Commit f44753e7 authored by nchernia's avatar nchernia
Browse files

change to call alignonly without chrom.sizes; merging moved to appropriate... 

change to call alignonly without chrom.sizes; merging moved to appropriate place; bug fix in countligations for stem
parent 9c55ecb1

CPU/common/countligations.sh

+2 −2
Changes for CPU/common/countligations.sh: 2 added lines, 2 removed lines.
Original line number Diff line number Diff line
@@ -33,5 +33,5 @@ else 
    num1=$(paste $file1 $file2 | grep -c $ligation)

    num2=$(wc -l $file1 | awk '{print $1}')

fi

echo -ne "$num1 " > ${ostem}_norm.txt.res.txt

echo "$num2" > ${ostem}_linecount.txt
 
echo -ne "$num1 " > ${curr_ostem}_norm.txt.res.txt

echo "$num2" > ${curr_ostem}_linecount.txt

CPU/juicer.sh

+45 −41
Changes for CPU/juicer.sh: 45 added lines, 41 removed lines.
Original line number Diff line number Diff line
@@ -173,7 +173,7 @@ then 
else

    # Reference sequence passed in, so genomePath must be set for the .hic file

    # to be properly created

    if [ -z "$genomePath" ]

    if [ -z "$genomePath" ] && [ -z "$alignonly" ]

    then

        echo "***! You must define a chrom.sizes file via the \"-p\" flag that delineates the lengths of the chromosomes in the genome at $refSeq";

        exit 1;
@@ -362,7 +362,7 @@ java -version 2>&1 | awk 'NR==1{printf("%s; ", $0);}' >> $headfile 
${juiceDir}/scripts/juicer_tools -V 2>&1 | awk '$1=="Juicer" && $2=="Tools"{printf("%s; ", $0);}' >> $headfile

echo "$0 $@" >> $headfile



## ALIGN FASTQ AS SINGLE END, SORT BY READNAME, HANDLE CHIMERIC READS

## ALIGN FASTQ IN SINGLE END MODE, SORT BY READNAME, HANDLE CHIMERIC READS

 

## Not in merge, dedup, final, or postproc stage, i.e. need to align files.

if [ -z $merge ] && [ -z $mergeonly ] && [ -z $final ] && [ -z $dedup ] && [ -z $deduponly ] && [ -z $postproc ]
@@ -376,97 +376,98 @@ then 


	echo $file1

	echo $file2

	ostem="$splitdir/$ostem"

	ostem="${splitdir}/${ostem}"

	

        if [ ${file1: -3} == ".gz" ]

        then

            usegzip=1

        fi



	curr_ostem=${ostem}_${i}

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



        # Align reads

        echo "Running command $bwa_cmd mem -SP5M $threadstring $refSeq $file1 $file2 > ${ostem}_${i}.sam" 

        $bwa_cmd mem -SP5M $threadstring $refSeq $file1 $file2 > ${ostem}_${i}.sam

        echo "Running command $bwa_cmd mem -SP5M $threadstring $refSeq $file1 $file2 > ${curr_ostem}.sam" 

        $bwa_cmd mem -SP5M $threadstring $refSeq $file1 $file2 > ${curr_ostem}.sam

        if [ $? -ne 0 ]

        then

            echo "***! Alignment of $file1 $file2 failed."

            exit 1

        else                                                            

	    echo "(-:  Align of ${ostem}_${i}.sam done successfully"

	    echo "(-:  Align of ${curr_ostem}.sam done successfully"

        fi

#	samtools view -hb $name$ext.sam > $name$ext.bam

	export LC_ALL=C

        # call chimeric_blacklist.awk to deal with chimeric reads; 

        # sorted file is sorted by read name at this point

	touch ${ostem}_${i}_collisions.sam ${ostem}_${i}_collisions_low_mapq.sam ${ostem}_${i}_unmapped.sam ${ostem}_${i}_mapq0.sam

	touch ${curr_ostem}_collisions.sam ${curr_ostem}_collisions_low_mapq.sam ${curr_ostem}_unmapped.sam ${curr_ostem}_mapq0.sam

	# chimeric takes in $name$ext

	awk -v "fname"=${ostem}_${i} -f ${juiceDir}/scripts/common/chimeric_blacklist.awk ${ostem}_${i}.sam

	awk -v "fname"=${curr_ostem} -f ${juiceDir}/scripts/common/chimeric_blacklist.awk ${curr_ostem}.sam

	if [ $? -ne 0 ]

	then

            echo "***! Failure during chimera handling of ${ostem}_${i}"

            echo "***! Failure during chimera handling of ${curr_ostem}"

            exit 1

	fi	

        # if any normal reads were written, find what fragment they correspond

	# to and store that

	if [ -e "${ostem}_${i}_norm.txt" ] && [ "$site" != "none" ]

	if [ -e "${curr_ostem}_norm.txt" ] && [ "$site" != "none" ]

	then

            ${juiceDir}/scripts/common/fragment.pl ${ostem}_${i}_norm.txt ${ostem}_${i}.frag.txt $site_file    

            ${juiceDir}/scripts/common/fragment.pl ${curr_ostem}_norm.txt ${curr_ostem}.frag.txt $site_file    

	elif [ "$site" == "none" ]

	then

            awk '{printf("%s %s %s %d %s %s %s %d", $1, $2, $3, 0, $4, $5, $6, 1); for (i=7; i<=NF; i++) {printf(" %s",$i);}printf("\n");}' ${ostem}_${i}_norm.txt > ${ostem}_${i}.frag.txt

            awk '{printf("%s %s %s %d %s %s %s %d", $1, $2, $3, 0, $4, $5, $6, 1); for (i=7; i<=NF; i++) {printf(" %s",$i);}printf("\n");}' ${curr_ostem}_norm.txt > ${curr_ostem}.frag.txt

	else

            echo "***! No ${ostem}_${i}_norm.txt file created"

            echo "***! No ${curr_ostem}_norm.txt file created"

            exit 1

	fi

	if [ $? -ne 0 ]

	then

            echo "***! Failure during fragment assignment of ${ostem}_${i}"

            echo "***! Failure during fragment assignment of ${curr_ostem}"

            exit 1

	fi                              



	# convert sams to bams and delete the sams

	samtools view -hb ${ostem}_${i}_collisions.sam > ${ostem}_${i}_collisions.bam

	samtools view -hb ${curr_ostem}_collisions.sam > ${curr_ostem}_collisions.bam

	if [ $? -ne 0 ]

	then

            echo "***! Failure during bam write of ${ostem}_${i}_collisions.sam"

            echo "***! Failure during bam write of ${curr_ostem}_collisions.sam"

            exit 1

	fi	

	samtools view -hb ${ostem}_${i}_collisions_low_mapq.sam > ${ostem}_${i}_collisions_low_mapq.bam

	samtools view -hb ${curr_ostem}_collisions_low_mapq.sam > ${curr_ostem}_collisions_low_mapq.bam

	if [ $? -ne 0 ]

	then

            echo "***! Failure during bam write of ${ostem}_${i}_collisions_low_mapq.sam"

            echo "***! Failure during bam write of ${curr_ostem}_collisions_low_mapq.sam"

            exit 1

	fi	

	samtools view -hb ${ostem}_${i}_unmapped.sam > ${ostem}_${i}_unmapped.bam

	samtools view -hb ${curr_ostem}_unmapped.sam > ${curr_ostem}_unmapped.bam

	if [ $? -ne 0 ]

	then

            echo "***! Failure during bam write of ${ostem}_${i}_unmapped.sam"

            echo "***! Failure during bam write of ${curr_ostem}_unmapped.sam"

            exit 1

	fi	

	samtools view -hb ${ostem}_${i}_mapq0.sam > ${ostem}_${i}_mapq0.bam

	samtools view -hb ${curr_ostem}_mapq0.sam > ${curr_ostem}_mapq0.bam

	if [ $? -ne 0 ]

	then

            echo "***! Failure during bam write of ${ostem}_${i}_mapq0.sam"

            echo "***! Failure during bam write of ${curr_ostem}_mapq0.sam"

            exit 1

	fi	

	samtools view -hb ${ostem}_${i}_alignable.sam > ${ostem}_${i}_alignable.bam

	samtools view -hb ${curr_ostem}_alignable.sam > ${curr_ostem}_alignable.bam

	if [ $? -ne 0 ]

	then

            echo "***! Failure during bam write of ${ostem}_${i}_alignable.sam"

            echo "***! Failure during bam write of ${curr_ostem}_alignable.sam"

            exit 1

	fi	

	# remove all sams EXCEPT alignable, which we need for deduping

	rm ${ostem}_${i}_collisions.sam ${ostem}_${i}_collisions_low_mapq.sam ${ostem}_${i}_unmapped.sam ${ostem}_${i}_mapq0.sam

	rm ${curr_ostem}_collisions.sam ${curr_ostem}_collisions_low_mapq.sam ${curr_ostem}_unmapped.sam ${curr_ostem}_mapq0.sam



        # sort by chromosome, fragment, strand, and position

	sort -T $tmpdir -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n ${ostem}_${i}.frag.txt > ${ostem}_${i}.sort.txt

	sort -T $tmpdir -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n ${curr_ostem}.frag.txt > ${curr_ostem}.sort.txt

	if [ $? -ne 0 ]

	then

            echo "***! Failure during sort of ${ostem}_${i}"

            echo "***! Failure during sort of ${curr_ostem}"

            exit 1

	else

            rm ${ostem}_${i}_norm.txt ${ostem}_${i}.frag.txt

            rm ${curr_ostem}_norm.txt ${curr_ostem}.frag.txt

	fi

    done

fi
@@ -483,6 +484,22 @@ then 
    then

        mv $donesplitdir/* $splitdir/.

    fi



    # combine bams

    if [ `ls -1 $splitdir/*_abnorm.bam 2>/dev/null | wc -l ` -gt 1 ]

    then

	samtools merge -n $outputdir/collisions.bam $splitdir/*_collisions.bam 

	samtools merge -n $outputdir/collisions_low_mapq.bam $splitdir/*_collisions_low_mapq.bam 

	samtools merge -n $outputdir/unmapped.bam $splitdir/*_unmapped.bam 

	samtools merge -n $outputdir/mapq0.bam $splitdir/*_mapq0.bam

    else

	cat $splitdir/*_collisions.bam > $outputdir/collisions.bam

	cat $splitdir/*_collisions_low_mapq.bam > $outputdir/collisions_low_mapq.bam

	cat $splitdir/*_unmapped.bam > $outputdir/unmapped.bam

	cat $splitdir/*_mapq0.bam > $outputdir/mapq0.bam

    fi





    if ! sort -T $tmpdir -m -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n $splitdir/*.sort.txt  > $outputdir/merged_sort.txt

    then 

        echo "***! Some problems occurred somewhere in creating sorted align files."
@@ -528,19 +545,6 @@ then 
    else

	cat ${splitdir}/*_alignable.bam > ${outputdir}/alignable.bam

    fi

    # combine bams

    if [ `ls -1 $splitdir/*_abnorm.bam 2>/dev/null | wc -l ` -gt 1 ]

    then

	samtools merge -n $outputdir/collisions.bam $splitdir/*_collisions.bam 

	samtools merge -n $outputdir/collisions_low_mapq.bam $splitdir/*_collisions_low_mapq.bam 

	samtools merge -n $outputdir/unmapped.bam $splitdir/*_unmapped.bam 

	samtools merge -n $outputdir/mapq0.bam $splitdir/*_mapq0.bam

    else

	cat $splitdir/*_collisions.bam > $outputdir/collisions.bam

	cat $splitdir/*_collisions_low_mapq.bam > $outputdir/collisions_low_mapq.bam

	cat $splitdir/*_unmapped.bam > $outputdir/unmapped.bam

	cat $splitdir/*_mapq0.bam > $outputdir/mapq0.bam

    fi

fi



if [ -n "$deduponly" ]

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