#!/bin/bash

for i in *bam
do
echo $i


bamToBed -split -i $1  |sort -k1,1 -k2,2n > bar
#rm aligned.bam 
genomeCoverageBed -i bar -bg  -g  hsa.b37.genome   |grep -v GL | sed 's/^/chr/g'> foo
rm bar
/data/results/tools/gbrowser/tools/bedGraphToBigWig foo /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome $1".bw"
#	-split	Report "split" BAM alignments as separate BED entries.
rm foo 

echo "track "$i >> trackDb.txt
echo "bigDataUrl "$i".bw" >> trackDb.txt
echo "shortLabel "$i >> trackDb.txt
echo "longLabel "$i >> 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
echo " " >> trackDb.txt

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

echo /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome|awk '{n=split($1,a,".");print "genome "a[n-1]}'> genomes.txt
echo /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome|awk '{n=split($1,a,".");print "trackDb "a[n-1]"/trackDb.txt"}'>> genomes.txt
done
ln -s . hg19
head -5 hub.txt > foo;
mv foo hub.txt