conda activate samtools_env

export WORKING_DIR=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output

cd $WORKING_DIR

#Sort alignments by name
for filename in $(ls *'.sam')

do

#echo $filename
 
fileID=`expr match "$filename" '\([0-9]*C_map_on_d427_hybridAB\)'`

#echo $fileID

export OUTPUT=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output/SAMTools/${fileID}_sort

samtools sort -o $OUTPUT.sam -n $filename 

done

#####################################################################################################################

#Convert SAM into BAM format

export WORKING_DIR=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output/SAMTools

cd $WORKING_DIR

for filename in $(ls *'.sam')

do

#echo $filename

samtools view -S -b $filename > $filename.bam  

done