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import os
import glob
import sys
import unittest
import pysam
import shutil
import gzip
import subprocess
import pytest
try:
from pathlib import Path
except ImportError:
Path = None
from TestUtils import get_temp_filename, check_lines_equal, load_and_convert, CBCF_DATADIR, get_temp_context
@pytest.fixture
def vcf_header():
vcf_header = pysam.VariantHeader()
vcf_header.add_sample("sample1")
vcf_header.add_sample("sample2")
vcf_header.contigs.add("1")
return vcf_header
## segfault without coordinates
def test_ascii_annotation_can_be_added(vcf_header):
vcf_header.formats.add("AN", 1, "String", "An annotation")
record = vcf_header.new_record(
contig="1",
start=12,
stop=13,
samples=[
{"AN": "anno1"},
{"AN": "anno2"}])
assert str(record)[:-1].split("\t")[-2:] == ["anno1", "anno2"]
def test_ascii_annotation_with_variable_length_can_be_added(vcf_header):
vcf_header.formats.add("AN", 1, "String", "An annotation")
record = vcf_header.new_record(
contig="1",
start=12,
stop=13,
samples=[
{"AN": "anno1b"},
{"AN": "anno1"}])
assert str(record)[:-1].split("\t")[-2:] == ["anno1b", "anno1"]
record = vcf_header.new_record(
contig="1",
start=12,
stop=13,
samples=[
{"AN": "anno2"},
{"AN": "anno2b"}])
assert str(record)[:-1].split("\t")[-2:] == ["anno2", "anno2b"]
def test_unicode_annotation_can_be_added(vcf_header):
vcf_header.formats.add("AN", 1, "String", "An annotation")
record = vcf_header.new_record(
contig="1",
start=12,
stop=13,
samples=[
{"AN": "anno1"},
{"AN": "Friedrich-Alexander-Universit\u00E4t_Erlangen-N\u00FCrnberg"}])
assert str(record)[:-1].split("\t")[-2:] == [
"anno1",
"Friedrich-Alexander-Universit\u00E4t_Erlangen-N\u00FCrnberg"]
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