Add BBTools Java implementation for fqcnt benchmark

[bbushnell]

This PR adds BBTools FastqScan as a Java implementation for the fqcnt benchmark.

Implementation Details

• Uses BBTools' FastqScan tool with multithreaded SIMD-accelerated parsing
• Wrapper script: fqcnt_java_bbtools.sh
• Output format matches biofast specification: <records>\t<bases>\t<qualities>

Testing

Tested with M_abscessus_HiSeq.fq (5,682,010 reads):

5682010	568201000	568201000

Requirements

• Java 18+ required (for jdk.incubator.vector SIMD support)
• Java 25 recommended for optimal performance
• BBTools: git clone --depth=1 https://github.com/bbushnell/BBTools

About BBTools

BBTools is a comprehensive suite of bioinformatics tools developed at the Joint Genome Institute (JGI). FastqScan provides high-performance FASTQ parsing optimized for modern hardware.

Repository: https://github.com/bbushnell/BBTools

[bbushnell]

Performance Note: FastqScan is fastest with larger files and BGZF compression

JVM Startup Overhead

Java has ~0.25s startup/JIT compilation overhead that dominates benchmarks on small files (like the 5.6M read test case). This overhead is:

• Amortized on production-scale files (100M+ reads)
• Irrelevant when called from Java code (JVM already running)

BGZF Multithreaded Decompression

FastqScan is actually faster on BGZF-compressed files than plaintext due to parallel decompression, if there are sufficient cores (~20). On 80M reads:

• Plaintext: ~4.2 GB/s (single-threaded)
• BGZF compressed: ~6.2 GB/s (multithreaded decompression)
• FastqScanMT (with t=2): ~9.5 GB/s on BGZF

Performance comparison showing FastqScanMT at 13.5x faster than Rust needletail on BGZF files