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Tag the H2009 ONT test uBAM with its read group (merge right after lrsomatic#207) - #5
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Every record of headered_H2009_ONT_UL_chr19_downsampled.bam now carries RG:Z:<the @rg ID already in its header>, as real dorado output does (samtools addreplacerg -m overwrite_all -R <ID>). Reads, qualities and all other tags are unchanged. test_sheet_2_rgtagged.csv is test_sheet_2.csv with sample3 reading this file. lrsomatic needs it to regression-test MINIMAP2_ALIGN's `samtools reset -x RG` (IntGenomicsLab/lrsomatic#207): none of the existing test uBAMs has a record-level RG tag, so dropping it could not be detected. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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clair_only now reads test_sheet_2_rgtagged.csv (IntGenomicsLab/test-datasets#5, must be merged first): test_sheet_2 with sample3's uBAM carrying dorado's RG on every record, as real dorado output does. None of the existing test uBAMs has a record-level RG tag, so the read-group assertion could not see a MINIMAP2_ALIGN that keeps it. Checked on Mindwell from dd3127f: with -x RG the test passes and the snapshot is byte-identical to the one from test_sheet_2; with ext.args3 = "" the read-group assertion fails, with all 3122 sample3 records carrying the undeclared dorado RG, while no other sample or snapshot entry changes. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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All six pipeline tests pass on Mindwell (apptainer) with 382ba38. The only change in every snapshot is LONGPHASE_MODCALL's longphase version (2.0.1 -> 2.0.2) plus the timestamp; no output md5 moves. So the chr19 test data is too small to trigger 2.0.1's CRAM misread, which is why the tests never showed it. clair_only was run on a local copy of test_sheet_2_rgtagged.csv, as IntGenomicsLab/test-datasets#5 is not merged yet. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
headered_H2009_ONT_UL_chr19_downsampled.bam (+ .bai) itself now carries RG:Z:<its header's dorado @rg ID> on every record, and the separate _rgtagged copy and test_sheet_2_rgtagged.csv are gone. Every lrsomatic pipeline test that reads this file (sample1 tumour and sample3 in samplesheet_lr-somatic.csv, sample1/3/5 in test_sheet_2.csv) now gets an RG-tagged uBAM, as real dorado output is. Merge only once IntGenomicsLab/lrsomatic#207 is in dev: without its `samtools reset -x RG`, the aligned records carry two RG tags and dev's BAM snapshots change. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Tags every record of
data/aligned/headered_H2009_ONT_UL_chr19_downsampled.bamwith the read group already declared in its header (RG:Z:df8348f0…_dna_r10.4.1_e8.2_400bps_sup@v5.0.0), as real dorado output does, and replaces the file (+.bai) in place.dev. Before that,devhas nosamtools reset -x RGinMINIMAP2_ALIGN: the uBAM'sRGtag would be carried through next to the pipeline's-Rread group, so dev's aligned BAMs (and their snapshot md5s) change, and every open lrsomatic PR'sdefaulttest would fail.Why: lrsomatic #207 drops the uBAM's own
RGtag before alignment. Without that, each aligned record carried twoRGtags; CRAM keeps one per record, and it kept dorado's, which has no@RGline in the aligned header. None of the test uBAMs had a record-levelRGtag (the ONT ones have dorado's@RGin the header only), so no test could see it. This file is sample1's tumour and sample3 insamplesheet_lr-somatic.csv(all-profile testtests) and sample1/3/5 intest_sheet_2.csv(clair_only, which asserts every record's RG is declared in its header).What:
samtools addreplacerg -m overwrite_all -R <ID> --no-PG, re-indexed. 2305 records before and after; read names, sequences, qualities and all other tags are identical; the header is unchanged.Validated on Mindwell (apptainer): with lrsomatic#207,
clair_onlypasses on the tagged file with its snapshot byte-identical to the untagged run; with-x RGremoved, the read-group assertion fails (all 3122 sample3 records carry the undeclared dorado RG) while no snapshot entry changes.(An earlier version of this PR added the tagged file as a copy plus a
test_sheet_2_rgtagged.csv; replaced by tagging the original in place.)🤖 Generated with Claude Code