public class HelloWord{
    public static void main(String []args) {  ## java程序总入口
        System.out.println("Hello World");
    }

}

//单行注释
/*多行注释
*多行注释第二行
/*多行注释第三行*/

public class Person{
String name;
int age;
boolean sex;
void eating(){ //方法1
    }
void running(){ //方法2
    }
void sleeping(){
    }
}

# 指定构造方法
class Name{
public sam(String name){ //默认了构造方法
    System.out.println("Sam");
}
}

# 构造对象
public class Car{
    public Puppy(String name){
        // 这个构造器仅有一个参数: name
        System.out.println("My car brand is :"+name);
    }
    public static void main(String []args){
        // 下面的语句将创建一个Car对象
        Puppy myPuppy=new Car( "Benz" );
    }
}

#output
My car brand is :Benz

public class Car {
    String brandname;
    public Car(String name){
        // 这个构造器有且仅有一个参数：name
        System.out.println("Car's brand is:" + name);
    }
    public void setbrand(String name){
        brandname = name;
        /void(空)方法不需要返回值/
    }
    public string getname(){
        System.out.println("Brand's name is :"+brandname);
        return brandname;
        /*设定为String类型的方法必须返回String类型的值*/
    }
    public static void main(String[] args){
        // 创建对象
        Car c=new Car("BMW");
        // 通过方法来设定车名
        c.setbrand("BMW");
        // 调用另外一个方法获取
        c.getname();
        //直接访问成员变量
        System.out.println("String Value :" + c.brandname);
    }
}


#otutput
Car's brand is:BMW
Brand's name is :BMW
String Value :abc

# top down
def fibonacci(n):
 if n==1 or n==2: return 1
 return fibonacci(n-1)+fibonacci(n-2)

 # bottom up
 def fibonacci(n):
 fib_table[1]=1
 fib_table[2]=1
 for i in range(3,n+1):
 fib_table[i]=fib_table[i-1]+fib_table[i-2]
 return fib_table[n]

ls -l | grep "^-" | wc -l

wc -l log.txt
wc -w log.txt

a=10
b=1
[ $a -lt $b ] # 注意括号两边需要留空格

# 报错:integer expression expected
int=${frac%.*} #需要将字符型或者num型的转化为int型
[ $int -lt $b]

if [ ! -d "$outfolder" ];then
    mkdir $outfolder
fi

find ./ -name unaligned_mc_tagged_polyA_filtered* | xargs rm

# 查看第九列为88的内容
samtools view human19.bam |awk -F'\t' 'function abs(x){return((x<0.0)? -x:x)} abs($9)==88{print $0}'

# 打印2-4行
sed -n '2~4p' human19_19bp_R1.fastq

# 打印具有固定字符的行
cat ../unaligned_human_R1.fastq| grep -A 3  'CAAGGCGACGAACTAGGCGC:E100019795L1C032R02303048097|CAAGGCGACGAACTAGGCGC:E100019795L1C032R02303048097|CAAGGCGACGAACTAGGCGC:E100019795L1C032R02303179234|CAAGGCGACGAACTAGGCGC:E100019795L1C032R02303179234|CAAGGCGACGAACTAGGCGC:E100019795L1C032R02400179922|CAAGGCGACGAACTAGGCGC:E100019795L1C032R02400179922' #-A：显示匹配到字符那行的后面n行 

cat ../unaligned_human_R1.fastq| egrep -A 3  'CAAGGCGACGAACTAGGCGC:E100019795L1C032R02303048097|CAAGGCGACGAACTAGGCGC:E100019795L1C032R02303048097‘ # 相当于grep -E,匹配比grep更多。

pkill Xorg #但是之前的进展看不多了

zcat H_R1.fq.gz | echo $((`wc -l`/4))

(
samtools view -H [bamfile];
samtools view -F 0x004 [bamfile] |
java -jar StreamSampler.jar [# of reads to sample] [total # reads]
) |
samtools -bS - > [sampled bam file]

function SubSample {
## Calculate the sampling factor based on the intended number of reads:
FACTOR=$(samtools idxstats $1 | cut -f3 | awk -v COUNT=$2 'BEGIN {total=0} {total += $1} END {print COUNT/total}')

if [[ $FACTOR > 1 ]]
  then 
  echo '[ERROR]: Requested number of reads exceeds total read count in' $1 '-- exiting' && exit 1
fi

sambamba view -s $FACTOR -f bam -l 5 $1

}

## Usage example, selecting 100.000 reads:
SubSample in.bam 100000 > subsampled.bam

## 需要额外下载StreamSampler.jar，并且有bam文件版本限制，不好用
(
samtools view -H [bamfile];
samtools view -F 0x004 [bamfile] |
java -jar StreamSampler.jar [# of reads to sample] [total # reads]
) |
samtools -bS - > [sampled bam file]

##在shell直接执行，存在一个问题就是subsample的不是正好1000，可能是999。因为flagstat里面有两个reads相加，所以需要double number。

frac=$( samtools flagstat $outbam | cut -f3 | awk 'BEGIN {total=0} {total += $1} END {frac=2000/total;{print frac}}')
int=${frac%.*}
if [ $int -eq 0 ];then
    samtools view -bs $frac $outbam > $outfolder3$samplebam
fi


## 原始网页写法，但是运行terminal会闪退。

function SubSample {
## Calculate the sampling factor based on the intended number of reads:
FACTOR=$(samtools idxstats $1 | cut -f3 | awk -v COUNT=$2 'BEGIN {total=0} {total += $1} END {print COUNT/total}')

if [[ $FACTOR > 1 ]]
  then 
  echo '[ERROR]: Requested number of reads exceeds total read count in' $1 '-- exiting' && exit 1
fi

samtools view -s $FACTOR -f bam -l 5 $1
}

## Usage example, selecting 100.000 reads:
SubSample in.bam 100000 > subsampled.bam

samtools view -bs 42.1 in.bam > subsampled.bam

samfile=out.sam
outbam=filtered.bam
samtools view -h -q 10 $samfile | samtools view -bS > $outbam

samtools rmdup in.bam -o rmdup.bam

samtools view -bS in.sam> out.bam
samtools view -h -o out.sam in.bam

/samtools view -h -f 0x002 file.bam |\
egrep "(^@|XT\:A\:U)"

cd /media/ggj/home/ggj/tmp/DarkReaction/barcode/nofilter
BAM_FILE="/media/ggj/home/ggj/tmp/DarkReaction/barcode/nofilter/unaligned_tagged_filtered.bam"
filter_file="/media/ggj/home/ggj/tmp/DarkReaction/barcode/barcode_88K_tag.txt"
# Save the header lines
samtools view -H $BAM_FILE > SAM_header

# Filter alignments using filter.txt. Use LC_ALL=C to set C locale instead of UTF-8
samtools view $BAM_FILE | LC_ALL=C grep -F -f $filter_file > filtered_SAM_body

# Combine header and body
cat SAM_header filtered_SAM_body > filtered.sam

# Convert filtered.sam to BAM format
samtools view -b filtered.sam > filtered.bam