#!/bin/bash
##  qsub -q batch velmakefa.sh
#PBS -N bamindx
#PBS -l mem=48gb,nodes=1:ppn=24,walltime=19:55:00
#PBS -o bamindx.$$.out
#PBS -e bamindx.$$.err
#PBS -V

ncpu=24

workd=$HOME/scratch/chrs/cacao
export scripts=$HOME/bio/evigene/scripts/rnaseq
export bindir=$HOME/bio/bin

cd $workd/rnas/bams7/

# env bamlist=xxxx qsub -q batch velmakefa.sh
bamlist1=`ls ncgr{0909,0910}*.bam`
bamlist2=`ls ncgr090[567]*.bam`
#bamlist3=`ls cgb*1-mars11s8p.bam`
#bamlist4=`ls cgb*1.bam`
bamlist4=`ls cgb*.bam`

bamlist=$bamlist4

for bam in $bamlist ; do {
 if [ ! -f $bam.bai ]; then 
   echo samtools index $bam
   ( $bindir/samtools index $bam ; $bindir/samtools idxstats $bam > $bam.count ) &
 fi
} done


wait