# 24 September 2010

#/Volumes/:home:grobertson/FindPeaks/Code/v4.0.15/fp4/FindPeaks.jar
FP=/home/grobertson/FindPeaks/Code/v4.0.15/fp4/FindPeaks.jar

# have to run this on xhost06, can't find java16 on xhost08 or 09
JAVA=/usr/local/bin/java16

BAM=/archive/solexa1_4/analysis/SC0002/FC6255_5/bwa/FC6255_5.fastq.bam
OUTDIR=/projects/remc_bigdata/S_cere/SC0002
NAME=SC0002-wt_sacCer2

#BAM=/archive/solexa1_4/analysis/SC0007/FC6360_2/bwa/FC6360_2.fastq.bam
#OUTDIR=/projects/remc_bigdata/S_cere/SC0007
#NAME=SC0007-Fpr3-ko_sacCer2

#BAM=/archive/solexa1_4/analysis/SC0008/FC6360_3/bwa/FC6360_3.fastq.bam
#OUTDIR=/projects/remc_bigdata/S_cere/SC0008
#NAME=SC0008-Fpr4-ko_sacCer2

FPWIG=SC0002-wt_sacCer2_triangle_standard.wig
# 'clean' has chrM, not chrMT; no header lines
CLEAN=$FPWIG.clean
BWFILE=$FPWIG.bigwig

#time java -Xmx2G -jar FindPeaks.jar -name test -input filename.map -output /output_path/ -aligner maq -one_per -dist_type 1 200
echo "time $JAVA -Xmx6G -jar $FP -name $NAME -input $BAM -output $OUTDIR/ -aligner sam-ignore-deletion -dist_type 1 200 -duplicatefilter -minimum 1 -qualityfilter 10"
time $JAVA -Xmx6G -jar $FP -name $NAME -input $BAM -output $OUTDIR/ -aligner sam-ignore-deletion -dist_type 1 200 -duplicatefilter -minimum 1 -qualityfilter 10

#echo; echo "change to 'chrMT' from 'chrM', then remove the first three lines"
#echo "zcat $OUTDIR/$FPWIG.gz | sed 's/chrom=MT/chrom=chrM/' | sed '1,3d' > $OUTDIR/$CLEAN"
#zcat $OUTDIR/$FPWIG.gz | sed 's/chrom=MT/chrom=chrM/' | sed '1,3d' > $OUTDIR/$CLEAN

#echo; echo "remove the first three lines"
#echo "zcat $OUTDIR/$FPWIG.gz | sed '1,3d' > $OUTDIR/$CLEAN"
#zcat $OUTDIR/$FPWIG.gz | sed '1,3d' > $OUTDIR/$CLEAN

#echo "gzipping..."
#gzip $OUTDIR/$CLEAN

#=============================================================================
#CHROMINFO=/projects/mapp_etc/Mappability/fastq/mm9/mm9.chromInfo.txt
CHROMINFO=/projects/remc_bigdata/S_cere/chromInfo.sacCer2.20100924.txt

echo "done"; echo "running wigToBigWig... (~/bin/x86_64/wigToBigWig)"
echo "wigToBigWig -clip $OUTDIR/$CLEAN.gz $CHROMINFO $OUTDIR/$BWFILE"
wigToBigWig -clip $OUTDIR/$CLEAN.gz $CHROMINFO $OUTDIR/$BWFILE