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Add BBTools Java implementation for fqcnt benchmark #25

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10 changes: 10 additions & 0 deletions fqcnt/fqcnt_java_bbtools.sh
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#!/bin/bash
# BBTools FastqScan for biofast benchmark
# Requirements:
# - Java 18+ required (for jdk.incubator.vector SIMD support)
# - Java 25 recommended for optimal performance
# Setup:
# git clone --depth=1 https://github.com/bbushnell/BBTools

BBTools/fastqscan.sh in="$1" 2>/dev/null | \
awk '/^Records:/{r=$2} /^Bases:/{b=$2} /^Quals:/{q=$2} END{print r"\t"b"\t"q}'