#!/bin/tcsh
# bam2bw.sh
#  bam2bw.sh $dmag2/genome/dmagna20100422assembly.fa.fai [134]*.bam

## fixme bpath
set bpath=/bio/bio-grid/mb/bin

if ( $?dgenomesize == 0 ) then 
  set dgenomesize=$1; shift; 
endif
if ( $?drna == 0 ) then 
  set drna=$1; shift; 
endif
if ( $drna == "" || $dgenomesize == "" ) then
  echo "usage: bam2bw.sh /path/to/genome.chr_size.tab rnaseqlib4{.bam}"; exit;
endif

while ($drna != "") 
  echo "# bed2bw chrsize=$dgenomesize bed=$drna"
  set brna=`basename $drna .bed | sed 's/.bam//'`

  if( -f $brna.bw ) then
    echo "# exists $brna.bw"; 
  else

    # nasty fails when read beyond end if dgenomesize.. filter
    $bpath/bedGraphToBigWig $drna $dgenomesize  $brna.bw

  endif

  set drna=""
  if( $# > 0 ) then
    set drna=$1; shift;
  endif

end