UNIX for Beginners Questions & Answers

#!/bin/bash
echo " I AM OUTSIDE THE LOOP"

infile="./calls.txt"

while IFS=',' read -r f1 f2
do
        echo " I AM INSIDE THE LOOP"

        foo=$f1
        bar=$f2

        #many program calls here

done < "$infile"

I AM OUTSIDE THE LOOP

foo1,bar1
foo2,bar2
foo3,bar3

./HiCoPi.sh

 I AM OUTSIDE THE LOOP
 I AM INSIDE THE LOOP
 I AM INSIDE THE LOOP
 I AM INSIDE THE LOOP

while IFS=',' read -r f1 f2 <&3
do
  ...
done 3< "$infile"

#!/bin/bash
echo " I AM OUTSIDE THE LOOP"

infile="calls.txt"

while IFS=',' read -r f1 f2 f3 f4 f5 f6 f7 f8 f9 f10 f11 f12 f13 f14 f15 f16 f17 f18 f19
do
        echo " I AM INSIDE THE LOOP"

        my_file1=$f1
        species1=$f2
        chrom1=$f3
        my_file2=$f4
        species2=$f5
        chrom2=$f6
        binSize=$f7
        foo1=$f8
        foo2=$f9
        foo3=$f10
        foo4=$f11
        variance=$f12
        bar1=$f13
        bar2=$f14
        java_jar=$f15
        bar3=$f16
        bar4=$f17
        unit=$f18
        bar5=$f19

        # program calls here

done < "$infile"

/path/to/my/file.txt,string1,string2,/path/to/my/other/file.txt,string3,string4,int1,string5,string6,int2,int3,int4,/path/to/a/third/file.txt,path/to/a/fourth/file.txt,/path/to/a/java.jar,anotherString,anotherString,anotherString,aFloatNumber