sequenceTools
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stschiff
We realised that the current damage model used in `--singleStrandMode` is not appropriate if the input pileup data contains alleles from unmerged R2 reads from paired-end sequencing. Currently, this means,...
v1.5.2 introduced a feature whereby lower-case letters in the pileup-input are automatically parsed as capital-letters and thereby fully considered when calling the alleles. This may be appropriate in many cases,...
Hi, I'm attempting to run sequenceTools to generate pseudo-haploid calls for a list of bamfiles. However I'm getting the following error: pileupCaller: SeqFormatException "cannot parse chromosome " Any suggestions? Thanks!
It has been suggested to me that in cases where diploid and haploid chromosomes are present, calling should ideally differentiate between the two. So for example, for human genomes, we...
I installed sequencetools 1.6.0.0 with conda (fresh env). However, when I am using pileupcaller and the --vcf option, I get an "invalid option --vcf" error and then it reports below...
``` [2 of 3] Compiling SequenceTools.Utils /home/curators/work/unpack-dir/unpacked/sequenceTools-1.5.3.1-54e9f0959a741bf603bcc485603f256e26a21f561f025ac7d572cd6a858bcc84/src/SequenceTools/Utils.hs:46:32: error: [GHC-83865] • Couldn't match type ‘Int’ with ‘(Int, Int)’ Expected: Maybe (Int, Int) -> GenoEntry Actual: Maybe Int -> GenoEntry • In...
As requested on Bioconda [here](https://github.com/bioconda/bioconda-recipes/pull/53566), we would like to add a linux-aarch64 built.