Add T2T-CHM13v2.0 reference genome support (CHM13-T2T)#250
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Register CHM13-T2T (nuclear chromosomes 1-22, X, Y; no mitochondrion) as a first-class supported genome. Adds CHECKSUMS entry, extends all chrom_orders dicts, updates CLI help, README, and CHANGELOG. FTP upload of CHM13-T2T.tar.gz is required before install works end-to-end. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Matrix generation reads transcript_path from the package directory (references/chromosomes/transcripts/<genome>/), not the volume, so the per-chromosome transcript files must ship in the repo like every other supported genome. These were missing for CHM13-T2T, causing SigProfilerMatrixGeneratorFunc to fail with FileNotFoundError. Adds the 24 transcript files (chr 1-22, X, Y) so end-to-end matrix generation works for CHM13-T2T. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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The previous TSB was built from chm13v2.0_maskedY_rCRS.fa, which hard-masks chrY PAR1 (positions 1-2,394,410) with Ns. This caused "reference base does not match" errors for any VCF called against the iGenomes UCSC CHM13 reference (unmasked PAR1). Rebuilt all 24 TSB files from the iGenomes CHM13 genome.fa (s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/CHM13/). Only chrY checksum changed; chr1-22 and X are identical between the two references. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Happy to share the .tar of the build for you to host if this looks good to you. Just let me know what the preferred sharing method is for you. |
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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Adding support for CHM13. Assisted with Claude, but of course verified personally. Is it possible to host the
.tar.gzalongside your other hosted genomes?Summary
CHM13-T2T(T2T-CHM13v2.0, nuclear chromosomes 1–22, X, Y) as a first-class supported genomeCHECKSUMSinreference_genome_manager.pyso the standardSigProfilerMatrixGenerator install CHM13-T2Tcommand works once the tarball is on the FTP serverCHM13-T2Tto allchrom_ordersdictionaries inSigProfilerMatrixGeneratorFunc.py(9 locations) andMutationMatrixGenerator.pyto preventKeyErroron any code path