Update expected test outputs for FreeBayes+minimap2; skip novoalign when not needed

Generate new expected FASTA files from FreeBayes+minimap2 pipeline:
- refine1: 6bp insertion at pos 1539 (82% of reads support it, QUAL=300)
- refine2: 49bp longer consensus (minimap2 maps more reads to ends)

Make novoalign instantiation conditional on already_realigned_bam so
refine_assembly works on ARM64 when using pre-aligned BAMs.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: dpark01

src/viral_ngs/assembly.py

@@ -699,8 +699,10 @@ def refine_assembly(
     picard_index = viral_ngs.core.picard.CreateSequenceDictionaryTool()
     picard_mkdup = viral_ngs.core.picard.MarkDuplicatesTool()
     samtools = viral_ngs.core.samtools.SamtoolsTool()
-    novoalign = viral_ngs.core.novoalign.NovoalignTool(license_path=novoalign_license_path)
     fb = viral_ngs.assemble.freebayes.FreeBayesTool()
+    novoalign = None
+    if not already_realigned_bam:
+        novoalign = viral_ngs.core.novoalign.NovoalignTool(license_path=novoalign_license_path)
 
     # Sanitize fasta header & create deambiguated genome for GATK
     deambigFasta = viral_ngs.core.file.mkstempfname('.deambig.fasta')
@@ -771,7 +773,8 @@ def refine_assembly(
     # has a non-zero size
     if (os.path.getsize(outFasta) > 0):
         samtools.faidx(outFasta, overwrite=True)
-        novoalign.index_fasta(outFasta)
+        if already_realigned_bam is None:
+            novoalign.index_fasta(outFasta)
 
     return 0
 

tests/input/TestRefineAssembly/expected.ebov.refine1.freebayes.fasta

@@ -24,7 +24,7 @@ GCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATC
 ACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCAACCCAAATGCAACCCC
 AATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGGATACCA
 TATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGT
-TTAATCTGTGGGTTGAGGCAGCTGGCCAACGAACAAGCTCTCCAACTGTTCCTGAGAGCC
-ACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTGCTGCAG
-CGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGG
-ACCAAGAACAT
+TTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCAACTGTTCCTG
+AGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTG
+CTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACAT
+GATTGGACCAAGAACAT

tests/input/TestRefineAssembly/expected.ebov.refine2.freebayes.fasta

@@ -1,22 +1,30 @@
 >test_sub-EBOV.genome-1
-ATTGAGATCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGGGCTTC
-AGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAA
-AACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGT
-ATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCC
-ACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCT
-TCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATA
-TCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCA
-AGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAAC
-TAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGA
-AAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAA
-CTTCTTCCGACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCA
-AGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACGAGTCCTCAACCTCCC
-ACAACCAAAACAGGTCCGGACAACAGCACCCGTAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTG
-GACAACATCACCGTAGAGCNGACAACGACNNNNNNGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAA
-AGCAGAGAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCAAAACTACAGCGAG
-ACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCA
-ATACTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCAACCCAA
-ATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGGATACCATATTTCGGG
-CCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCA
-ACGAAACGACTCAAGCTCTCCAACTGTTCCTGAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGC
-AATTGACTTCCTGCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAAC
+TCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAA
+TGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCC
+ACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAAT
+CAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCC
+CCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTT
+CCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGG
+AACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTT
+CTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTA
+TTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTT
+GTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCT
+GCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACT
+AATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAAC
+TAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAAC
+GGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAAC
+ACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTG
+CACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACG
+AGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCGTAATACACCCGTG
+TATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGCNGACAAC
+GNCNNNNNNGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAAAGCAGAG
+AACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCAA
+AACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGT
+GCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATC
+ACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCAACCCAAATGCAACCCC
+AATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGGATACCA
+TATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGT
+TTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCAACTGTTCCTG
+AGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTG
+CTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACAT
+GATTGGACCAAGAACAT