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design.txt
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# Example inputs and outputs
# input_file.list
/hgsccl/next-gen/Illumina/Instruments/D00341/171220_D00341_0575_AH3GFMBCX2/Results/Project_171220_D00341_0575_AH3GFMBCX2/Sample_H3GFMBCX2-1-IDMB46/SNP/*SNPs_Annotated.vcf
/hgsccl/next-gen/Illumina/Instruments/D00341/171220_D00341_0575_AH3GFMBCX2/Results/Project_171220_D00341_0575_AH3GFMBCX2/Sample_H3GFMBCX2-1-IDMB37/SNP/*SNPs_Annotated.vcf
/hgsccl/next-gen/Illumina/Instruments/D00341/171220_D00341_0575_AH3GFMBCX2/Results/Project_171220_D00341_0575_AH3GFMBCX2/Sample_H3GFMBCX2-1-IDMB29/SNP/*SNPs_Annotated.vcf
/hgsccl/next-gen/Illumina/Instruments/D00341/171220_D00341_0575_AH3GFMBCX2/Results/Project_171220_D00341_0575_AH3GFMBCX2/Sample_H3GFMBCX2-1-IDMB99/SNP/*SNPs_Annotated.vcf # multi-hit
# stdout
LINE: -rw-rw-rw- 2 blah blah /hgsccl/next-gen/Illumina/Instruments/D00341/171220_D00341_0575_AH3GFMBCX2/Results/Project_171220_D00341_0575_AH3GFMBCX2/Sample_H3GFMBCX2-1-IDMB46/SNP/foo_SNPs_Annotated.vcf
LINE: -rw-rw-rw- 2 blah blah /hgsccl/next-gen/Illumina/Instruments/D00341/171220_D00341_0575_AH3GFMBCX2/Results/Project_171220_D00341_0575_AH3GFMBCX2/Sample_H3GFMBCX2-1-IDMB29/SNP/bar_SNPs_Annotated.vcf
count is: 2
# script.sh
#!/bin/bash
count=0
while read LINE;
do
if [ -f $LINE ]; then
echo -n "LINE: "
ls -lF $LINE
count=`expr $count + 1`
fi
done < ./05_8_2018.resultPath.txt
echo "count is: $count"
fglob input_file.list
/hgsccl/next-gen/Illumina/Instruments/D00341/171220_D00341_0575_AH3GFMBCX2/Results/Project_171220_D00341_0575_AH3GFMBCX2/Sample_H3GFMBCX2-1-IDMB46/SNP/foo_SNPs_Annotated.vcf
/hgsccl/next-gen/Illumina/Instruments/D00341/171220_D00341_0575_AH3GFMBCX2/Results/Project_171220_D00341_0575_AH3GFMBCX2/Sample_H3GFMBCX2-1-IDMB29/SNP/bar_SNPs_Annotated.vcf
fglob --bad input_file.list
/hgsccl/next-gen/Illumina/Instruments/D00341/171220_D00341_0575_AH3GFMBCX2/Results/Project_171220_D00341_0575_AH3GFMBCX2/Sample_H3GFMBCX2-1-IDMB37/SNP/*SNPs_Annotated.vcf
fglob --multi input_file.list
/hgsccl/next-gen/Illumina/Instruments/D00341/171220_D00341_0575_AH3GFMBCX2/Results/Project_171220_D00341_0575_AH3GFMBCX2/Sample_H3GFMBCX2-1-IDMB99/SNP/*SNPs_Annotated.vcf
fglob --table input_file.list
...46/SNP/*SNPs_Annotated.vcf good ...46/SNP/foo_SNPs_Annotated.vcf
...37/SNP/*SNPs_Annotated.vcf missing (empty)
...29/SNP/*SNPs_Annotated.vcf good ...29/SNP/bar_SNPs_Annotated.vcf
...99/SNP/*SNPs_Annotated.vcf multi ...99/SNP/spam_SNPs_Annotated.vcf
...99/SNP/*SNPs_Annotated.vcf multi ...99/SNP/eggs_SNPs_Annotated.vcf