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trichelab / spiky

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More issues with scanning bam files into a ssb_res like objects #25

Open prisnir-zz opened 3 years ago

prisnir-zz commented 3 years ago

I have noticed a few issues while working with some more functions: scan_spiked_bam

res <- scan_spiked_bam(sb, bins=GRanges()) ERROR message below:

# > res <- scan_spiked_bam(sb, bins=GRanges())
# Error in h(simpleError(msg, call)) : 
#   error in evaluating the argument 'table' in selecting a method for function '%in%': invalid class “PhredQuality” object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL")
# methylation_specificity(ssb_res)pending test

Also, I am running into a similar issue with ScanBamParam() fl <- scanBamFlag(isDuplicate=FALSE, isPaired=TRUE, isProperPair=TRUE)

> fl
keep0 keep1 
 4092  3071

bp <- ScanBamParam(flag=fl)

# Error in h(simpleError(msg, call)) : 
#   error in evaluating the argument 'table' in selecting a method for function '%in%': invalid class “PhredQuality” object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL")

Looks like a Rsamtools bug. Can you help sort this out please?