v2.10.5: fix silent extract segfault on unusual MM/ML layouts

Bug fix

fiberhmm-extract --all produced silently empty output on certain BAMs from pangenome-graph-surjection pipelines (e.g. vg surject onto linear reference). Root cause was a C-level segfault inside pysam.AlignedSegment.modified_bases on reads with unusual MM/ML layouts — invisible because the SIGSEGV kills the worker before Python's exception handler can run, and the main process reports it blandly as "A process in the process pool was terminated abruptly" with zero rows emitted per region.

Localized via faulthandler: segfault at _extract_m6a line 505 during read.modified_bases. pysam has had this class of bug intermittently for years; we already worked around it in v2.9.0 for the apply/call path by using our own numpy MM/ML parser (fiberhmm.core.bam_reader.parse_mm_ml_per_mod_type, validated against pysam on 500+ real reads).

Fix

Swap read.modified_bases for the safe parser in all three extract sites:

• _extract_m6a
• _extract_m5c
• _extract_deam priority-1 (MM/ML u dU code)

No API change; output format unchanged. Single-char mod codes work identically. The rare ChEBI 55797 numeric code is no longer auto-detected in extract (explicitly unsupported — users needing it can rely on the R/Y or MD fallback paths, or run samtools calmd + fiberhmm-daf-encode).

Side fix: worker exception handler now flushes stderr explicitly so Python-level errors surface during multiprocessing crashes instead of getting buffer-swallowed.

Verified on real surjected fiber-seq CRAMs

Full pipeline: CRAM → BAM → fiberhmm-call → ft fire → fiberhmm-extract --all -c 8 --block-scores

Both of two test samples now produce full output across all 5 tracks (footprint / msp / tf / m6a / m5c), each around 1.8M rows. One of the two samples was silently emitting zero rows on v2.10.4 with identical config; v2.10.5 fixes it.

Tests

292 pass. Three deam priority-1 tests rewritten to construct real MM/ML tag strings instead of faking modified_bases dicts.

Install

pip install --upgrade fiberhmm