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fix: repair CITATION.cff and clarify BAM contig-map comment #73

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Merged
nextgenusfs merged 2 commits into from
Jun 10, 2026
Merged

fix: repair CITATION.cff and clarify BAM contig-map comment #73

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09d8f1a
fix: repair malformed CITATION.cff fields
Jun 9, 2026
61b89c8
docs: correct inv_contig_map comment in predict
Jun 9, 2026
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4 changes: 2 additions & 2 deletions CITATION.cff
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
cff-version: version = "26.5.22"
cff-version: 1.2.0
title: 'funannotate2: eukaryotic genome annotation'
message: >-
If you use this software, please cite it using the
Expand All @@ -17,5 +17,5 @@ keywords:
- functional annotation
- consensus gene models
license: BSD-2-Clause
version: version = "26.5.22"
version: 26.5.22
date-released: '2026-05-24'
6 changes: 5 additions & 1 deletion funannotate2/predict.py
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Expand Up @@ -205,7 +205,11 @@ def predict(args):
contig_name_map = simplify_headers_drop(
args.fasta, GenomeFasta, GenomeMito, drop=list(mito_contigs.keys())
)
# Create inverse contig map for BAM processing (maps simplified names back to original)
# Build the BAM->simplified contig map for annorefine.bam2hints. The BAM
# file references the user's original contig names, but everything
# downstream (per-contig FASTAs, hints files) uses the simplified names
# produced by simplify_headers_drop, so we need {original: simplified}.
# contig_name_map is {simplified: original}, so invert it here.
inv_contig_map = {value: key for key, value in contig_name_map.items()}
maskedRegions = os.path.join(misc_dir, "softmasked-regions.bed")
asmGaps = os.path.join(misc_dir, "assembly-gaps.bed")
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