ATGC")
for pos in range(10000, 200011000):
h = chileup.pileup(bam, "1", pos, config)
#print(pos, h.bases, len(h.bqs), len(h.deletions), len(h.insertions))
if set(h.bases.decode()) - actg:
print(pos, h.bases, set(h.bases.decode()) - actg)
break
h.rbp(h)
def test_insertion():
bam = pysam.AlignmentFile("tests/three.bam", "rb")
pos = 1585270
h = chileup.pileup(bam, "1", pos, config)
assert h.bases == 'tt', h.bases
assert len(h.deletions) == 2
def test_off_by_one():
bam = pysam.AlignmentFile("tests/soft.bam", "rb")
pos = 10080
h = chileup.pileup(bam, "1", pos, config)
assert h.bases == "", h.bases
actg = set("ATGCatgc")
for pos in range(10000, 200011000):
h = chileup.pileup(bam, "1", pos, config)
if len(h.insertions) > 0:
print(pos, len(h.bases), h.insertions)
#print(pos, h.bases, len(h.bqs), len(h.deletions), len(h.insertions))
if set(h.bases) - actg:
print(pos, h.bases, set(h.bases) - actg)
break
h.rbp(h)
if __name__ == "__main__":
bam = pysam.AlignmentFile("/data/human/hg002.cram", "rc",
reference_filename="/data/human/g1k_v37_decoy.fa")
config = chileup.Config(tags=[], track_read_names=True,
track_base_qualities=True, track_mapping_qualities=True,
exclude_flags=pysam.FQCFAIL | pysam.FSECONDARY | pysam.FSUPPLEMENTARY | pysam.FDUP,
min_base_quality=10, min_mapping_quality=10)
pos = 10080
h = chileup.pileup(bam, "1", pos, config)
print(h)
#print(pos, h.bases)
test_off_by_one()
print("off by one")
test_insertion()
print("insertion")
main(bam, config)
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), ".."))
import pysam
import cyvcf2
import chileup
import time
config = chileup.Config(tags=[], track_read_names=False,
track_base_qualities=False, track_mapping_qualities=False,
exclude_flags=pysam.FQCFAIL | pysam.FSECONDARY | pysam.FSUPPLEMENTARY | pysam.FDUP,
min_base_quality=10, min_mapping_quality=10)
bam = pysam.AlignmentFile(sys.argv[1], "rb",
reference_filename="/data/human/g1k_v37_decoy.fa")
vcf = cyvcf2.VCF(sys.argv[2])
t0 = time.time()
for v in vcf("1"):
h = chileup.pileup(bam, v.CHROM, v.start, config)
print(repr(v).strip(), h.bases)
print("hileup time: %.2f", time.time() - t0)
# now do pysam pileup.