thread=1

make clean; make -j 32

#n1=~/data/dataset/D2/n1.fq.gz
#n2=~/data/dataset/D2/n2.fq.gz
n1=~/data/dataset/D2/d1.fq
n2=~/data/dataset/D2/d2.fq

#n1=~/data/SRR25735656_1.fastq.gz
#n2=~/data/SRR25735656_2.fastq.gz

#n1=/file-data/zzh/dataset/D1/45mr1.fq.gz
#n2=/file-data/zzh/dataset/D1/45mr2.fq.gz

reference=~/data/reference/fmt/human_g1k_v37_decoy.fasta

#out=/dev/null
#out=./oldsam-D2-out.sam
#out=./D2-1.sam
out=./d.sam
prog=./fastalign
#prog=/home/zzh/fastbwa

time $prog mem -t $thread -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
    $reference \
    $n1 \
    $n2 \
    -o $out -2