more renames

Author: Psy-Fer

.github/workflows/release.yml

@@ -402,7 +402,7 @@ jobs:
         run: |
           gh release create "${{ needs.check-release.outputs.version }}" \
             --target "${{ github.sha }}" \
-            --title "ruSTAR ${{ needs.check-release.outputs.version }}" \
+            --title "rustar-aligner ${{ needs.check-release.outputs.version }}" \
             --notes-file /tmp/release-notes.md
 
       - name: Create release (auto-generated notes)
@@ -412,7 +412,7 @@ jobs:
         run: |
           gh release create "${{ needs.check-release.outputs.version }}" \
             --target "${{ github.sha }}" \
-            --title "ruSTAR ${{ needs.check-release.outputs.version }}" \
+            --title "rustar-aligner ${{ needs.check-release.outputs.version }}" \
             --generate-notes
 
   # ------------------------------------------------------------------

CHANGELOG.md

@@ -1,10 +1,10 @@
-# ruSTAR Changelog
+# rustar-aligner Changelog
 
 <!--
 Release notes are extracted from this file by the release workflow.
 Each released version needs a heading of the form:
 
-    ## [Version X.Y.Z](https://github.com/Psy-Fer/ruSTAR/releases/tag/vX.Y.Z) - YYYY-MM-DD
+    ## [Version X.Y.Z](https://github.com/Psy-Fer/rustar-aligner/releases/tag/vX.Y.Z) - YYYY-MM-DD
 
 Sections commonly used: Features, Bug fixes, Other changes.
 -->

CLAUDE.md

@@ -1,4 +1,4 @@
-# Contributing to ruSTAR
+# Contributing to rustar-aligner
 
 ## Building and testing
 
@@ -20,7 +20,7 @@ Small synthetic and yeast test data lives in `test/`. Integration tests in `test
 
 ## Project history
 
-ruSTAR was written as a faithful port of [STAR](https://github.com/alexdobin/STAR) by Alexander Dobin. Up to the initial release, the goal was behavioral parity with STAR — matching its algorithms, thresholds, and output formats as closely as possible. Notes from that development phase are in `docs/dev/`.
+rustar-aligner was written as a faithful port of [STAR](https://github.com/alexdobin/STAR) by Alexander Dobin. Up to the initial release, the goal was behavioral parity with STAR — matching its algorithms, thresholds, and output formats as closely as possible. Notes from that development phase are in `docs/dev/`.
 
 Future development is not bound by that constraint. Adding STARsolo, new features, or diverging from STAR behavior is entirely welcome.
 

CONTRIBUTING.md

@@ -6,7 +6,7 @@ rust-version = "1.88"
 authors = ["James Ferguson"]
 description = "A Rust reimplementation of STAR (Spliced Transcripts Alignment to a Reference), the RNA-seq aligner"
 license = "MIT"
-repository = "https://github.com/Psy-Fer/ruSTAR"
+repository = "https://github.com/Psy-Fer/rustar-aligner"
 readme = "README.md"
 keywords = ["bioinformatics", "rna-seq", "aligner", "sequencing", "star"]
 categories = ["command-line-utilities", "science"]

Cargo.toml

@@ -16,8 +16,8 @@ RUN HOST_TRIPLE=$(rustc -vV | awk '/^host:/ {print $2}') && \
     GIT_SHORT_HASH="${GIT_SHORT_HASH}" \
     cargo build --release --target "$HOST_TRIPLE" \
         ${CPU_TARGET:+--config "target.'$HOST_TRIPLE'.rustflags=['-C', 'target-cpu=$CPU_TARGET']"} \
-    && strip "target/$HOST_TRIPLE/release/ruSTAR" \
-    && cp "target/$HOST_TRIPLE/release/ruSTAR" /ruSTAR
+    && strip "target/$HOST_TRIPLE/release/rustar-aligner" \
+    && cp "target/$HOST_TRIPLE/release/rustar-aligner" /rustar-aligner
 
 # ---- Runtime stage ----
 FROM debian:bookworm-slim
@@ -27,7 +27,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     procps \
     && rm -rf /var/lib/apt/lists/*
 
-COPY --from=builder /ruSTAR /usr/local/bin/ruSTAR
-COPY --from=builder /ruSTAR /usr/local/bin/STAR
+COPY --from=builder /rustar-aligner /usr/local/bin/rustar-aligner
+COPY --from=builder /rustar-aligner /usr/local/bin/STAR
 
-CMD ["ruSTAR"]
+CMD ["rustar-aligner"]

Dockerfile

@@ -1,4 +1,4 @@
-# ruSTAR Implementation Roadmap
+# rustar-aligner Implementation Roadmap
 
 Tracks implementation progress across sessions. Each phase lists its deliverables, files touched, and completion status. Detailed notes for later phases are in `docs/`.
 
@@ -197,18 +197,18 @@ See [docs/phase16_algorithm.md](docs/phase16_algorithm.md) for sub-phase notes (
 | Fixable algorithm differences | 26 | 0.29% | Yes |
 | **Parity excl. unavoidable ties** | **8800/8826** | **99.70%** | — |
 
-**Adjusted SE summary (post Phase 16.29)**: 99.7% position agreement, 99.9% CIGAR, 2.2% splice rate (= STAR), 99.9% MAPQ, 26 actionable disagreements, 1 STAR-only / 1 ruSTAR-only. MAPQ inflation: 4 reads, MAPQ deflation: 4 reads.
+**Adjusted SE summary (post Phase 16.29)**: 99.7% position agreement, 99.9% CIGAR, 2.2% splice rate (= STAR), 99.9% MAPQ, 26 actionable disagreements, 1 STAR-only / 1 rustar-aligner-only. MAPQ inflation: 4 reads, MAPQ deflation: 4 reads.
 
 **PE parity (10k yeast pairs, 150 bp, post Phase G2):**
 
-| Metric | ruSTAR | STAR |
+| Metric | rustar-aligner | STAR |
 |--------|--------|------|
 | Both-mapped pairs | **8390** | 8390 |
 | Half-mapped pairs | **0** | 0 |
 | Net gap | **0 (exact match)** | — |
 | PE faithfulness (tie-adj, pos+CIGAR+MAPQ+proper+NH) | **99.883%** (16,284/16,306) | — |
 | Tie-breaking diffs (excluded) | 475 | — |
-| ruSTAR-only false positives | 1 (`.6302610`) | — |
+| rustar-aligner-only false positives | 1 (`.6302610`) | — |
 | STAR-only missed | 1 (`.18919121`) | — |
 | MAPQ inflations | **0** | — |
 | MAPQ deflations | **0** | — |
@@ -248,7 +248,7 @@ All 127 SE position disagreements (100 diff-chr + 27 same-chr) verified as **gen
 | Issue | Count | Difficulty |
 |-------|-------|------------|
 | SE CIGAR insertion placement | 1 | Hard — `ERR12389696.13573895` (AS=133 both, same pos, homopolymer seed-level tie) |
-| PE ruSTAR-only FP | 1 | `.6302610` — adapter contamination at mate2 pos 40, seeding-level |
+| PE rustar-aligner-only FP | 1 | `.6302610` — adapter contamination at mate2 pos 40, seeding-level |
 | PE STAR-only | 1 | `.18919121` — SA construction diff (EX_R=0 vs 1), SA-level |
 | PE AS diffs | 6 | Residual combined-score parity gaps |
 
@@ -268,7 +268,7 @@ STAR ... 2>star_debug.log
 
 Helper script: `test/debug_star.sh`
 ```bash
-./debug_star.sh pe <rustar.sam> <star.sam> [n_reads]  # extract & trace false positives
+./debug_star.sh pe <rustar-aligner.sam> <star.sam> [n_reads]  # extract & trace false positives
 ./debug_star.sh reads "read1,read2"                    # trace specific reads
 ```
 

ROADMAP.md

@@ -6,11 +6,11 @@
 
 ## Executive Summary
 
-Fixed critical bugs preventing alignments from working. ruSTAR now successfully aligns reads to the genome with valid SAM output, though performance and unique/multi classification need improvement.
+Fixed critical bugs preventing alignments from working. rustar-aligner now successfully aligns reads to the genome with valid SAM output, though performance and unique/multi classification need improvement.
 
 ### Test Results (Yeast, 100 reads)
 
-| Metric | STAR | ruSTAR | Status |
+| Metric | STAR | rustar-aligner | Status |
 |--------|------|--------|--------|
 | Time | <0.1s | ~5s | ⚠️ 50x slower |
 | Uniquely mapped | 88% | 0% | ⚠️ Classification broken |
@@ -215,7 +215,7 @@ if alignment_end < read_seq.len() {
 
 **Profiling Needed**:
 ```bash
-perf record -g ./target/release/ruSTAR --runMode alignReads ...
+perf record -g ./target/release/rustar-aligner --runMode alignReads ...
 perf report
 ```
 
@@ -239,7 +239,7 @@ perf report
 ### Working Test (100 reads):
 ```bash
 cd test/data/small/yeast
-ruSTAR --runMode alignReads \
+rustar-aligner --runMode alignReads \
   --genomeDir indices_rustar \
   --readFilesIn reads/ERR12389696_sub_1_100.fastq.gz \
   --readFilesCommand zcat \

docs/dev/ALIGNMENT_FIXES.md

@@ -100,7 +100,7 @@ Always try to merge with previous Match operation before pushing new one:
 - **Root Cause:** Internal representation uses global genome coordinates (cumulative across all chromosomes), but SAM/SJ format requires per-chromosome coordinates
 
 ### Coordinate Systems
-**Internal (ruSTAR):**
+**Internal (rustar-aligner):**
 - Global genome coordinates: cumulative across all chromosomes
 - Example: chr1 [0, 100k), chr2 [100k, 300k), chr3 [300k, 450k)
 - Position 350k → chr3, position 50k within chr3
@@ -212,7 +212,7 @@ if negative_value < 0 {
 
 ### 2. Coordinate System Documentation is Critical
 Internal representation vs external format:
-- **Internal:** Whatever is most efficient (global coords for ruSTAR)
+- **Internal:** Whatever is most efficient (global coords for rustar-aligner)
 - **External:** Whatever the standard requires (per-chr for SAM/BAM)
 - **Critical:** Convert at I/O boundaries
 
@@ -244,7 +244,7 @@ cargo build --release
 cargo test  # 170/170 passing
 
 # Test 100 reads
-./target/release/ruSTAR \
+./target/release/rustar-aligner \
   --runMode alignReads \
   --genomeDir test/data/small/yeast/indices_rustar \
   --readFilesIn test/data/small/yeast/reads/ERR12389696_sub_1_100.fastq.gz \

docs/dev/BUGFIX_2026-02-09.md

@@ -51,7 +51,7 @@ Phase 12 is now fully functional for single-end reads!
 
 Enable chimeric detection with:
 ```bash
-./target/release/ruSTAR \
+./target/release/rustar-aligner \
   --runMode alignReads \
   --genomeDir /path/to/index \
   --readFilesIn reads.fq \