v0.2.0

What's Changed

• fix: add fgumi-simd-fastq to publish list and verify completeness by @nh13 in #257
• feat(consensus): add EM-Seq methylation-aware consensus calling by @nh13 in #168
• feat(filter): add EM-Seq methylation filters and performance improvements by @nh13 in #169
• feat(zipper): add --restore-unconverted-bases flag for EM-seq by @nh13 in #170
• docs: add EM-Seq guide and clean up redundant docs by @nh13 in #171
• feat(consensus): add --methylation-mode for EM-Seq/TAPs consensus by @nh13 in #172
• feat(filter): add --methylation-mode to filter for conversion fraction by @nh13 in #173
• docs: add TAPs guide and update EM-Seq guide by @nh13 in #174
• feat(simulate): add --methylation-mode to simulate subcommands by @nh13 in #263
• fix(extract): take last :-separated field as UMI from read name by @nh13 in #264
• feat(zipper): auto-detect BAM input on stdin via BGZF magic by @nh13 in #267
• perf(zipper): speed up --restore-unconverted-bases hot path by @nh13 in #271
• fix(zipper)!: rename sort-key tag from pa to tc to avoid bwa-mem pa:f collision by @nh13 in #270
• fix(group): emit consecutive MI integers 0..N-1 by @nh13 in #273
• perf(io): async prefetch reader with POSIX_FADV_WILLNEED for BAM/FASTQ inputs by @nh13 in #258
• perf(zipper): restore unconverted bases on raw BAM bytes by @nh13 in #274
• feat(compare): add --command preset for per-stage compare defaults by @nh13 in #276
• feat(sort): add --async-reader for prefetch I/O on input BAM by @nh13 in #261
• docs(reorder-buffer): correct insert complexity and add micro-bench by @nh13 in #265
• feat(raw-bam): unified view/editor API + close #272 gaps by @nh13 in #278
• refactor: migrate fgumi to new raw-bam view/editor API by @nh13 in #279
• refactor(raw-bam)!: narrow re-exports + partial free-fn demotion by @nh13 in #280
• test(raw-bam): benchmarks + proptests + edge cases by @nh13 in #281
• perf(raw-bam): follow-up speedups + SIMD nibble2base by @nh13 in #282
• fix(group): cap metric memory with per-thread accumulators (#285) by @nh13 in #287
• refactor(zipper): use RawRecord methods in restore_unconverted_bases_in_raw_record by @nh13 in #286
• refactor(pipeline): PerThreadAccumulator for all per-batch metric collection by @nh13 in #290
• feat(sort): distribute spill files across multiple temp dirs by @nh13 in #284
• feat(raw-bam): additive API surface by @nh13 in #288
• feat(sam): raw-byte record_utils + RawRecordClipper by @nh13 in #289
• refactor(consensus): migrate internals to RawRecord; drop RecordBuf variants by @nh13 in #291
• refactor(lib): migrate commands, storage, and pipeline to raw-byte records by @nh13 in #292
• fix(unified-pipeline): suppress deadlock false positive when all queues empty by @nh13 in #297
• fix(consensus): preserve BA-only orientation for methylation tags by @nh13 in #298
• docs: fix broken doctests in commands modules by @nh13 in #300
• refactor(consensus): rename duplex-filter tier locals to best/worst by @nh13 in #299
• refactor(lib)!: collapse Template/DecodedRecord to raw-only; drop dead RecordBuf helpers by @nh13 in #294
• refactor(test): migrate workspace tests to fgumi_raw_bam SamBuilder by @nh13 in #295
• fix(pipeline): stream rejects to disk in simplex/duplex/codec/correct by @nh13 in #293
• fix(simulate): apply --unmapped-fraction to mapped-reads output by @nh13 in #304
• refactor!: delete vendored bam_codec; migrate simulate to SamBuilder by @nh13 in #296
• perf: migrate RecordBuf hot paths to raw-byte accessors by @nh13 in #305
• fix(metrics): use htsjdk-compatible Murmur3 for downsample selection by @nh13 in #306
• feat(compare): restore --command preset for per-stage compare defaults by @nh13 in #307
• fix(compare): preserve /A /B strand suffix in paired-UMI MI keys by @nh13 in #308
• chore: release v0.2.0 by @nh13 in #259
• fix(ci): exclude non-publishable crates from publish-workflow guard by @nh13 in #310
• fix(raw-bam): gate cigar_op_kind behind noodles feature by @nh13 in #311

Full Changelog: v0.1.3...v0.2.0