#!/usr/bin/env bash


screen -R dupradar

export NGS_TOOLS="/projects/bioinfo/$(whoami)/scripts/ngs_tools"

source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
export PATH=${NGS_TOOLS}/dge_workflow:$PATH

PRJ_DATA=/projects/bioinfo/misc/dup_radar_refs


mcdir ${PRJ_DATA}

## fam72d_transfection_seq
mcdir ${PRJ_DATA}/fam72d_transfection_seq
export IGENOME=/projects/bioinfo/igenomes/Mus_musculus/Ensembl_v81/GRCm38
bamFiles=$(ls /projects/bioinfo/brandl/data/fam72d_transfection_seq/alignments/*bam)
#ll ${IGENOME} $bamFiles
dge_analyze_duplicates.sh  ${bamFiles} &


## meyer_rnaseq
mcdir ${PRJ_DATA}/meyer_rnaseq
export IGENOME=/projects/bioinfo/igenomes/Mus_musculus/Ensembl_v81/GRCm38
bamFiles=$(ls /projects/bioinfo/brandl/data/meyer_rnaseq/alignments/*bam)
#ls $bamFiles
dge_analyze_duplicates.sh ${bamFiles} &



## xing_rnaseq
mcdir ${PRJ_DATA}/xing_rnaseq
export IGENOME=/projects/bioinfo/igenomes/Mus_musculus/Ensembl_v81/GRCm38
bamFiles=$(ls /projects/bioinfo/data/xing_11b_rnaseq/alignments/*bam)
#ls $bamFiles
dge_analyze_duplicates.sh -${bamFiles} &

wait

mailme "dupradar refs done"

## integrate stats for report overlay
rendr_snippet "dupstats_integration" <<"EOF"
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.39/R/core_commons.R")


EOF