test v0.1.6

fix bugs related to merge
pirl-unc · Feb 1, 2024 · 3563214 · 3563214
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Showing 16 changed files with 3,580 additions and 3,553 deletions.
diff --git a/examples/outputs/hg002_cutesv.tsv b/examples/outputs/hg002_cutesv.tsv
diff --git a/examples/outputs/hg002_intersecting_variants.tsv b/examples/outputs/hg002_intersecting_variants.tsv
diff --git a/examples/outputs/hg002_merged_variants.tsv b/examples/outputs/hg002_merged_variants.tsv
diff --git a/examples/outputs/hg002_merged_variants.vcf b/examples/outputs/hg002_merged_variants.vcf
diff --git a/examples/outputs/hg002_merged_variants_collapsed.tsv b/examples/outputs/hg002_merged_variants_collapsed.tsv
diff --git a/examples/outputs/hg002_merged_variants_passed.tsv b/examples/outputs/hg002_merged_variants_passed.tsv
diff --git a/examples/outputs/hg002_merged_variants_private.tsv b/examples/outputs/hg002_merged_variants_private.tsv
diff --git a/examples/outputs/hg002_merged_variants_rejected.tsv b/examples/outputs/hg002_merged_variants_rejected.tsv
diff --git a/examples/outputs/hg002_sniffles2.tsv b/examples/outputs/hg002_sniffles2.tsv
diff --git a/examples/outputs/hg002_sniffles2_ensembl_annotated.tsv b/examples/outputs/hg002_sniffles2_ensembl_annotated.tsv
diff --git a/examples/outputs/hg002_sniffles2_gencode_annotated.tsv b/examples/outputs/hg002_sniffles2_gencode_annotated.tsv
diff --git a/examples/outputs/hg002_sniffles2_overlap.tsv b/examples/outputs/hg002_sniffles2_overlap.tsv
@@ -1,3 +1,3 @@
 variant_id	variant_call_id	sample_id	chromosome_1	position_1	chromosome_2	position_2	variant_type	reference_allele	alternate_allele	source_id	phase_block_id	clone_id	nucleic_acid	variant_calling_method	sequencing_platform	filter	quality_score	precise	variant_subtype	variant_size	reference_allele_read_count	alternate_allele_read_count	total_read_count	alternate_allele_fraction	alternate_allele_read_ids	variant_sequences	tags	attributes	position_1_annotation_annotator	position_1_annotation_annotator_version	position_1_annotation_gene_id	position_1_annotation_gene_id_stable	position_1_annotation_gene_name	position_1_annotation_gene_strand	position_1_annotation_gene_type	position_1_annotation_gene_version	position_1_annotation_region	position_1_annotation_species	position_2_annotation_annotator	position_2_annotation_annotator_version	position_2_annotation_gene_id	position_2_annotation_gene_id_stable	position_2_annotation_gene_name	position_2_annotation_gene_strand	position_2_annotation_gene_type	position_2_annotation_gene_version	position_2_annotation_region	position_2_annotation_species
-1	HG002_dna_sniffles2_INS_1_chr1:10863_chr1:10863	HG002	chr1	10863	chr1	10863	INS	N	CAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA	hg002			dna	sniffles2	PACBIO	PASS	45.0	True		48	5	8	13	0.615	m64012_190921_234837/58460920/ccs;m64011_190830_220126/131269927/ccs;m64012_190921_234837/125634487/ccs;m64011_190830_220126/102304431/ccs;m64011_190901_095311/166070209/ccs;m64011_190830_220126/70254798/ccs;m64011_190901_095311/23725469/ccs;m64011_190901_095311/150538373/ccs	CAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA		ID=Sniffles2.INS.5S0;PRECISE=True;SVTYPE=INS;SVLEN=48;END=10863;SUPPORT=8;RNAMES=m64011_190901_095311/166070209/ccs,m64012_190921_234837/125634487/ccs,m64011_190830_220126/70254798/ccs,m64011_190901_095311/150538373/ccs,m64011_190830_220126/102304431/ccs,m64012_190921_234837/58460920/ccs,m64011_190830_220126/131269927/ccs,m64011_190901_095311/23725469/ccs;COVERAGE=11,12,13,13,13;STRAND=-;AF=0.615;STDEV_LEN=14.341;STDEV_POS=0.0;SUPPORT_LONG=0;GT=0/1;GQ=27;DR=5;DV=8																				
-2	HG002_dna_sniffles2_INS_2_chr1:10863_chr1:10863	HG002	chr1	10863	chr1	10863	INS	N	CAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGGGCCGGCGCAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA	hg002			dna	sniffles2	PACBIO	PASS	51.0	True		134	8	5	13	0.385	m64011_190901_095311/14353347/ccs;m64011_190901_095311/142478143/ccs;m64011_190830_220126/95815702/ccs;m64011_190901_095311/177932654/ccs;m64011_190901_095311/101253601/ccs	CAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGGGCCGGCGCAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA		ID=Sniffles2.INS.6S0;PRECISE=True;SVTYPE=INS;SVLEN=134;END=10863;SUPPORT=5;RNAMES=m64011_190901_095311/177932654/ccs,m64011_190901_095311/101253601/ccs,m64011_190901_095311/14353347/ccs,m64011_190901_095311/142478143/ccs,m64011_190830_220126/95815702/ccs;COVERAGE=11,12,13,13,13;STRAND=+-;AF=0.385;STDEV_LEN=0.0;STDEV_POS=0.0;SUPPORT_LONG=0;GT=0/1;GQ=27;DR=8;DV=5																				
+1	HG002_dna_sniffles2_INS_1_chr1:10863_chr1:10863	HG002	chr1	10863	chr1	10863	INS	N	CAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA	hg002			dna	sniffles2	PACBIO	PASS	45.0	True		48	5	8	13	0.615	m64011_190901_095311/23725469/ccs;m64011_190830_220126/102304431/ccs;m64011_190830_220126/131269927/ccs;m64012_190921_234837/58460920/ccs;m64011_190901_095311/150538373/ccs;m64011_190901_095311/166070209/ccs;m64012_190921_234837/125634487/ccs;m64011_190830_220126/70254798/ccs	CAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA		ID=Sniffles2.INS.5S0;PRECISE=True;SVTYPE=INS;SVLEN=48;END=10863;SUPPORT=8;RNAMES=m64011_190901_095311/166070209/ccs,m64012_190921_234837/125634487/ccs,m64011_190830_220126/70254798/ccs,m64011_190901_095311/150538373/ccs,m64011_190830_220126/102304431/ccs,m64012_190921_234837/58460920/ccs,m64011_190830_220126/131269927/ccs,m64011_190901_095311/23725469/ccs;COVERAGE=11,12,13,13,13;STRAND=-;AF=0.615;STDEV_LEN=14.341;STDEV_POS=0.0;SUPPORT_LONG=0;GT=0/1;GQ=27;DR=5;DV=8																				
+2	HG002_dna_sniffles2_INS_2_chr1:10863_chr1:10863	HG002	chr1	10863	chr1	10863	INS	N	CAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGGGCCGGCGCAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA	hg002			dna	sniffles2	PACBIO	PASS	51.0	True		134	8	5	13	0.385	m64011_190901_095311/101253601/ccs;m64011_190901_095311/177932654/ccs;m64011_190830_220126/95815702/ccs;m64011_190901_095311/14353347/ccs;m64011_190901_095311/142478143/ccs	CAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGGGCCGGCGCAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA		ID=Sniffles2.INS.6S0;PRECISE=True;SVTYPE=INS;SVLEN=134;END=10863;SUPPORT=5;RNAMES=m64011_190901_095311/177932654/ccs,m64011_190901_095311/101253601/ccs,m64011_190901_095311/14353347/ccs,m64011_190901_095311/142478143/ccs,m64011_190830_220126/95815702/ccs;COVERAGE=11,12,13,13,13;STRAND=+-;AF=0.385;STDEV_LEN=0.0;STDEV_POS=0.0;SUPPORT_LONG=0;GT=0/1;GQ=27;DR=8;DV=5																				
diff --git a/examples/outputs/hg002_sniffles2_private.tsv b/examples/outputs/hg002_sniffles2_private.tsv