v0.1.3

What's Changed

• feat(sort): add CB (cellular barcode) to template-coordinate sort key by @nh13 in #160
• docs: improve cell barcode documentation by @nh13 in #177
• fix(sort): use monotonic counter for chunk file naming during consolidation by @nh13 in #178
• refactor(sort): introduce ChunkNamer to centralize temp file naming by @nh13 in #179
• feat(zipper): accept BAM input for mapped reads by @nh13 in #183
• feat(extract): add SIMD-accelerated FASTQ parsing by @nh13 in #180
• docs(vendored): update bam_codec comments to reflect noodles#364 closure by @nh13 in #182
• refactor(vendored): remove vendored BAM decoder, use noodles Reader API by @nh13 in #185
• feat(sort): add fgumi merge command with loser tree by @nh13 in #186
• perf(sort): improve multi-threaded sort scaling by @nh13 in #187
• doc: update fulcrum genomics logo with light/dark theme support by @nh13 in #194
• perf(sort): MSD hybrid radix sort for template-coordinate sorting by @nh13 in #191
• perf(compare): replace RecordBuf with raw byte comparison for compare-bams by @nh13 in #197
• feat: add --includelist option to simulate fastq-reads by @nh13 in #198
• feat: add simplex-metrics command for simplex sequencing QC by @nh13 in #195
• fix(compare): exclude BAM bin field from core field comparison by @nh13 in #208
• Remove unused --sort-order flag from codec and simplex by @nh13 in #209
• fix(cli): allow explicit true/false values on all boolean flags and remove dead code by @nh13 in #210
• ci: pin GitHub Actions to full-length commit SHAs by @nh13 in #215
• fix(raw-bam): use minimal unsigned BAM integer types for non-negative tag values by @nh13 in #213
• fix(compare): use semantic integer comparison for BAM tag values by @nh13 in #214
• refactor(clip): use ClippingMode enum instead of String for --clipping-mode by @nh13 in #218
• perf(sort): reuse buffers in merge phase via producer-consumer buffer pool by @nh13 in #219
• perf(sort): optimize sort pipeline with LoserTree merge, EMBEDDED_IN_RECORD, and queryname specifiers by @nh13 in #217
• docs: add trait overview table and extension guide for unified pipeline by @nh13 in #222
• refactor(correct): eliminate RecordBuf duplication via raw-byte processing by @nh13 in #229
• ci: add cargo-audit security job to CI workflow by @nh13 in #221
• fix: dedup --no-umi OOM on production WES data by @nh13 in #231
• feat(group): add position group size metrics and --metrics prefix output by @nh13 in #232
• fix: replace panic!() with graceful error handling by @nh13 in #223
• refactor: replace all unwrap() calls in crates/ with expect() by @nh13 in #225
• test: add end-to-end regression tests using simulate and compare by @nh13 in #227
• refactor: replace all unwrap() calls in src/commands/ with expect() by @nh13 in #224
• refactor: replace all unwrap() calls in src/lib/ with expect() by @nh13 in #226
• perf(zipper): eliminate RecordBuf re-encode bottleneck with raw-byte merge by @nh13 in #228
• Accept yes/no/y/n/t/f as boolean flag values by @nh13 in #235
• feat(sort): add --max-memory=auto with system memory detection by @nh13 in #236
• docs: add mdBook documentation site with FG branding by @nh13 in #243
• refactor: remove customizable tag options in favor of SAM spec standard tags by @nh13 in #240
• perf(sort): implement N+2 worker-pool model for parallel sort I/O by @nh13 in #242
• refactor(sort): remove dead rayon code paths superseded by N+2 pool by @nh13 in #246
• refactor: introduce SamTag newtype for two-character BAM tag fields by @nh13 in #241
• revert(sort): restore --max-memory default to 768M by @nh13 in #245
• docs: describe fgumi as a research preview instead of alpha by @nh13 in #248
• perf(sort): redesign phase 2 work stealing and bound rayon to --threads by @nh13 in #247
• perf(sort): add memory probes and force mimalloc arena collection by @nh13 in #249
• fix(docs): correct Zenodo DOI badge link in README by @nh13 in #250
• fix: abort pipeline on deadlock detection when recovery is disabled by @nh13 in #252
• fix: prevent pipeline deadlock when held items block reorder buffer progress by @nh13 in #251
• perf(extract): bounded BGZF FASTQ pipeline with memory backpressure by @nh13 in #244
• fix: prevent OOM and group flush timeout in unified pipeline by @nh13 in #253
• chore: release v0.1.3 by @nh13 in #163

Full Changelog: v0.1.2...v0.1.3