feat(io): native CBQ input support

Cargo.toml

@@ -65,6 +65,7 @@ mimalloc = { version = "0.1", default-features = false }
 libmimalloc-sys = { version = "0.1.49", features = ["extended"] } # mi_option_set (purge_delay); see main.rs
 libdeflater = "1.25.2"
 noodles-bgzf = { version = "0.49", features = ["libdeflate"] }
+binseq = { version = "0.9.4", default-features = false, features = ["anyhow"] }
 
 [dev-dependencies]
 assert_cmd = "2"

README.md

@@ -45,6 +45,26 @@ target/release/rustar-aligner \
   --outFileNamePrefix /path/to/output_
 ```
 
+### CBQ input
+
+CBQ is detected from the file header, so the filename extension is irrelevant.
+A paired-end CBQ stores both mates in one file.
+CBQ is currently limited to ordinary alignment input; it cannot be combined
+with `--readFilesCommand`, STARsolo/SmartSeq workflows, or qualityless
+unmapped-FASTQ output.
+
+`--readFilesNthreads` controls decoder concurrency only (`0` derives a bounded
+default from `--runThreadN`); it does not affect how much input is held in
+memory, which is fixed by the window budget.
+
+```bash
+target/release/rustar-aligner \
+  --genomeDir /path/to/genome_index \
+  --readFilesIn reads.cbq \
+  --readFilesNthreads 4 \
+  --outFileNamePrefix /path/to/output_
+```
+
 ### BAM output
 
 ```bash
@@ -207,6 +227,7 @@ resident; the 16 GB sparse index is stable at ~54 s.</sub>
 ## Supported Features
 
 - Single-end and paired-end alignment with mate rescue
+- Native single-file CBQ input (single-end or interleaved paired-end), with parallel decoding controlled by `--readFilesNthreads`. Decoded reads are bounded by a fixed per-window record budget, so peak input memory is independent of both the thread count and the input file's block size
 - Read-end alignment mode (`--alignEndsType Local` (default) / `EndToEnd` / `Extend5pOfRead1` / `Extend5pOfReads12` / `Extend3pOfRead1`)
 - SAM, unsorted BAM, and coordinate-sorted BAM output (`--outSAMtype SAM`, `BAM Unsorted`, or `BAM SortedByCoordinate`)
 - Multi-threaded parallel alignment (`--runThreadN`)