modernized dge_merge_treps

dge_workflow/dge_utils.sh

@@ -259,36 +259,26 @@ fi
 
 
 local bam_dir=$1; # bam_dir=$baseDir/mapped_trim/
-local bio_reps=$2; # bio_samples="test,lala"
+local bio_samples=$2; # bio_samples="test,lala"
 
 if [ ! -d "$bam_dir" ]; then
     echo "bam file directory does not exist! $usage'" >&2 ; return;
 fi
 
-if [ $(echo "$bio_samples" | grep "," | wc -l )  -ne 1 ]; then
+if [ $(echo "${bio_samples}" | grep "," | wc -l )  -ne 1 ]; then
     echo "Invalid biosample spec! $usage'" >&2 ; return;
 fi
 
-#for sample in aRG bRG N; do
-for sample in $(echo $bio_samples | tr ",", " "); do
-    # DEBUG sample=Insm1_1103
-
-    ## todo use joblist instead here
-    (
-    sampleBams=$(find $bam_dir -name '*bam'  | grep -v unmapped | grep $sample)
-    echo "merging $sample with $sampleBams"
-
-    ## todo add read-groups to bam files
-    if [ 1 -eq $(echo "$sampleBams" | wc -l) ]; then
-        cp $sampleBams $sample.bam
-    else
-        samtools merge - $(echo $sampleBams | xargs echo) | samtools sort - $sample
-    fi
-
-    samtools index $sample.bam
-    )&
+for condition in $(echo ${bio_samples} | tr ",", " "); do
+    echo merging ${condition}
+    bamFiles=$(ls ${bam_dir}/${condition}*.bam | xargs echo)
+    jl submit --jl .merge_reps "
+    samtools merge --threads 10 - ${bamFiles} | samtools sort -T ${condition} -o ${condition}.bam -
+    samtools index ${condition}.bam
+    "
 done
 
+jl wait .merge_reps
 }
 export -f dge_merge_treps