Carry aligned reads as CRAM, with --aligned_format cram|bam - #207

Draft

ljwharbers wants to merge 13 commits into

devfrom

experiment/cram-io

Commits on Sep 23, 2026

Carry aligned and haplotagged reads as CRAM (prototype)

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claude
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83fff3e
Drop the uBAM's RG tag before alignment

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5dff4f1
Write CRAM 3.0 with the reference embedded

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1569c5e
Document the CRAM outputs

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5481adb

Commits on Sep 24, 2026

Give ASCAT no FASTA again

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77bcf54
Find ClairS-TO's intermediate directory under its sample-named path

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28965de

Commits on Sep 25, 2026

Add --aligned_format (cram, default, or bam)

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51323c8
Regenerate pipeline-test snapshots for the CRAM default

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2cd3e56

Commits on Sep 28, 2026

Merge remote-tracking branch 'origin/dev' into experiment/cram-io
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f01a25b
Fill in PR number in CHANGELOG entry

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ef82aa0
Stop snapshotting CRAM/CRAI md5s in the pipeline tests

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e2aca1b
Correct the CHANGELOG and give longphase haplotag samtools under conda

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f342092
Test the CRAM merge in clair_only and run deep_only on BAM

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d5b9d7b