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WIP #3

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c1708e6
Merge tag '0.1.4' into develop
Dec 7, 2021
2baae40
Merge tag '0.1.5' into develop
Dec 14, 2021
8976c9d
Merge tag '0.1.6' into develop
Dec 17, 2021
ca4302c
Merge tag '0.1.7' into develop
Feb 17, 2022
87535ae
Add confidence calls to merged VCF
Mar 1, 2022
419790c
Update tests initial changes
Mar 1, 2022
2724de1
Update tests inline with MNV confidence score addition
Mar 3, 2022
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58 changes: 41 additions & 17 deletions python/casmsmartphase/MNVMerge.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,6 @@ def parse_homs_bed_to_dict(bed_file: str) -> Dict:
while line:
line = line.rstrip()
split_line = line.split("\t")
print(split_line)
hom = False if len(split_line) == 3 else True
if hom:
bed_entry = (int(split_line[1]) + 1, int(split_line[2]), hom)
Expand Down Expand Up @@ -116,8 +115,6 @@ def parse_sphase_output(
line = line.rstrip()
try:
(mnv_id, pair1, pair2, flag, confidence) = re.split(r"\s+", line, 5)
(_id_contig, id_start_region, _id_stop) = mnv_id.split("-")
print(_id_contig, id_start_region, _id_stop)
if float(confidence) < cutoff or int(flag) & exclude_flags:
continue
(contig, startpos, _tmp) = pair1.split("-", maxsplit=2)
Expand All @@ -130,22 +127,26 @@ def parse_sphase_output(
if not contig in mnvs:
mnvs[contig] = {}
# Check for adjacent MNV
if startpos in mnvs[contig].values():
if startpos in [t[0] for t in mnvs[contig].values()]:
# Check if startpos in mnv_id is already stored and see if these are adjacent to an already recorded MNV
# Find key for mnv that adjoins this one
key = None
for k, v in mnvs[contig].items():
if v == startpos:
for k, (end_pos, conf_score_list) in mnvs[contig].items():
if end_pos == startpos:
key = k
break
# Check if current end_pos is adjacent, if so, extend this MNV
mnvs[contig][key] = endpos
(end_pos, conf_score_list) = mnvs[contig].pop(key)
conf_score_list.append(confidence)
mnvs[contig][key] = (endpos, conf_score_list)
mnv_len = (endpos - key) + 1
if max_len < mnv_len:
max_len = mnv_len
else:
# Otherwise this is a new MNV
mnvs[contig][startpos] = endpos
conf_list = list()
conf_list.append(confidence)
mnvs[contig][startpos] = (endpos, conf_list)
mnv_len = (endpos - startpos) + 1
if max_len < mnv_len:
max_len = mnv_len
Expand All @@ -168,8 +169,8 @@ def parse_sphase_output(
for store in hom_bed_parsed[contig]:
# (start, stop, hom)
(start, stop, _hom) = store
mnvs[contig][start] = stop
mnv_len = (stop - start) + 1
mnvs[contig][start] = (stop, ["1.0"] * (mnv_len - 1))
if max_len < mnv_len:
max_len = mnv_len
mnvs[contig] = {
Expand Down Expand Up @@ -242,7 +243,6 @@ def generate_new_increment_header(
line with the key and description updates to include said
incremental int
"""
print(f"headerline {n}")
new_line = existing_line.copy()
new_line.mapping["ID"] = new_line.mapping["ID"] + f"_{n}"
new_line.mapping["Description"] = (
Expand Down Expand Up @@ -274,9 +274,27 @@ def parse_header_add_merge_and_process(
for new_head_line in lines_to_add:
writer_header.add_line(new_head_line)

# Add confidence score info headerline
##INFO=<ID=SPCONF,Number=.,Type=String,Description="Smart-Phase confidence scores of the form score_MNV_base_1to2,score_MNV_base_2to3 etc.">
writer_header.add_info_line(
vcfpy.OrderedDict(
[
("ID", "SPCONF"),
("Number", "1"),
("Type", "String"),
(
"Description",
"Smart-Phase confidence scores of the form score_MNV_base_1to2,score_MNV_base_2to3 etc.",
),
]
)
)

return writer_header

def merge_snv_to_mnv(self, snv_list: List[vcfpy.Record]) -> vcfpy.Record:
def merge_snv_to_mnv(
self, snv_list: List[vcfpy.Record], conf_calls: List[str]
) -> vcfpy.Record:
"""
Merge snvs from list into a single variant and output to VCF
"""
Expand Down Expand Up @@ -305,7 +323,7 @@ def merge_snv_to_mnv(self, snv_list: List[vcfpy.Record]) -> vcfpy.Record:
id = [] # list of SNV IDs?
ref = ""
alt_str = ""
info = {}
info = {"SPCONF": str(",".join(conf_calls))}
format = []
# Setup new call objects
calls_dict = {}
Expand Down Expand Up @@ -393,24 +411,30 @@ def perform_mnv_merge_to_vcf(self):
start_pos_mnv = 0
start_contig_mnv = ""
in_mnv = False
mnv_end_pos = 0
mnv_conf_calls = None
for variant in reader:
if variant.CHROM in mnvs:
# Start position in an mnv
if int(variant.POS) in mnvs[variant.CHROM]:
in_mnv = True
(mnv_end_pos, mnv_conf_calls) = mnvs[variant.CHROM][
int(variant.POS)
]
start_pos_mnv = int(variant.POS)
start_contig_mnv = variant.CHROM
snvs.append(variant)
# In an MNV and waiting for finish
elif (
in_mnv and int(variant.POS) <= mnvs[start_contig_mnv][start_pos_mnv]
):
elif in_mnv and int(variant.POS) <= mnv_end_pos:
snvs.append(variant)
if int(variant.POS) == mnvs[start_contig_mnv][start_pos_mnv]:
mnv_rec = self.merge_snv_to_mnv(snvs)
if int(variant.POS) == mnv_end_pos:
mnv_rec = self.merge_snv_to_mnv(snvs, mnv_conf_calls)
writer.write_record(mnv_rec)
snvs.clear()
in_mnv = False
mnv_end_pos = 0
mnv_conf_calls = None

else:
writer.write_record(variant)
else:
Expand Down
3 changes: 2 additions & 1 deletion python/test_data/test_exp_result.vcf
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Original file line number Diff line number Diff line change
Expand Up @@ -3426,11 +3426,12 @@
##FORMAT=<ID=RTZ_2,Number=1,Type=Integer,Description="Reads presenting a T for this position, reverse strand (MNV allele 2 in series)">
##FORMAT=<ID=PM_1,Number=1,Type=Float,Description="Proportion of mut allele (MNV allele 1 in series)">
##FORMAT=<ID=PM_2,Number=1,Type=Float,Description="Proportion of mut allele (MNV allele 2 in series)">
##INFO=<ID=SPCONF,Number=1,Type=String,Description="Smart-Phase confidence scores of the form score_MNV_base_1to2,score_MNV_base_2to3 etc.">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOUR
chr1 1291220 8adb6b0a-a8ac-11eb-a08f-58fa0906d930 G A . . DP=105;MP=1.0;GP=2.6e-18;TG=GG/AGGGG;TP=0.99;SG=GG/AAGGG;SP=0.0071 GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:0:0:32:0:0:0:32:0:0.0 0|1:3:0:23:0:3:0:12:0:0.15
chr1 1321114 8adb6fb0-a8ac-11eb-a08f-58fa0906d930 G A . . DP=201;MP=1.0;GP=3.7e-39;TG=GG/AGGGG;TP=1.0;SG=GG/AAGGG;SP=0.00062 GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:0:0:6:1:0:0:129:0:0.0 0|1:1:0:5:0:9:0:50:0:0.15
chr1 1324702 8adb7104-a8ac-11eb-a08f-58fa0906d930 G A . . DP=179;MP=1.0;GP=7.9e-29;TG=GG/AGGGG;TP=0.99;SG=GG/AAGGG;SP=0.0089 GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:0:0:19:0:2:0:96:0:0.017 0|1:4:0:13:0:8:0:37:0:0.19
chr1 1341593 8adb7244-a8ac-11eb-a08f-58fa0906d930 G C . . DP=304;MP=1.0;GP=6.4e-17;TG=GG/CGGGG;TP=1.0;SG=GG/CCGGG;SP=1.2e-06 GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:0:5:157:0:0:7:42:0:0.057 0|1:0:6:57:0:0:5:25:0:0.12
chr1 1341778 8adb737a-a8ac-11eb-a08f-58fa0906d930 C T . . DP=143;MP=1.0;GP=2.6e-27;TG=CC/CCCCT;TP=1.0;SG=CC/CCCTT;SP=0.003 GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:0:17:0:0:0:78:0:0:0.0 0|1:0:8:0:2:0:33:0:5:0.15
chr1 1627262 8adb74a6-a8ac-11eb-a08f-58fa0906d930;8adb75c8-a8ac-11eb-a08f-58fa0906d930 GG AA . . DP_1=266;MP_1=1.0;GP_1=4.6e-51;TG_1=GG/AGGGG;TP_1=1.0;SG_1=GG/AAGGG;SP_1=9.4e-07;DP_2=271;MP_2=1.0;GP_2=7.1e-49;TG_2=GG/AGGGG;TP_2=1.0;SG_2=GG/AAGGG;SP_2=1.6e-06 GT_1:FAZ_1:FCZ_1:FGZ_1:FTZ_1:RAZ_1:RCZ_1:RGZ_1:RTZ_1:PM_1:GT_2:FAZ_2:FCZ_2:FGZ_2:FTZ_2:RAZ_2:RCZ_2:RGZ_2:RTZ_2:PM_2 0|0:0:0:88:0:0:0:88:0:0.0:0|0:0:1:88:0:1:0:88:0:0.0056 0|1:6:0:40:0:4:0:40:0:0.11:0|1:6:0:41:0:5:1:40:0:0.12
chr1 1627262 8adb74a6-a8ac-11eb-a08f-58fa0906d930;8adb75c8-a8ac-11eb-a08f-58fa0906d930 GG AA . . SPCONF=0.1999724805754193;DP_1=266;MP_1=1.0;GP_1=4.6e-51;TG_1=GG/AGGGG;TP_1=1.0;SG_1=GG/AAGGG;SP_1=9.4e-07;DP_2=271;MP_2=1.0;GP_2=7.1e-49;TG_2=GG/AGGGG;TP_2=1.0;SG_2=GG/AAGGG;SP_2=1.6e-06 GT_1:FAZ_1:FCZ_1:FGZ_1:FTZ_1:RAZ_1:RCZ_1:RGZ_1:RTZ_1:PM_1:GT_2:FAZ_2:FCZ_2:FGZ_2:FTZ_2:RAZ_2:RCZ_2:RGZ_2:RTZ_2:PM_2 0|0:0:0:88:0:0:0:88:0:0.0:0|0:0:1:88:0:1:0:88:0:0.0056 0|1:6:0:40:0:4:0:40:0:0.11:0|1:6:0:41:0:5:1:40:0:0.12
chr1 1866692 8adb76ea-a8ac-11eb-a08f-58fa0906d930 C T . . DP=25;MP=1.0;GP=0.00015;TG=CC/CCTTT;TP=0.44;SG=CC/CCCTT;SP=0.36 GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:0:9:0:0:0:8:0:0:0.0 0|1:0:2:0:0:0:2:0:4:0.5
3 changes: 2 additions & 1 deletion python/test_data/test_exp_result_trinuc.vcf
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Original file line number Diff line number Diff line change
Expand Up @@ -3462,5 +3462,6 @@
##FORMAT=<ID=PM_2,Number=1,Type=Float,Description="Proportion of mut allele (MNV allele 2 in series)">
##FORMAT=<ID=PM_3,Number=1,Type=Float,Description="Proportion of mut allele (MNV allele 3 in series)">
##FORMAT=<ID=PM_4,Number=1,Type=Float,Description="Proportion of mut allele (MNV allele 4 in series)">
##INFO=<ID=SPCONF,Number=1,Type=String,Description="Smart-Phase confidence scores of the form score_MNV_base_1to2,score_MNV_base_2to3 etc.">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOUR
chr12 9420710 8bfa48aa-37d4-11ec-b209-ac832c775300;8bfa48fa-37d4-11ec-b209-ac832c775300;8bfa495e-37d4-11ec-b209-ac832c775300;8bfa49a4-37d4-11ec-b209-ac832c775300 GGAG CCCC . . DP_1=60;MP_1=1;GP_1=5e-15;TG_1=GG/CCGGG;TP_1=0.44;SG_1=GG/CCCGG;SP_1=0.34;DP_2=62;MP_2=1;GP_2=1.3e-15;TG_2=GG/CCGGG;TP_2=0.45;SG_2=GG/CCCGG;SP_2=0.32;DP_3=62;MP_3=1;GP_3=1.3e-15;TG_3=AA/AAACC;TP_3=0.45;SG_3=AA/AACCC;SP_3=0.32;DP_4=63;MP_4=1;GP_4=6.8e-16;TG_4=GG/CCGGG;TP_4=0.45;SG_4=GG/CCCGG;SP_4=0.32 GT_1:FAZ_1:FCZ_1:FGZ_1:FTZ_1:RAZ_1:RCZ_1:RGZ_1:RTZ_1:PM_1:GT_2:FAZ_2:FCZ_2:FGZ_2:FTZ_2:RAZ_2:RCZ_2:RGZ_2:RTZ_2:PM_2:GT_3:FAZ_3:FCZ_3:FGZ_3:FTZ_3:RAZ_3:RCZ_3:RGZ_3:RTZ_3:PM_3:GT_4:FAZ_4:FCZ_4:FGZ_4:FTZ_4:RAZ_4:RCZ_4:RGZ_4:RTZ_4:PM_4 0|0:0:0:29:0:0:0:24:0:0:0|0:0:0:31:0:0:0:24:0:0:0|0:31:0:0:0:24:0:0:0:0:0|0:0:0:32:0:0:0:24:0:0 0|1:0:0:2:0:1:3:1:0:0.43:0|1:0:0:2:0:0:3:2:0:0.43:0|1:2:0:0:0:2:3:0:0:0.43:0|1:0:0:2:0:0:3:2:0:0.43
chr12 9420710 8bfa48aa-37d4-11ec-b209-ac832c775300;8bfa48fa-37d4-11ec-b209-ac832c775300;8bfa495e-37d4-11ec-b209-ac832c775300;8bfa49a4-37d4-11ec-b209-ac832c775300 GGAG CCCC . . SPCONF=0.39992018950740127,0.15993615797563573,0.15993615797563573;DP_1=60;MP_1=1;GP_1=5e-15;TG_1=GG/CCGGG;TP_1=0.44;SG_1=GG/CCCGG;SP_1=0.34;DP_2=62;MP_2=1;GP_2=1.3e-15;TG_2=GG/CCGGG;TP_2=0.45;SG_2=GG/CCCGG;SP_2=0.32;DP_3=62;MP_3=1;GP_3=1.3e-15;TG_3=AA/AAACC;TP_3=0.45;SG_3=AA/AACCC;SP_3=0.32;DP_4=63;MP_4=1;GP_4=6.8e-16;TG_4=GG/CCGGG;TP_4=0.45;SG_4=GG/CCCGG;SP_4=0.32 GT_1:FAZ_1:FCZ_1:FGZ_1:FTZ_1:RAZ_1:RCZ_1:RGZ_1:RTZ_1:PM_1:GT_2:FAZ_2:FCZ_2:FGZ_2:FTZ_2:RAZ_2:RCZ_2:RGZ_2:RTZ_2:PM_2:GT_3:FAZ_3:FCZ_3:FGZ_3:FTZ_3:RAZ_3:RCZ_3:RGZ_3:RTZ_3:PM_3:GT_4:FAZ_4:FCZ_4:FGZ_4:FTZ_4:RAZ_4:RCZ_4:RGZ_4:RTZ_4:PM_4 0|0:0:0:29:0:0:0:24:0:0:0|0:0:0:31:0:0:0:24:0:0:0|0:31:0:0:0:24:0:0:0:0:0|0:0:0:32:0:0:0:24:0:0 0|1:0:0:2:0:1:3:1:0:0.43:0|1:0:0:2:0:0:3:2:0:0.43:0|1:2:0:0:0:2:3:0:0:0.43:0|1:0:0:2:0:0:3:2:0:0.43
3 changes: 2 additions & 1 deletion python/test_data/test_filt_qual_exp_result.vcf
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Original file line number Diff line number Diff line change
Expand Up @@ -3427,11 +3427,12 @@
##FORMAT=<ID=RTZ_2,Number=1,Type=Integer,Description="Reads presenting a T for this position, reverse strand (MNV allele 2 in series)">
##FORMAT=<ID=PM_1,Number=1,Type=Float,Description="Proportion of mut allele (MNV allele 1 in series)">
##FORMAT=<ID=PM_2,Number=1,Type=Float,Description="Proportion of mut allele (MNV allele 2 in series)">
##INFO=<ID=SPCONF,Number=1,Type=String,Description="Smart-Phase confidence scores of the form score_MNV_base_1to2,score_MNV_base_2to3 etc.">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOUR
chr1 1291220 8adb6b0a-a8ac-11eb-a08f-58fa0906d930 G A . . DP=105;MP=1.0;GP=2.6e-18;TG=GG/AGGGG;TP=0.99;SG=GG/AAGGG;SP=0.0071 GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:0:0:32:0:0:0:32:0:0.0 0|1:3:0:23:0:3:0:12:0:0.15
chr1 1321114 8adb6fb0-a8ac-11eb-a08f-58fa0906d930 G A . . DP=201;MP=1.0;GP=3.7e-39;TG=GG/AGGGG;TP=1.0;SG=GG/AAGGG;SP=0.00062 GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:0:0:6:1:0:0:129:0:0.0 0|1:1:0:5:0:9:0:50:0:0.15
chr1 1324702 8adb7104-a8ac-11eb-a08f-58fa0906d930 G A . . DP=179;MP=1.0;GP=7.9e-29;TG=GG/AGGGG;TP=0.99;SG=GG/AAGGG;SP=0.0089 GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:0:0:19:0:2:0:96:0:0.017 0|1:4:0:13:0:8:0:37:0:0.19
chr1 1341593 8adb7244-a8ac-11eb-a08f-58fa0906d930 G C . . DP=304;MP=1.0;GP=6.4e-17;TG=GG/CGGGG;TP=1.0;SG=GG/CCGGG;SP=1.2e-06 GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:0:5:157:0:0:7:42:0:0.057 0|1:0:6:57:0:0:5:25:0:0.12
chr1 1341778 8adb737a-a8ac-11eb-a08f-58fa0906d930 C T . . DP=143;MP=1.0;GP=2.6e-27;TG=CC/CCCCT;TP=1.0;SG=CC/CCCTT;SP=0.003 GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:0:17:0:0:0:78:0:0:0.0 0|1:0:8:0:2:0:33:0:5:0.15
chr1 1627262 8adb74a6-a8ac-11eb-a08f-58fa0906d930;8adb75c8-a8ac-11eb-a08f-58fa0906d930 GG AA 5 MNP DP_1=266;MP_1=1.0;GP_1=4.6e-51;TG_1=GG/AGGGG;TP_1=1.0;SG_1=GG/AAGGG;SP_1=9.4e-07;DP_2=271;MP_2=1.0;GP_2=7.1e-49;TG_2=GG/AGGGG;TP_2=1.0;SG_2=GG/AAGGG;SP_2=1.6e-06 GT_1:FAZ_1:FCZ_1:FGZ_1:FTZ_1:RAZ_1:RCZ_1:RGZ_1:RTZ_1:PM_1:GT_2:FAZ_2:FCZ_2:FGZ_2:FTZ_2:RAZ_2:RCZ_2:RGZ_2:RTZ_2:PM_2 0|0:0:0:88:0:0:0:88:0:0.0:0|0:0:1:88:0:1:0:88:0:0.0056 0|1:6:0:40:0:4:0:40:0:0.11:0|1:6:0:41:0:5:1:40:0:0.12
chr1 1627262 8adb74a6-a8ac-11eb-a08f-58fa0906d930;8adb75c8-a8ac-11eb-a08f-58fa0906d930 GG AA 5 MNP SPCONF=0.1999724805754193;DP_1=266;MP_1=1.0;GP_1=4.6e-51;TG_1=GG/AGGGG;TP_1=1.0;SG_1=GG/AAGGG;SP_1=9.4e-07;DP_2=271;MP_2=1.0;GP_2=7.1e-49;TG_2=GG/AGGGG;TP_2=1.0;SG_2=GG/AAGGG;SP_2=1.6e-06 GT_1:FAZ_1:FCZ_1:FGZ_1:FTZ_1:RAZ_1:RCZ_1:RGZ_1:RTZ_1:PM_1:GT_2:FAZ_2:FCZ_2:FGZ_2:FTZ_2:RAZ_2:RCZ_2:RGZ_2:RTZ_2:PM_2 0|0:0:0:88:0:0:0:88:0:0.0:0|0:0:1:88:0:1:0:88:0:0.0056 0|1:6:0:40:0:4:0:40:0:0.11:0|1:6:0:41:0:5:1:40:0:0.12
chr1 1866692 8adb76ea-a8ac-11eb-a08f-58fa0906d930 C T . . DP=25;MP=1.0;GP=0.00015;TG=CC/CCTTT;TP=0.44;SG=CC/CCCTT;SP=0.36 GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:0:9:0:0:0:8:0:0:0.0 0|1:0:2:0:0:0:2:0:4:0.5
99 changes: 93 additions & 6 deletions python/tests/01_MNVMerge_test.py
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Expand Up @@ -157,24 +157,106 @@ def test_get_last_vcf_process_index(in_head, key_prefix, exp_idx):

@pytest.mark.parametrize(
"sphaseout,cutoff,exclude_flags,hom_dict,exp_result",
# SPOUT = "test_data/sample.phased.output"
# SPOUT_TRINUC = "test_data/sample.phased.trinuc.output"
# BAD_SPOUT = "test_data/bad_sample.phased.output"
# SPOUT_EXCEPT = "test_data/sample.phased.except.output"
# BED_INPUT_HOM = "test_data/expected_output_hethom.bed"
# BED_INPUT_NOHOM = "test_data/expected_output.bed"
# SPOUT_TRINUC_2 = "test_data/test_phase_triplet.out"
[
(SPOUT, 0.0, 2, {}, ({"chr1": {1627262: 1627263}}, 2)),
(
SPOUT,
0.0,
2,
{},
(
{"chr1": {1627262: (1627263, ["0.1999724805754193"])}},
2,
),
),
(SPOUT, 0.1, 1, {}, ({}, 1)),
(SPOUT_EXCEPT, 0.0, 2, {}, ({"chr1": {1627262: 1627263}}, 2)),
(SPOUT_TRINUC, 0.0, 2, {}, ({"chr12": {9420710: 9420713}}, 4)),
(
SPOUT_EXCEPT,
0.0,
2,
{},
({"chr1": {1627262: (1627263, ["0.1999724805754193"])}}, 2),
),
(
SPOUT_TRINUC,
0.0,
2,
{},
(
{
"chr12": {
9420710: (
9420713,
[
"0.39992018950740127",
"0.15993615797563573",
"0.15993615797563573",
],
)
}
},
4,
),
),
(
SPOUT_TRINUC,
0.0,
2,
{"chr1": [(1627262, 1627263, "hom")]},
({"chr1": {1627262: 1627263}, "chr12": {9420710: 9420713}}, 4),
(
{
"chr1": {
1627262: (
1627263,
["1.0"],
)
},
"chr12": {
9420710: (
9420713,
[
"0.39992018950740127",
"0.15993615797563573",
"0.15993615797563573",
],
)
},
},
4,
),
),
(
SPOUT_TRINUC,
0.0,
2,
{"chr1": [(1627262, 1627269, "hom")]},
({"chr1": {1627262: 1627269}, "chr12": {9420710: 9420713}}, 8),
(
{
"chr1": {
1627262: (
1627269,
["1.0", "1.0", "1.0", "1.0", "1.0", "1.0", "1.0"],
)
},
"chr12": {
9420710: (
9420713,
[
"0.39992018950740127",
"0.15993615797563573",
"0.15993615797563573",
],
)
},
},
8,
),
),
(
SPOUT_TRINUC_2,
Expand All @@ -183,7 +265,12 @@ def test_get_last_vcf_process_index(in_head, key_prefix, exp_idx):
{},
(
{
"chr17": {42760364: 42760366},
"chr17": {
42760364: (
42760366,
["0.27489430479697324", "0.06933530763570786"],
)
},
},
3,
),
Expand Down