更新 .gitignore，添加 run.status.json；删除旧的 mapping.sh 脚本并添加新的 01.mapping.sh 脚本

2025-12-17 23:27:49 +08:00
parent d8888b8589
commit e8ba2ed962
3 changed files with 20 additions and 16 deletions
@@ -0,0 +1,18 @@
+#! /bin/bash
+set -e
+THREADS=${THREADS:-6}
+if [ "$#" -ne 4 ]; then
+    echo "Usage: $0 <reference_genome> <fastq_1> <fastq_2> <output_prefix>"
+    exit 1
+fi
+
+ref=$1
+fq1=$2
+fq2=$3
+out=$4
+outdir=$(dirname "$out")
+mkdir -p "$outdir"
+hisat2 -p "$THREADS" --dta -x "$ref" -1 "$fq1" -2 "$fq2" -S "${out}.sam"
+samtools view -b -@ "$THREADS" "${out}.sam" | samtools sort -@ "$THREADS" -o "${out}.sorted.bam" --write-index
+rm "${out}.sam"
+echo "Mapping completed. Sorted BAM file is at ${out}.sorted.bam"