Add dna-playground — k-mer offset histogram DNA alignment playground

[Copilot]

Introduces a new dna-playground workspace crate for experimenting with k-mer based DNA alignment against hg38 FASTA. Generates synthetic reads with configurable mutations, aligns them via offset histogram voting across multiple k values, then resolves candidates with Needleman-Wunsch local alignment and evaluates against ground truth.

New crate: dna-playground

Core modules

Module	Purpose
fasta.rs	needletail FASTA reader (plain + gz), batch and streaming
dna.rs	Complement/RC, hard/soft masking; Orientation + SoftmaskMode enums
kmer.rs	2-bit packed k-mers; PackedKmer::U64 (k≤31) / PackedKmer::U128 (k≥32); overlapping KmerIter (stride 1)
index.rs	Per-chromosome k-mer index; frequency filter drops high-occurrence k-mers (repeat noise)
generate.rs	Synthetic reads: SNPs, indels, hard/soft masking, optional RC; serde ground-truth JSONL
align.rs	Multi-k offset voting (offset = ref_pos − query_pos), clustering, weighted scoring (weight(k) = k)
local_align.rs	Needleman-Wunsch over a reference window extracted around the histogram peak
cigar.rs	CIGAR string from aligned strings (SAM M/I/D)
metrics.rs	Identity, query/reference coverage, MAPQ-like confidence, ground-truth error
report.rs	Aligned FASTA pairs, JSONL alignment report, debug offset-vote CSV, text visual alignment
main.rs	CLI: generate, align, evaluate, index subcommands

CLI usage

# Generate synthetic reads with ground truth
dna-playground generate \
  --reference hg38/hg38.fa \
  --read-count 1000 --read-len 150 \
  --snp-rate 0.001 --insertion-rate 0.0005 --deletion-rate 0.0005 \
  --out reads.fa --truth reads.truth.jsonl

# Align reads (index built in memory)
dna-playground align \
  --reference hg38/hg38.fa \
  --reads reads.fa \
  --k 17 --k 21 --k 25 \
  --out-aligned aligned.fa \
  --out-report aligned.jsonl

# Evaluate predicted vs ground truth
dna-playground evaluate \
  --truth reads.truth.jsonl \
  --report aligned.jsonl

Workspace additions

• rand = "0.10.1", serde = "1.0.228", serde_json = "1.0.149" added to [workspace.dependencies]
• "dna-playground" added to workspace members

Verification

• cargo build --workspace ✅
• cargo clippy -p dna-playground ✅ (zero warnings)
• cargo test -p dna-playground ✅ (10/10 tests pass)