Variable error in QDNA_from_bam_no_chrX.R

aeeckhou / shallowHRD

This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination Deficiency of a tumor based on the number of Large-scale Genomic Alterations (LGAs).

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Variable error in QDNA_from_bam_no_chrX.R #6

Closed DucoG closed 1 year ago

DucoG commented 2 years ago

Hello,

I noticed the following small error while running QDNA_from_bam_no_chrX.R

Line 50 uses outputPath but I think instead inputPath would be the correct variable. The error is present only in this file and not in QDNA_from_bam_chrX.R

Line 50:

readCounts <- binReadCounts(bins, bamfiles=paste0(outputPath,"/",NAMEEE,".bam"))

should be changed to:

readCounts <- binReadCounts(bins, bamfiles=paste0(inputPath,"/",NAMEEE,".bam"))

Kind regards, Duco Gaillard

aeeckhou commented 1 year ago

Dear Duco,

Sorry for the delayed answer... Thank you for spotting the mistake. I corrected this in QDNA_from_bam_no_chrX.R.

Best regards, Alexandre Eeckhoutte