fix: replace twobitreader with py2bit to support large genomes#107
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alejandrogzi merged 2 commits intohillerlab:mainfrom Apr 4, 2026
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twobitreader only handles version-0 .2bit files. faToTwoBit -long produces version-1 (64-bit) .2bit files required for genomes larger than 4 GB (e.g. lungfish ~40 GB, salamander ~21 GB). This caused crashes during LASTZ jobs. py2bit supports both version-0 and version-1 .2bit files, fixing issue hillerlab#56. Changes: - standalone_scripts/run_lastz.py: import py2bit; use py2bit.open() and two_bit_conn.sequence() instead of TwoBitFile and dict-style access - pyproject.toml: twobitreader -> py2bit in dependencies Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…, writer side) The previous commit fixed the reader (twobitreader → py2bit), but faToTwoBit was still writing version-0 (32-bit) .2bit files without -long, causing an index overflow abort on genomes with sequences larger than 4 GB. Adding -long to both faToTwoBit call sites in project_setup_procedures.py so it writes version-1 (64-bit) .2bit files that py2bit can then read. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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twobitreader only handles version-0 .2bit files. faToTwoBit -long produces version-1 (64-bit) .2bit files required for larger genomes (e.g., lungfish ~40 GB, salamander ~21 GB). This caused crashes during the partition step.
py2bit supports both version-0 and version-1 .2bit files, fixes #56.
I have tested this fix on my side with large input data, and it works well.