all_sam_to_bam_3.sh

#!/bin/bash

# A first example of 'for loop' to iterate a set of commands over a list of files

SamFilesCount=$(ls *.sam | wc -l);
echo "In this directory you have ${SamFilesCount}"

# Loop throught all .sam files (note: won't work if no .sam files are present!)
for SamFile in *.sam
do
        echo -n "Converting ${SamFile}... "
        if [[ -s "${SamFile}" ]]
        then
          samtools view -bS ${SamFile} | samtools sort -o ${SamFile/.sam/.bam} -
          samtools index ${SamFile/.sam/.bam}.bam
          echo "Done!"
        else 
          echo "Skipping $SamFile: it's empty!"
        fi  
done