Merge pull request #18 from martinghunt/apply_variants_to_probe_flanks

Apply variants to probe flanks
iqbal-lab-org · Oct 9, 2020 · be60d7c · be60d7c
2 parents bfe49f0 + 53a62ba
commit be60d7c
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Showing 53 changed files with 1,031 additions and 1,481 deletions.
diff --git a/tests/data/probe_mapping/annotate_vcf_with_probe_mapping.expect.rev.vcf b/tests/data/probe_mapping/annotate_vcf_with_probe_mapping.expect.rev.vcf
diff --git a/tests/data/probe_mapping/annotate_vcf_with_probe_mapping.expect.vcf b/tests/data/probe_mapping/annotate_vcf_with_probe_mapping.expect.vcf
diff --git a/tests/data/probe_mapping/annotate_vcf_with_probe_mapping.in.vcf b/tests/data/probe_mapping/annotate_vcf_with_probe_mapping.in.vcf
@@ -1,154 +1,16 @@
 ##contig=<ID=ref,length=430>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
-ref	37	1	T	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	37	2	T	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	37	3	T	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	38	4	G	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	38	5	G	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	38	6	G	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	39	7	T	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	39	8	T	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	39	9	T	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	40	10	A	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	40	11	A	G	.	PASS	.	GT:EXPECT	1/1:TP
-ref	40	12	A	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	41	13	C	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	41	14	C	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	41	15	C	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	42	16	A	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	42	17	A	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	42	18	A	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	43	19	G	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	43	20	G	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	43	21	G	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	57	22	G	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	57	23	G	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	57	24	G	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	58	25	C	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	58	26	C	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	58	27	C	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	59	28	A	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	59	29	A	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	59	30	A	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	60	31	A	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	60	32	A	G	.	PASS	.	GT:EXPECT	1/1:TP
-ref	60	33	A	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	61	34	A	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	61	35	A	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	61	36	A	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	62	37	G	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	62	38	G	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	62	39	G	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	63	40	A	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	63	41	A	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	63	42	A	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	77	43	G	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	77	44	G	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	77	45	G	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	78	46	C	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	78	47	C	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	78	48	C	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	79	49	C	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	79	50	C	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	79	51	C	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	80	52	T	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	80	53	T	C	.	PASS	.	GT:EXPECT	1/1:TP
-ref	80	54	T	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	81	55	C	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	81	56	C	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	81	57	C	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	82	58	C	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	82	59	C	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	82	60	C	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	83	61	G	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	83	62	G	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	83	63	G	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	106	64	G	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	106	65	G	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	106	66	G	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	107	67	T	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	107	68	T	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	107	69	T	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	108	70	C	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	108	71	C	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	108	72	C	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	109	73	G	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	109	74	G	C	.	PASS	.	GT:EXPECT	1/1:TP
-ref	109	75	G	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	110	76	C	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	110	77	C	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	110	78	C	T	.	PASS	.	GT:EXPECT	1/1:TP
-ref	111	79	A	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	111	80	A	G	.	PASS	.	GT:EXPECT	1/1:TP
-ref	111	81	A	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	112	82	T	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	112	83	T	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	112	84	T	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	113	85	A	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	113	86	A	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	113	87	A	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	114	88	G	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	114	89	G	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	114	90	G	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	137	91	C	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	137	92	C	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	137	93	C	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	138	94	T	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	138	95	T	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	138	96	T	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	139	97	C	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	139	98	C	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	139	99	C	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	140	100	G	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	140	101	G	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	140	102	G	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	140	103	GT	AC	.	PASS	.	GT:EXPECT	1/1:FP
-ref	140	104	GT	G	.	PASS	.	GT:EXPECT	1/1:TP
-ref	160	105	A	AG	.	PASS	.	GT:EXPECT	1/1:Partial_TP
-ref	160	106	A	AT	.	PASS	.	GT:EXPECT	1/1:TP
-ref	160	107	A	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	160	108	A	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	161	109	A	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	161	110	A	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	161	111	A	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	161	112	AAC	ACGTACGGGTGGTGTGTTTGAAAGATAG	.	PASS	.	GT:EXPECT	1/1:Partial_TP
-ref	161	113	AACAAGACGTCCTCT	ACG	.	PASS	.	GT:EXPECT	1/1:Partial_TP
-ref	162	114	A	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	162	115	A	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	162	116	A	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	163	117	C	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	163	118	C	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	163	119	C	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	164	120	A	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	164	121	A	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	164	122	A	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	230	123	TG	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	250	124	.	G	.	PASS	.	GT:EXPECT	1/1:VFR_FILTER_NO_REF_SEQ
-ref	250	125	C	G	.	PASS	.	GT:EXPECT	1/1:VFR_FILTER_REF_STRING_MISMATCH
-ref	250	126	G	.	.	PASS	.	GT:EXPECT	1/1:VFR_FILTER_NO_ALTS
-ref	250	127	G	C	.	FILTER_X	.	GT:EXPECT	1/1:TP
-ref	250	128	G	C	.	MISMAPPED_UNPLACEABLE	.	GT:EXPECT	1/1:TP
-ref	250	129	G	C	.	PASS	.	EXPECT	VFR_FILTER_NO_GT
-ref	250	130	G	C	.	PASS	.	GT:EXPECT	./.:VFR_FILTER_CANNOT_USE_GT
-ref	250	131	G	C	.	PASS	.	GT:EXPECT	0/1:VFR_FILTER_CANNOT_USE_GT
-ref	298	132	G	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	298	133	G	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	298	134	G	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	299	135	C	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	299	136	C	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	299	137	C	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	300	138	A	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	300	139	A	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	300	140	A	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	300	141	ATGCGTATCG	AGGTAACCCC	.	PASS	.	GT:EXPECT	1/1:Partial_TP
-ref	300	142	ATGCGTATCG	AGGTACGAGA	.	PASS	.	GT:EXPECT	1/1:TP
-ref	301	143	T	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	301	144	T	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	302	145	G	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	302	146	G	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	302	147	G	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	303	148	C	A	.	PASS	.	GT:EXPECT	1/1:FP
-ref	303	149	C	G	.	PASS	.	GT:EXPECT	1/1:FP
-ref	304	150	G	C	.	PASS	.	GT:EXPECT	1/1:FP
-ref	304	151	G	T	.	PASS	.	GT:EXPECT	1/1:FP
-ref	400	152	G	AAAAA	.	PASS	.	GT:EXPECT	1/1:FP_PROBE_UNMAPPED
+ref	40	1	A	G	.	PASS	.	GT:EXPECT	1/1:TP
+ref	60	2	A	G	.	PASS	.	GT:EXPECT	1/1:TP
+ref	80	3	T	C	.	PASS	.	GT:EXPECT	1/1:TP
+ref	109	4	G	C	.	PASS	.	GT:EXPECT	1/1:TP
+ref	110	5	C	T	.	PASS	.	GT:EXPECT	1/1:TP
+ref	111	6	A	G	.	PASS	.	GT:EXPECT	1/1:TP
+ref	140	7	GT	AC	.	PASS	.	GT:EXPECT	1/1:FP
+ref	140	8	GT	G	.	PASS	.	GT:EXPECT	1/1:TP
+ref	160	9	A	AG	.	PASS	.	GT:EXPECT	1/1:Partial_TP
+ref	160	10	A	AT	.	PASS	.	GT:EXPECT	1/1:TP
+ref	230	11	TG	T	.	PASS	.	GT:EXPECT	1/1:FP
+ref	300	12	ATGCGTATCG	AGGTAACCCC	.	PASS	.	GT:EXPECT	1/1:Partial_TP
+ref	300	13	ATGCGTATCG	AGGTACGAGA	.	PASS	.	GT:EXPECT	1/1:TP
+ref	400	14	G	AAAAA	.	PASS	.	GT:EXPECT	1/1:FP_PROBE_UNMAPPED
diff --git a/tests/data/probe_mapping/annotate_vcf_with_probe_mapping.truth.fa b/tests/data/probe_mapping/annotate_vcf_with_probe_mapping.truth.fa
@@ -3,7 +3,7 @@ CTGACTGGCCGAATAGGTCAGATATAGGCAACGACATGTGCAGTGCGGCGACCCTTGCAG
 AGACAGTGACGCTTTCGCCCCCGTTGCCTAAACCTATTTGAAGGAGTCCTGTAGCAGCCG
 CAGTAAGGCACAATACCTCGGTCCGTGTTACCAGACCAATAACAAGACGTCCTCTTCAAT
 GTTTAAATGACCCTCTCGTCATAAAACCTTTCTACTATGTGTTCCGCAATGATCAACAAC
-TACAATGGCCCGTCGTGAATAACGCGACGGCTGAGACGAACGGCGCGTGAATGAAGCGCA
+TACAATGGCGCGTCGTGAATAACGCGACGGCTGAGACGAACGGCGCGTGAATGAAGCGCA
 GGTACGAGATTAAACAGCTCAGGAGCCAGTTTTCCAATCCTACATCTGTTTCTTGCGTCG
 TAGCGGGACCCTCCATTGTTACTTATTAGGTTCTCGTTATGTCTCATAATCTCAGTGCTG
 GTGTGATAAG
diff --git a/tests/data/probe_mapping/annotate_vcf_with_probe_mapping.truth.revcomp.fa b/tests/data/probe_mapping/annotate_vcf_with_probe_mapping.truth.revcomp.fa
@@ -2,7 +2,7 @@
 CTTATCACACCAGCACTGAGATTATGAGACATAACGAGAACCTAATAAGTAACAATGGAG
 GGTCCCGCTACGACGCAAGAAACAGATGTAGGATTGGAAAACTGGCTCCTGAGCTGTTTA
 ATCTCGTACCTGCGCTTCATTCACGCGCCGTTCGTCTCAGCCGTCGCGTTATTCACGACG
-GGCCATTGTAGTTGTTGATCATTGCGGAACACATAGTAGAAAGGTTTTATGACGAGAGGG
+CGCCATTGTAGTTGTTGATCATTGCGGAACACATAGTAGAAAGGTTTTATGACGAGAGGG
 TCATTTAAACATTGAAGAGGACGTCTTGTTATTGGTCTGGTAACACGGACCGAGGTATTG
 TGCCTTACTGCGGCTGCTACAGGACTCCTTCAAATAGGTTTAGGCAACGGGGGCGAAAGC
 GTCACTGTCTCTGCAAGGGTCGCCGCACTGCACATGTCGTTGCCTATATCTGACCTATTC

diff --git a/tests/data/probe_mapping/make_test_data.py → ...otate_vcf_with_probe_mapping_make_data.py b/tests/data/probe_mapping/make_test_data.py → ...otate_vcf_with_probe_mapping_make_data.py
@@ -97,9 +97,11 @@ def add_fp_snps(positions, vcf_lines, ref_seq, truth_seq):
 
 # These two make sure we hit lines in the code where the cigar string has I or D
 # while the probe position that is tracked is inside the allele of interest.
-# The other variants in this test file don't fo that.
-vcf_lines.append(["ref", 161, ".", "".join(ref_seq[160:163]), "ACGTACGGGTGGTGTGTTTGAAAGATAG", ".", "PASS", ".", "GT:EXPECT", "1/1:Partial_TP"])
-vcf_lines.append(["ref", 161, ".", "".join(ref_seq[160:175]), "ACG", ".", "PASS", ".", "GT:EXPECT", "1/1:Partial_TP"])
+# The other variants in this test file don't do that.
+# EDIT: have to remove these because they mess up the previous variants at position 160.
+# Added this case into the cluster_snp_indel test instead
+#vcf_lines.append(["ref", 161, ".", "".join(ref_seq[160:163]), "ACGTACGGGTGGTGTGTTTGAAAGATAG", ".", "PASS", ".", "GT:EXPECT", "1/1:Partial_TP"])
+#vcf_lines.append(["ref", 161, ".", "".join(ref_seq[160:175]), "ACG", ".", "PASS", ".", "GT:EXPECT", "1/1:Partial_TP"])
 
 fp_positions.extend(range(159, 164))
 assert len(ref_seq) == len(truth_seq) == 299
@@ -131,24 +133,17 @@ def add_fp_snps(positions, vcf_lines, ref_seq, truth_seq):
 ref_seq[230] = truth_seq[230] = "G"
 vcf_lines.append(["ref", 230, ".", "TG", "T", ".", "PASS", ".", "GT:EXPECT", "1/1:FP"])
 
-
 # SNP so near the end that probe won't map
 vcf_lines.append(["ref", 400, ".", ref_seq[399], "AAAAA", ".", "PASS", ".", "GT:EXPECT", "1/1:FP_PROBE_UNMAPPED"])
 
-# Add in records that can't be evaluated for various reasons
-ref_seq[249] = "G"
-truth_seq[249] = "C"
-vcf_lines.append(["ref", 250, ".", "G", "C", ".", "FILTER_X", ".", "GT:EXPECT", "1/1:TP"])
-vcf_lines.append(["ref", 250, ".", "G", "C", ".", "MISMAPPED_UNPLACEABLE", ".", "GT:EXPECT", "1/1:TP"])
-vcf_lines.append(["ref", 250, ".", "G", "C", ".", "PASS", ".", "GT:EXPECT", "0/1:VFR_FILTER_CANNOT_USE_GT"])
-vcf_lines.append(["ref", 250, ".", "G", "C", ".", "PASS", ".", "GT:EXPECT", "./.:VFR_FILTER_CANNOT_USE_GT"])
-vcf_lines.append(["ref", 250, ".", "C", "G", ".", "PASS", ".", "GT:EXPECT", "1/1:VFR_FILTER_REF_STRING_MISMATCH"])
-vcf_lines.append(["ref", 250, ".", "G", "C", ".", "PASS", ".", "EXPECT", "VFR_FILTER_NO_GT"])
-vcf_lines.append(["ref", 250, ".", "G", ".", ".", "PASS", ".", "GT:EXPECT", "1/1:VFR_FILTER_NO_ALTS"])
-vcf_lines.append(["ref", 250, ".", ".", "G", ".", "PASS", ".", "GT:EXPECT", "1/1:VFR_FILTER_NO_REF_SEQ"])
-
-
-add_fp_snps(fp_positions, vcf_lines, ref_seq, truth_seq)
+# We now have an underlying assumption that the input VCF does not contain a
+# large number of errors, allowing us to apply called variants in the flanks
+# of probes. This is to correctly call clusters of variants. This means that
+# we can no longer add in all these FP SNPs at every position in this test -
+# it results in flanks having junk and messing up the TP/FP call that
+# we're testing. So don't do it for now (but leave here commented out in case
+# we change the method again the future).
+#add_fp_snps(fp_positions, vcf_lines, ref_seq, truth_seq)
 
 
 with open("annotate_vcf_with_probe_mapping.in.vcf", "w") as f:

diff --git a/tests/data/probe_mapping/clustered_snp_indel.expect.vcf b/tests/data/probe_mapping/clustered_snp_indel.expect.vcf
@@ -0,0 +1,32 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##contig=<ID=ref,length=2000>
+##FORMAT=<ID=VFR_IN_MASK,Number=1,Type=String,Description="Whether or not the variant is in the truth genome mask">
+##FORMAT=<ID=VFR_RESULT,Number=1,Type=String,Description="FP, TP, or Partial_TP when part of the allele matches the truth reference">
+##FORMAT=<ID=VFR_ALLELE_LEN,Number=1,Type=Integer,Description="Number of positions in allele that were checked if they match the truth">
+##FORMAT=<ID=VFR_ALLELE_MATCH_COUNT,Number=1,Type=String,Description="Number of positions in allele that match the truth">
+##FORMAT=<ID=VFR_ALLELE_MATCH_FRAC,Number=1,Type=String,Description="Fraction of positions in allele that match the truth">
+##FORMAT=<ID=VFR_ED_RA,Number=1,Type=String,Description="Edit distance between ref and alt allele (using the called allele where more than one alt)">
+##FORMAT=<ID=VFR_ED_TR,Number=1,Type=String,Description="Edit distance between truth and ref allele">
+##FORMAT=<ID=VFR_ED_TA,Number=1,Type=String,Description="Edit distance between truth and alt allele">
+##FORMAT=<ID=VFR_ED_SCORE,Number=1,Type=String,Description="Edit distance score">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
+NC_000962	1001	.	A	T	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1004	.	T	C	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1005	.	GGAGA	G	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1013	.	G	C	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1015	.	A	AC	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:0:0:2:2:1.0:0:TP
+NC_000962	1019	.	C	G	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1022	.	T	TAG	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:0:0:3:3:1.0:0:TP
+NC_000962	1024	.	T	TGC	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:0:0:3:3:1.0:0:TP
+NC_000962	1026	.	G	A	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1028	.	GC	G	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1033	.	A	T	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1035	.	A	G	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1038	.	A	C	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1041	.	G	A	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1044	.	G	A	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1045	.	G	C	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1046	.	A	T	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:1:0:1:1:1.0:0:TP
+NC_000962	1048	.	C	CG	.	PASS	.	GT:VFR_ED_RA:VFR_ED_TR:VFR_ED_TA:VFR_ALLELE_LEN:VFR_ALLELE_MATCH_COUNT:VFR_ALLELE_MATCH_FRAC:VFR_IN_MASK:VFR_RESULT	1/1:1:0:0:2:2:1.0:0:TP
diff --git a/tests/data/probe_mapping/clustered_snp_indel.in.vcf b/tests/data/probe_mapping/clustered_snp_indel.in.vcf
@@ -0,0 +1,23 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##contig=<ID=ref,length=2000>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
+NC_000962	1001	.	A	T	.	PASS	.	GT	1/1
+NC_000962	1004	.	T	C	.	PASS	.	GT	1/1
+NC_000962	1005	.	GGAGA	G	.	PASS	.	GT	1/1
+NC_000962	1013	.	G	C	.	PASS	.	GT	1/1
+NC_000962	1015	.	A	AC	.	PASS	.	GT	1/1
+NC_000962	1019	.	C	G	.	PASS	.	GT	1/1
+NC_000962	1022	.	T	TAG	.	PASS	.	GT	1/1
+NC_000962	1024	.	T	TGC	.	PASS	.	GT	1/1
+NC_000962	1026	.	G	A	.	PASS	.	GT	1/1
+NC_000962	1028	.	GC	G	.	PASS	.	GT	1/1
+NC_000962	1033	.	A	T	.	PASS	.	GT	1/1
+NC_000962	1035	.	A	G	.	PASS	.	GT	1/1
+NC_000962	1038	.	A	C	.	PASS	.	GT	1/1
+NC_000962	1041	.	G	A	.	PASS	.	GT	1/1
+NC_000962	1044	.	G	A	.	PASS	.	GT	1/1
+NC_000962	1045	.	G	C	.	PASS	.	GT	1/1
+NC_000962	1046	.	A	T	.	PASS	.	GT	1/1
+NC_000962	1048	.	C	CG	.	PASS	.	GT	1/1
diff --git a/tests/data/probe_mapping/clustered_snp_indel.ref.fa b/tests/data/probe_mapping/clustered_snp_indel.ref.fa
@@ -0,0 +1,35 @@
+>NC_000962
+TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTT
+AACGGCGACCCTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTG
+ACCCCTCAGCAAAGGGCTTGGCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTT
+GCTCTGTTATCCGTGCCGAGCAGCTTTGTCCAAAACGAAATCGAGCGCCATCTGCGGGCC
+CCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGATCCAACTCGGGGTCCGCATC
+GCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGAAAATCCTGCT
+ACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG
+GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCACAATACCGATTCC
+GCTACCGCTGGCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGC
+GCCTCCAACCGGTTCGCGCACGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCT
+TACAACCCCCTGTTCATCTGGGGCGAGTCCGGTCTCGGCAAGACACACCTGCTACACGCG
+GCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGGTCAAATATGTCTCCACCGAG
+GAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGCATTCAAACGC
+AGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG
+GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATC
+GTCATCTCATCTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACC
+CGCTTTGAGTGGGGGCTGATCACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCC
+ATCTTGCGCAAGAAAGCACAGATGGAACGGCTCGCGGTCCCCGACGATGTCCTCGAACTC
+ATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGGGCGCGCTGATCCGGGTCACC
+GCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGATTGTGCTTCGC
+GATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC
+GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTG
+GCCCAGTCACGACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCC
+AAAATCGGCCAAGCGTTCGGCCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATC
+CTGTCCGAGATGGCCGAGCGCCGTGAGGTCTTTGATCACGTCAAAGAACTCACCACTCGC
+ATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCCGACAACGTTCTTAAAAAAAC
+TTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCTGTGCACAAAC
+CGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG
+ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACC
+TGCACCAAGACCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCT
+TCGTCGTTTGTTCTTGGAAAGACAGCGCTGGGGATCGTTCGCTGGATACCACCCGCATAA
+CTGGCTCGTCGCGGTGGGTCAGAGGTCAATGATGAACTTTCAAGTTGACGTGAGAAGCTC
+TACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGGGTCACGCGTCATGGGCATTC
+GTCGTTGGCAGTCCCCACGC