#!/bin/sh
#/mnt/raid/tools/align/tophat-2.0.8b.Linux_x86_64/bam_merge -Q aligned.bam unmapped.bam   accepted_hits.bam 
#time bamToBed -split -i aligned.bam  |sort -k1,1 -k2,2n > bar
#samtools view -b -s $3 $1 > foo
#/data/results/tools/samtools/samtools-1.0/samtools sort -@20 $1 srt
#/data/results/tools/samtools/samtools-1.0/samtools view -b -s $3 srt.bam > foo
/data/results/tools/samtools/samtools-1.0/samtools view -b -s $3 $1 > foo
/data/results/tools/bedtools/bedtools2/bin/bamToBed -split -i foo >bar1

#/data/results/tools/samtools/samtools-1.0/samtools sort -@20 $4 srt
#/data/results/tools/samtools/samtools-1.0/samtools view -b -s $3 srt.bam > foo
/data/results/tools/samtools/samtools-1.0/samtools view -b -s $3 $4 > foo
/data/results/tools/bedtools/bedtools2/bin/bamToBed -split -i foo >bar2
cat bar1 bar2 |sort -k1,1 -k2,2n > bar
#cat bar1 |sort -k1,1 -k2,2n > bar
rm foo bar1 bar2
#rm aligned.bam 
/data/results/tools/bedtools/bedtools2/bin/genomeCoverageBed -strand + -i bar -bg  -g  $2  > foo
/data/results/tools/gbrowser/tools/bedGraphToBigWig foo $2 $1"-plus.samp.bw"
#err
#chr5	100947571	100947734	181
#update new bedtools:
#/data/results/tools/bedtools/bedtools2/bin/genomeCoverageBed -split -strand + -ibam srt.bam -bg  -g  /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome  > foo
#chr5	100947568	100947569	202
#chr5	100947569	100947571	7
#chr5	100947571	100947734	1

/data/results/tools/bedtools/bedtools2/bin/genomeCoverageBed -strand - -i bar -bg  -g  $2  > foo
/data/results/tools/gbrowser/tools/bedGraphToBigWig foo $2 $1"-minus.samp.bw"
rm bar
#	-split	Report "split" BAM alignments as separate BED entries.

echo "track "$1"plus" >> SStrackDb.txt
echo "bigDataUrl "$1"-plus.samp.bw" >> SStrackDb.txt
echo "shortLabel "$1"plus" >> SStrackDb.txt
echo "longLabel "$1"plus" >> SStrackDb.txt
echo "color 0,0,255" >> SStrackDb.txt
echo "maxHeightPixels 128:30:11" >> SStrackDb.txt
echo "autoScale on" >> SStrackDb.txt
echo "visibility full" >> SStrackDb.txt
echo "type bigWig" >> SStrackDb.txt
echo " " >> SStrackDb.txt

echo "track "$1"minus" >> SStrackDb.txt
echo "bigDataUrl "$1"-minus.samp.bw" >> SStrackDb.txt
echo "shortLabel "$1"minus" >> SStrackDb.txt
echo "longLabel "$1"minus" >> SStrackDb.txt
echo "color 0,0,255" >> SStrackDb.txt
echo "maxHeightPixels 128:30:11" >> SStrackDb.txt
echo "autoScale on" >> SStrackDb.txt
echo "visibility full" >> SStrackDb.txt
echo "type bigWig" >> SStrackDb.txt
echo " " >> SStrackDb.txt

rm hub.txt
echo "hub "$1 >> hub.txt
echo "shortLabel "$1 >> hub.txt
echo "longLabel "$1 >> hub.txt
echo "genomesFile genomes.txt" >> hub.txt
echo "email reczko@fleming.gr" >> hub.txt

echo $2|awk '{n=split($1,a,".");print "genome "a[n-1]}'> genomes.txt
echo $2|awk '{n=split($1,a,".");print "trackDb "a[n-1]"/SStrackDb.txt"}'>> genomes.txt

echo $2|awk '{n=split($1,a,".");print "http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db="a[n-1]"&hubUrl=http://genomics-lab.fleming.gr/fleming/MFlab/run42/hub-raw.txt"}' > hub-link.txt

exit
echo "track "$1 >> ../trackDb.txt
echo "bigDataUrl "$1".samp.bw" >> ../trackDb.txt
echo "shortLabel "$1 >> ../trackDb.txt
echo "longLabel "$1 >> ../trackDb.txt
echo "color 0,0,255" >> ../trackDb.txt
echo "maxHeightPixels 128:30:11" >> ../trackDb.txt
echo "autoScale on" >> ../trackDb.txt
echo "visibility full" >> ../trackDb.txt
echo "type bigWig" >> ../trackDb.txt

exit
echo "track name="$2" color=0,0,255 visibility=full maxHeightPixels=11:30:128 type=bigWig bigDataUrl=http://estia/fleming/run5/tracks/VK/"$2".samp.bw"
echo "track name="DENTCP_sens" color=0,0,255 visibility=full maxHeightPixels=11:30:128 type=bigWig bigDataUrl=http://estia/fleming/proton/run9/tophat_out/DENTCP.samp.bw 
echo "mv *bw  /var/www/genomebrowser/fleming/..."