diff --git a/exec/SplitFusion.1_fastq-bam.sh b/exec/SplitFusion.1_fastq-bam.sh index 37f14cd..fdc8892 100755 --- a/exec/SplitFusion.1_fastq-bam.sh +++ b/exec/SplitFusion.1_fastq-bam.sh @@ -72,20 +72,12 @@ SampleId=$( pwd | sed "s:.*/::") sort --parallel=$thread -k1,1b -u uniq.ligateUmi > _consolidated.readID #=== join raw sam with consolidated ID === - sed -e 's:\t\t:\t*\t:g' _raw.sam | sed -e 's/umi:/umi\t/' > _raw.samC - sort --parallel=$thread -k1,1b _raw.samC > _raw.sam.s - rm _raw.samC - - join _consolidated.readID _raw.sam.s > _consolidated.sam0 - cp header consolidated.sam - sed -e 's/ /:/' _consolidated.sam0 | tr ' ' '\t' | cut -f1,3- >> consolidated.sam - rm _raw.sam.s + cp header consolidated.sam + sed -e 's:\t\t:\t*\t:g' _raw.sam | sed -e 's/umi:/umi\t/' | sort --parallel=$thread -k1,1b | \ + join _consolidated.readID - | sed -e 's/ /:/' | tr ' ' '\t' | cut -f1,3- >> consolidated.sam rm _* grep -P '\tSA:Z:' consolidated.sam > _sa.sam - -$samtools view -@ $thread -T $refGenome -bS consolidated.sam > _consolidated.bam -$samtools sort -@ $thread _consolidated.bam -o $SampleId.consolidated.bam - rm consolidated.sam _consolidated.bam -$samtools index $SampleId.consolidated.bam +$samtools view -@ $thread -T $refGenome -bS consolidated.sam | $samtools sort -@ $thread -o $SampleId.consolidated.bam - +$samtools index $SampleId.consolidated.bam