Fixed chromosome comparison in createNormalizedCoverageFiles() #40
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added 2 commits
March 4, 2019 17:10
Chromosomes in BED and BAM files start with "chr". createNormalizedCoverageFiles() was trying to compare chromosome names in samples and control files as if these names were numerics. The subroutine now treats both as strings for comparison.
Fixed chromosome comparison in createNormalizedCoverageFiles()
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Dear Richard, Cheers, |
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Hi Freerk, If this is in active development, you may want to remove lines 2025-2028 in CoNVaDING.pl v1.2.1. Now that the chromosome name is processed in string context, there is no need to replace the non-numerical identifiers with numbers. I was planning on doing this, but did not want to Commit and submit a Pull-Request until I had time to make sure that this change worked. Best wishes, |
…nd autoSD to raw output
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Other option is to convert number to string by interpolation and use "eq" |
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Chromosomes in BED and BAM files start with "chr". createNormalizedCoverageFiles() was trying to compare chromosome names in samples and control files as if these names were numerics. The subroutine now treats both as strings for comparison.