# 19 December 2010

JAVA=/usr/local/bin/java16

# Trying v4.0.16-dev.interval
FPDIR=/home/afejes/workspace/Vancouver_Package/jars/fp4
FP=$FPDIR/FindPeaks.jar
SEPR=$FPDIR/SeparateReads.jar
SRTF=$FPDIR/SortFiles.jar

WTBW=/home/grobertson/bin/x86_64/wigToBigWig

# have to run this on xhost06, can't find java16 on xhost08 or 09
# 2.8GB meta .map file, 4 lanes
MAP=/archive/solexa1_5/analysis/MM0507/meta_maq/MM0507_4_lanes.map
NAME=MM0507_H3K9me3_ChIP-seq.mm9_ht5_q10
WIGNAME=MM0507_H3K9me3_ChIP-seq.mm9_ht5_q10_triangle_standard
BASEDIR=/projects/remc_bigdata/MORGEN/MM0507_H3K9me3_liver_adult_4L/bigWig

WIGDIR=$BEDDIR/wig
# 'clean' has chrM, not chrMT; no header lines
CLEAN=$FPWIG.clean
CHRM=$FPWIG.chrM.wig
BWFILE=$WIGNAME.bigwig


echo "findpeaks in 'maq' mode"
echo "$JAVA -Xmx6G -jar $FP -input $MAP -aligner maq -output $BASEDIR/ -dist_type 1 200 -name $NAME -qualityfilter 10 -duplicatefilter -minimum 5"
$JAVA -Xmx6G -jar $FP -input $MAP -aligner maq -output $BASEDIR/ -dist_type 1 200 -name $NAME -qualityfilter 10 -duplicatefilter -minimum 5


#=============================================================================
#echo "changing to 'chrMT' from 'chrM', removing header lines..."
#less $OUTDIR/$FPWIG.gz | sed 's/chrom=MT/chrom=chrM/' | sed '1,3d' > $OUTDIR/$CLEAN
#echo "less $OUTDIR/$FPWIG.gz | sed 's/chrom=MT/chrom=chrM/' > $OUTDIR/$CHRM"
#less $OUTDIR/$FPWIG.gz | sed 's/chrom=MT/chrom=chrM/' > $OUTDIR/$CHRM
#echo "gzipping"
#gzip $OUTDIR/$CHRM

#=============================================================================

#CHROMINFO=/projects/mapp_etc/Mappability/fastq/mm9/mm9.chromInfo.txt
CHROMINFO=/home/grobertson/bin/x86_64/mm9.chrom.sizes
#CHROMINFO=/home/grobertson/bin/x86_64/mm8.chrom.sizes
#GENOMEFA=/projects/mapp_etc/Mappability/fastq/mm9/36mer/bwa_ind/mm9_build37_mouse.fasta
# 'chr1' is '1'
#GENOMEFA=/projects/wtsspipeline/resources/Mus_musculus/bfa_NCBI-37/all_mouse_no_chr.fasta
GENOMEFA=/projects/wtsspipeline/resources/Mus_musculus/bfa_NCBI-37/all_mouse.fasta
#echo "sed '1,3d'..."
#echo "less $WIGDIR/$WIGNAME.wig.gz | sed '1,3d' > $WIGDIR/$WIGNAME.sed13.wig"
#less $WIGDIR/$WIGNAME.wig.gz | sed '1,3d' > $WIGDIR/$WIGNAME.sed13.wig
#echo "gzipping..."
#gzip $WIGDIR/$WIGNAME.sed13.wig

#echo "done"; 
#echo "running wigToBigWig... (~/bin/x86_64/wigToBigWig)"
#echo "$WTBW -clip $WIGDIR/$WIGNAME.sed13.wig.gz $CHROMINFO $WIGDIR/$BWFILE"
#$WTBW -clip $WIGDIR/$WIGNAME.sed13.wig.gz $CHROMINFO $WIGDIR/$BWFILE