Add scripts/refbuild: build GOR chromSeq reference builds from FASTA

[gorfather]

What

Adds scripts/refbuild/ — tooling to build GOR chromSeq reference builds from standard FASTA.

GOR's reference-build commands and functions (VARJOIN, VARMERGE, VARNORM and refbase() / refbases()) read reference bases from a build folder holding one <contig>.txt per chromosome (one byte per base, no newlines) plus buildsize.gor and buildsplit.txt. GOR does not read FASTA directly, and there was no in-repo tool to produce that layout. This fills that gap.

Contents

• fasta_to_chromseq.py — stream a FASTA (plain or gzipped) into <contig>.txt, measure buildsize.gor, emit buildsplit.txt from GOR's built-in split tables, and write gor_config.txt. Handles Ensembl vs UCSC contig naming (--chr-prefix, --mt) and primary-assembly filtering (--primary). Streams, so memory stays flat on whole genomes.
• download_build.sh — one-shot download + convert for hg38/hg19 (Ensembl by default, UCSC alternative); bundles the source URLs.
• chromseq_to_gor.py + validate.sh — drive gorpipe against a build to prove GOR reads it correctly: refbase() vs the stored bytes, and VCF REF alleles vs refbases() (e.g. a GIAB cross-check).
• README.md — download URLs, conversion, config wiring, validation, and a buildsize vs buildsplit explanation.

Notes

• The split tables mirror ReferenceBuildDefaults.java (hg19 shares hg18's table); buildsize.gor is measured from the FASTA.
• Reference data is intentionally kept out of the repo — only the scripts and URLs live here; builds go to a user-chosen root.
• Verified: converter round-trips tests/data/ref_mini byte-for-byte, and full Ensembl GRCh38/GRCh37 builds pass genome-wide self-consistency and GIAB chr21 REF cross-checks.

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