#!/bin/bash
#SBATCH -t 12:00:00
#SBATCH --nodes 1
#SBATCH --export=NONE
#SBATCH --mail-user=kramsey@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

cd /data/kramseylab/sam/2304_TnSeq/

for f in *.sam;

do
        PREFIX="${f%.sam}"
	DIRPATH=/data/kramseylab/bam/2304_TnSeq_bam
	
	#Convert sam to bam

	module load bio/SAMtools/1.9-foss-2018b
	
	samtools view -bT /data/kramseylab/genomefiles/NC_007880_short.fasta -o $DIRPATH/$PREFIX.bam /data/kramseylab/sam/2304_TnSeq/$PREFIX.sam
	samtools sort -o $DIRPATH/$PREFIX\-sorted.bam $DIRPATH/$PREFIX.bam 
	samtools index $DIRPATH/$PREFIX\-sorted.bam

	rm /data/kramseylab/bam/2302_TnSeq_bam/$PREFIX.bam

	module unload bio/SAMtools/1.9-foss-2018b

shift
done