#!/usr/bin/bash

export PATH=/bioinfo/guests/nriddifo/miniconda2/bin:$PATH
source activate picard

bam_files=/data/kdi_prod/project_result/948/01.00/Analysis/Bwa/visor

for b in $( ls -1 "$bam_files"/*.filt.SC.RG.bam )
do
  file_name=$( basename "${b}" )
  output_base=$(echo $file_name | cut -d '.' -f 1)

  echo """
  picard AddOrReplaceReadGroups \
    INPUT=${b} \
    OUTPUT=$bam_files/${output_base}.tagged.filt.SC.RG.bam \
    VALIDATION_STRINGENCY=LENIENT \
    RGID=$output_base \
    RGLB=visor \
    RGPL=illumina \
    RGPU=1 \
    RGSM=$output_base
    """

    samtools index $bam_files/${output_base}.tagged.filt.SC.RG.bam
done
