Merge branch 'hotfix/0.9.1'

CHANGELOG.md

@@ -8,6 +8,12 @@ and this project adheres to
 
 ## [Unreleased]
 
+## [0.9.1] - 2022-08-01
+
+## Fixed
+
+- Errors from incorrect CliqueSNV VCF output
+
 ## [0.9.0] - 2022-07-29
 
 ## Added
@@ -262,7 +268,8 @@ This is a major overhaul of YAVSAP to make it use nf-core's DSL2 modules.
 - Krona graphs of Kraken2 output
 - BLAST of assemblies and unclassified reads
 
-[unreleased]: https://github.com/ksumngs/yavsap/compare/v0.9.0...HEAD
+[unreleased]: https://github.com/ksumngs/yavsap/compare/v0.9.1...HEAD
+[0.9.1]: https://github.com/ksumngs/yavsap/compare/v0.9.0...v0.9.1
 [0.9.0]: https://github.com/ksumngs/yavsap/compare/v0.8.0...v0.9.0
 [0.8.0]: https://github.com/ksumngs/yavsap/compare/v0.7.1...v0.8.0
 [0.7.1]: https://github.com/ksumngs/yavsap/compare/v0.7.0...v0.7.1

bin/vartable

@@ -41,7 +41,12 @@ for vcf_file in ARGS
     variants = Dict[]
 
     for vcf_record in vcf_reader
-        first(VCF.filter(vcf_record)) == "PASS" || continue
+        try
+            first(VCF.filter(vcf_record)) == "PASS" || continue
+        catch
+            # This is fine: someone forgot to read the spec and created
+            # an empty FILTER instead of marking it as PASS, unless it isn't
+        end #try
 
         variant = Dict()
 
@@ -53,7 +58,11 @@ for vcf_file in ARGS
         variant["pos"] = VCF.pos(vcf_record)
         variant["ref"] = VCF.ref(vcf_record)
         variant["alt"] = first(VCF.alt(vcf_record))
-        variant["qual"] = VCF.qual(vcf_record)
+        variant["qual"] = try
+            VCF.qual(vcf_record)
+        catch
+            nothing
+        end
 
         push!(variants, variant)
     end #for

nextflow.config

@@ -238,7 +238,7 @@ manifest {
     description = 'Identification and analysis of viral haplotypes in metagenomic NGS reads'
     mainScript = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version = '0.9.0'
+    version = '0.9.1'
     recurseSubmodules = true
 }