## Download and install Scalpel

cd ~/biosoft

mkdir Scalpel && cd Scalpel

wget [url]https://downloads./project/scalpel/scalpel-0.5.3.tar.gz[/url]

tar zxvf scalpel-0.5.3.tar.gz

cd scalpel-0.5.3

make

~/biosoft/Scalpel/scalpel-0.5.3/scalpel-discovery --help

~/biosoft/Scalpel/scalpel-0.5.3/scalpel-export --help

cat ~/reference/genome/hg19/hg19.chr.bed |while read id

do

arr=($id)

# arr=($a) will split the $a to $arr , ${arr[0]} ${arr[1]} ~~~, but ${arr[@]} is the whole array .

# OLD_IFS="$IFS"

# IFS=","

# arr=($a)

# IFS="$OLD_IFS"

#arr=($a)用于將字符串$a分割到數(shù)組$arr ${arr[0]} ${arr[1]} ... 分別存儲分割后的數(shù)組第1 2 ... 項 ，${arr[@]}存儲整個數(shù)組。

#變量$IFS存儲著分隔符，這里我們將其設(shè)為逗號 "," OLD_IFS用于備份默認的分隔符，使用完后將之恢復(fù)默認。

echo ${arr[0]}:${arr[1]}-${arr[2]}

date

start=`date +%s`

~/biosoft/Scalpel/scalpel-0.5.3/scalpel-discovery --single \

--bam ~/data/project/myGenome/fastq/bamFiles/jmzeng.filter.rmdup.bam \

--ref ~/reference/genome/hg19/hg19.fa \

--bed ${arr[0]}:${arr[1]}-${arr[2]} \

--window 600 --numprocs 5 --dir ${arr[0]}

end=`date +%s`

runtime=$((end-start))

echo "Runtime for ${arr[0]}:${arr[1]}-${arr[2]} was $runtime"

done