#!/bin/bash
# RNAseq bigWigs moeten in de rnaWig directory staan

function addTrack {	
	echo "  track multi_$1" >> rnaseq_trackDb.txt
  	echo "  parent RNAseq" >> rnaseq_trackDb.txt
    	echo "  aggregate solidOverlay">> rnaseq_trackDb.txt
      	echo "  container multiWig"  >> rnaseq_trackDb.txt
        echo "  viewLimits -127:127">> rnaseq_trackDb.txt
	echo "  type bigWig">> rnaseq_trackDb.txt
      	echo "  visibility full" >> rnaseq_trackDb.txt
	echo "  showSubtrackColorOnUi on">> rnaseq_trackDb.txt
	echo "  maxHeightPixels 500:100:9">> rnaseq_trackDb.txt
	echo "  shortLabel $1">> rnaseq_trackDb.txt
	echo "  longLabel multiWig $1">> rnaseq_trackDb.txt
	echo -e "\n" >> rnaseq_trackDb.txt

	echo "    track ${1}_rev" >> rnaseq_trackDb.txt
    	echo "    bigDataUrl rnaWig/${1}.reverse.bw">> rnaseq_trackDb.txt
        echo "    color 255,51,0">> rnaseq_trackDb.txt
	echo "    visibility full" >> rnaseq_trackDb.txt
	echo "    longLabel $1 reverse">> rnaseq_trackDb.txt
	echo "    parent multi_$1">> rnaseq_trackDb.txt
	echo "    shortLabel ${1}_rev">> rnaseq_trackDb.txt
	echo "    type bigWig">> rnaseq_trackDb.txt
	echo -e "\n">> rnaseq_trackDb.txt

	echo "    track ${1}_for">> rnaseq_trackDb.txt
	echo "    bigDataUrl rnaWig/${1}.forward.bw">> rnaseq_trackDb.txt
	echo "    parent multi_$1">> rnaseq_trackDb.txt
	echo "    visibility full" >> rnaseq_trackDb.txt
	echo "    color 255,51,0">> rnaseq_trackDb.txt
	echo "    longLabel $1 forward">> rnaseq_trackDb.txt
	echo "    shortLabel ${1}_for">> rnaseq_trackDb.txt
	echo "    type bigWig">> rnaseq_trackDb.txt
	echo -e "\n">> rnaseq_trackDb.txt
}

function addSuperTrack {
	echo "track RNAseq" > rnaseq_trackDb.txt
	echo "shortLabel RNAseq" >> rnaseq_trackDb.txt
	echo "longLabel Inhouse RNAseq data" >> rnaseq_trackDb.txt
	echo "superTrack on show" >> rnaseq_trackDb.txt
	echo "priority 1" >> rnaseq_trackDb.txt
	echo -e "\n" >> rnaseq_trackDb.txt
}


"$@"

addSuperTrack
for i in rnaWig/*.bw
do
	echo $i
	addTrack $i
done