#!/bin/bash
#PBS -l walltime=48:00:00
#PBS -l ncpus=16,mem=8gb
#PBS -q sgp
#PBS -N trio_whole_exome_cram_compression
#PBS -j oe

# enable running singletons
if [ -z $PBS_ARRAY_INDEX ]
then
  if [ -z $INDEX ]
  then
    export PBS_ARRAY_INDX=1
  else
    export PBS_ARRAY_INDEX=$INDEX
  fi
fi

# Expects environment variables to be set
# PROJECT_ID - e.g. 12345_LastnameFirstname
# CONFIG_SH - absolute path to configuration script setting environment variables

source $CONFIG_SH

FAMILY_ID=`head -n $PBS_ARRAY_INDEX $PARAMS_DIR/$PROJECT_ID.family_ids.txt | tail -n 1`

# This assumes that ${PROJECT_ID}_${FAMILY_ID} is unique, and it should be - if there was
# a re-run of a family, it should have a new project id.
cd $OUTPUT_DIR/*${PROJECT_ID}_${FAMILY_ID}*

for BAM in */*.bam
do

  # 1. Compress to CRAM format without quality score binning
  CRAM=${BAM%.bam}.cram
  samtools view -@ 16 -T $REFERENCE_GENOME -C -o $CRAM $BAM

  # 2. Index the CRAM file - good sanity check
  samtools index $CRAM
  
  # 3. Compare the stats from the BAM and CRAM files
  samtools flagstat $BAM > $BAM.flagstat.txt
  samtools flagstat $CRAM > $CRAM.flagstat.txt
  diff $BAM.flagstat.txt $CRAM.flagstat.txt

done
