
# Injected Samples
##############################
PREFIXES=(
# Old MAC fragments
PTET_FRAG_Inj40_ND7_REGN-17_S12
# Sorted anlagens
PTET_Nuc_33N_Inj40_ND7_REGN-14_S9
PTET_Nuc_53N_Inj40_ND7_REGN-16_S11
)

NB_PREF=${#PREFIXES[@]}



# MAC genome
GENOME=/data/PARAMECIUM/REFERENCES/tetraurelia/ptetraurelia_mac_51.fa

DIR_MAPPING=/data/PARAMECIUM/MAPPING/tetraurelia/ptetraurelia_mac_51/DNAseq/anlagen/
REF_PREF=pt_51


OUT_DIR=results/
mkdir -p $OUT_DIR


# SNP calculation
for (( N=0; N<${NB_PREF}; N++ )); do

    PREFIX=${PREFIXES[$N]}
    BAM=`find $DIR_MAPPING/ -name $PREFIX.BOWTIE.pt_51.pe.sorted.bam`
    echo $BAM
    FILE=`basename $BAM`
    if [ ! -f $OUT_DIR/`basename $FILE`.findSNP.tab ]; then
        echo "Processing $FILE file..."
        findSNP.pl -seq_id scaffold51_5 -bam $BAM -genome $GENOME -consensus_cutoff 0.001 -max_coverage 10000 -remove_aln_ends -threads 15 > $OUT_DIR/`basename $FILE`.findSNP.tab &
    fi
done






BINSIZE=20
SMOOTH=50
REGION=scaffold51_5:592000:598000

# ND7 gene coverage in the different samples
for (( N=0; N<${NB_PREF}; N++ )); do

    PREFIX=${PREFIXES[$N]}
    BAM=`find $DIR_MAPPING/ -name $PREFIX.BOWTIE.pt_51.pe.sorted.bam`
    
    FILE=`basename $BAM`
    echo "Processing $FILE file..."
    PREFIX=`echo ${FILE%.pe.sorted.bam}`
    if [ ! -f "$OUT_DIR/$PREFIX.bin$BINSIZE.smooth$SMOOTH.bedgraph" ]; then
        bamCoverage --bam $BAM --outFileName $OUT_DIR/$PREFIX.bin$BINSIZE.smooth$SMOOTH.bedgraph --outFileFormat bedgraph --binSize $BINSIZE --smoothLength $SMOOTH --region $REGION
    fi
done


# contamination.R


