#!/bin/bash

#BSUB -J "align[1-56]"
#BSUB -q small
#BSUB -W 00:30
#BSUB -o output.%I
#BSUB -e error.%I

WD=/lustre/scratch116/casm/cgp/users/tn5/julia

cd $WD
BWA=~/work/irap_install/bin/bwa/bin/bwa
SAMTOOLS=~/apps/samtools/samtools

FQ1=`ls *_1.fastq.gz | head -n $LSB_JOBINDEX | tail -n 1`
FQ2=${FQ1%_1.fastq.gz}_2.fastq.gz
BASE=${FQ1%_1.fastq.gz}

echo KRAS
zcat $FQ1 $FQ2 | grep -c GCAGGTCGAGGGACCTAATA
zcat $FQ1 $FQ2 | grep -c TATTAGGTCCCTCGACCTGC
echo ROSA
zcat $FQ1 $FQ2 | grep -c AAGACCGCGAAGAGTTTGTC
zcat $FQ1 $FQ2 | grep -c GACAAACTCTTCGCGGTCTT
