thread=64

## d1
#n_r1=~/data/fastq/dataset/na12878_wes_144/s_1.fq
#n_r2=~/data/fastq/dataset/na12878_wes_144/s_2.fq
#n_r1=~/data/fastq/dataset/na12878_wes_144/45m_r1.fq
#n_r2=~/data/fastq/dataset/na12878_wes_144/45m_r2.fq
#n_r1=~/data/fastq/dataset/na12878_wes_144/45mr1.fq.gz
#n_r2=~/data/fastq/dataset/na12878_wes_144/45mr2.fq.gz
## d2
#n_r1=~/data/fastq/dataset/na12878_wgs_101/s_1.fq
#n_r2=~/data/fastq/dataset/na12878_wgs_101/s_2.fq
n_r1=~/data/fastq/dataset/na12878_wgs_101/45m_r1.fq
n_r2=~/data/fastq/dataset/na12878_wgs_101/45m_r2.fq
# d3
#n_r1=~/data/fastq/dataset/na12878_wgs_150/s_1.fq
#n_r2=~/data/fastq/dataset/na12878_wgs_150/s_2.fq
#n_r1=~/data/fastq/dataset/na12878_wgs_150/45mr1.fq.gz
#n_r2=~/data/fastq/dataset/na12878_wgs_150/45mr2.fq.gz
## d4
#n_r1=~/data/fastq/dataset/zy_wes/s_1.fq
#n_r2=~/data/fastq/dataset/zy_wes/s_2.fq
#n_r1=~/data/fastq/dataset/zy_wes/45mr1.fq.gz
#n_r2=~/data/fastq/dataset/zy_wes/45mr2.fq.gz
## d5
#n_r1=~/data/fastq/dataset/zy_wgs/45mr1.fq.gz
#n_r2=~/data/fastq/dataset/zy_wgs/45mr2.fq.gz
#n_r1=~/data/fastq/dataset/zy_wgs/s_1.fq
#n_r2=~/data/fastq/dataset/zy_wgs/s_2.fq
#n_r1=~/data1/fastq/dataset/zy_wgs/E150010395_L01_690_1.fq
#n_r2=~/data1/fastq/dataset/zy_wgs/E150010395_L01_690_2.fq

reference=~/data1/fmt_ref/human_g1k_v37_decoy.fasta
#reference=~/reference/bwa/human_g1k_v37_decoy.fasta
#reference=~/data/reference/human_g1k_v37_decoy.fasta
#out=./all.sam
#out=./sn.sam
#out=./ssn-x1.sam
out=~/data1/d2-45m.sam
#out=~/data/out1.sam
#out=/dev/null
#out=./na12878.sam
#time ./bwa mem -t 12 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
#    /home/zzh/data/reference/human_g1k_v37_decoy.fasta \
#    /home/zzh/data/fastq/nm1.fq \
#    /home/zzh/data/fastq/nm2.fq -o /dev/null

#time ./bwa mem -t 12 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
#    /home/zzh/data/reference/human_g1k_v37_decoy.fasta \
#    /mnt/d/data/fastq/ZY2105177532213000/ZY2105177532213010_L4_1.fq.gz \
#    /mnt/d/data/fastq/ZY2105177532213000/ZY2105177532213010_L4_2.fq.gz \
#    -o /dev/null

time ./fastbwa mem -t $thread -b 256 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
    $reference \
    $n_r1 \
    $n_r2 \
    -o $out -2