Adding in the f field to the sort so that problems with .1 versus .10 are resolved appropriately

#             script will not work. The error will often manifest itself

#             through a "*" in the name because the wildcard was not able to

#             match any files with the read1str.   

set -e

#set -e ## This is causing problems; need better error detection

shopt -s extglob

juicer_version="1.5.6" 

### LOAD BWA AND SAMTOOLS

# fastq files should look like filename_R1.fastq and filename_R2.fastq 

# if your fastq files look different, change this value

read1str="_R1" 

        then

            usegzip=1

        fi

	source ${juiceDir}/scripts/common/countligations.sh

        # Align read1 

            fi

	fi

        # sort read 1 aligned file by readname

	sort -T $tmpdir -k1,1 $name1$ext.sam > $name1${ext}_sort.sam

	sort -T $tmpdir -k1,1f $name1$ext.sam > $name1${ext}_sort.sam

	if [ $? -ne 0 ]

	then

            echo "***! Error while sorting $name1$ext.sam"

            echo "(-: Sort read 1 aligned file by readname completed."

	fi

        # sort read 2 aligned file by readname

	sort -T $tmpdir -k1,1 $name2$ext.sam > $name2${ext}_sort.sam

	sort -T $tmpdir -k1,1f $name2$ext.sam > $name2${ext}_sort.sam

	if [ $? -ne 0 ]

	then

            echo "***! Error while sorting $name2$ext.sam"

	awk 'BEGIN{OFS="\t"}NF>=11{$1=$1"/1"; print}' $name1${ext}_sort.sam > $name1${ext}_sort1.sam

	awk 'BEGIN{OFS="\t"}NF>=11{$1=$1"/2"; print}' $name2${ext}_sort.sam > $name2${ext}_sort1.sam

	sort -T $tmpdir -k1,1 -m $name1${ext}_sort1.sam $name2${ext}_sort1.sam > ${name}${ext}.sam

	sort -T $tmpdir -k1,1f -m $name1${ext}_sort1.sam $name2${ext}_sort1.sam > ${name}${ext}.sam

	if [ $? -ne 0 ]

	then