Open ptrebert opened 2 years ago
@daewoooo
re your email: for one, which version of StrandPhaseR did you run? another point: you are using a different parameter setting, see at least recall.phased
(I guess lookup.bp
has this default value as given below):
correctInvertedRegionPhasing(
input.bams = bam.folder,
outputfolder = output.folder,
inv.bed = NULL,
recall.phased = TRUE,
het.genotype = 'strict',
snv.positions = variant.calls,
breakpointR.data = breakpointr.data,
strandphaseR.data = strandphaser.data,
pairedEndReads = TRUE,
min.mapq = 10,
background = 0.1,
vcfs.files = strandphaser.vcf,
lookup.bp = 1000000,
ref.fasta = clustered.assm,
assume.biallelic = TRUE
)
Apparently, I am not enough of an R programmer to understand how I have updated the documentation of the StrandPhaser function
would affect the runtime behavior of a function?
@daewoooo what is the status here, could you reproduce this problem with StrandPhaseR #8b93668 ?
Hi Peter, I'm sorry I was attending a conference this week. I will resolve this issue tomorrow. David
No problem; it's the last sample that's causing trouble, the light at the end of the tunnel is probably not a train...
@daewoooo I am still waiting for feedback on this one
Hi David,
in the call for
correctInvertedRegionPhasing
, I get the following error:I am copying the input data to the Globus share for debugging. Best, Peter