Repository: iqbal-lab-org/varifier (language: python)

Issue:
Empty 01.merged.vcf
This is a copy of a post in the covid-pipeline slack channel, reproduced here to better track issues.

Here's a sample I spiked a 6bp deletion and a SNP into, `ERR5246334-varifier` with:
```
$ cat 00.dnadiff.vcf 
##fileformat=VCFv4.2
##contig=<ID=ERR5246334,length=29884>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
ERR5246334	26431	.	A	T	.	.	SVTYPE=DNADIFF_SNP	GT	1/1
ERR5246334	27690	.	GGCAATA	G	.	.	SVTYPE=DNADIFF_DEL	GT	1/1
```
and
```
$ cat 00.minimap2.vcf 
##fileformat=VCFv4.1
##contig=<ID=ERR5246334,length=29884>
##INFO=<ID=QNAME,Number=1,Type=String,Description="Query name">
##INFO=<ID=QSTART,Number=1,Type=Integer,Description="Query start">
##INFO=<ID=QSTRAND,Number=1,Type=String,Description="Query strand">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
ERR5246334	26431	.	A	T	60	.	QNAME=assembly;QSTART=26401;QSTRAND=+	GT	1/1
ERR5246334	27690	.	GGCAATA	G	60	.	QNAME=assembly;QSTART=27661;QSTRAND=+	GT	1/1
```
but
```
$ cat 01.merged.vcf
##fileformat=VCFv4.2
##contig=<ID=ERR5246334,length=29884>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
```


Discussion / hints:

Fix patch:
diff --git a/requirements.txt b/requirements.txt
index 1766ac6..49199a2 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 biopython
-cluster_vcf_records >= 0.13.1
+cluster_vcf_records >= 0.13.2
 mappy >= 2.17
 pandas
 pyfastaq >= 3.14.0


Test patch:
diff --git a/tests/data/truth_variant_finding/merge_vcf_files_for_probe_mapping.ref.fa b/tests/data/truth_variant_finding/merge_vcf_files_for_probe_mapping.ref.fa
index 8b68d3e..9abea40 100644
--- a/tests/data/truth_variant_finding/merge_vcf_files_for_probe_mapping.ref.fa
+++ b/tests/data/truth_variant_finding/merge_vcf_files_for_probe_mapping.ref.fa
@@ -1,4 +1,4 @@
->ref
+>ref foo
 AAGCCCAATAAACCACTAGTGATATAGGCAACGACATGTACAGTGCGGCGACCCTTGCAA
 AGACAGTGACGCTTTCGCCTCCGTTGCCTAAACCTATTTGAAGGAGTCGCATAGCAGCCG
 CAGTAAGGCACAATACCTCGTGTCCGTGTTACCAGACCAAAACAAGACGTCCTCTTCAAT
diff --git a/tests/data/truth_variant_finding/merge_vcf_files_for_probe_mapping.ref.fa.fai b/tests/data/truth_variant_finding/merge_vcf_files_for_probe_mapping.ref.fa.fai
index 1d6da42..35a2f76 100644
--- a/tests/data/truth_variant_finding/merge_vcf_files_for_probe_mapping.ref.fa.fai
+++ b/tests/data/truth_variant_finding/merge_vcf_files_for_probe_mapping.ref.fa.fai
@@ -1,1 +1,1 @@
-ref	430	5	60	61
+ref	430	9	60	61