DamageProfiler

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How to run in Computing Cluster?

2

Hi, Thanks for a cool tool I am struggling to use it in computing clusters I uploaded tar.gz and opened it with the following command: > tar -xzvf v1.1.tar.gz I...

sultandromeda

When running DamageProfiler (`0.4.9`, within nf-core/eager `2.4.6`) on larger bam files, the rate at which reads are processed becomes slower and slower. At first: ``` 2023-07-28 12:12:04 INFO StartCalculations:115 -...

TCLamnidis

Add an option to subsample the input

1

Currently, there is no way to randomly subsample an input bam within DamageProfiler. When the input bams are very large, this can increase the runtime considerably, while the damage rates...

TCLamnidis

rescale

1

can damaeprofiler rescale qulity scores like mapdamage2? my samples are not udg treated so i need to rescale bam

atongsa

OutOfMemoryError: Java heap space

6

Hi there! I am using DamageProfiler 1.1 via the [conda package](https://anaconda.org/bioconda/damageprofiler), which means that the call to run the command line version simply is damageprofiler [options] instead of the call...

lczech

Performance improvements required

1

We should improve the overall performance of the application.

apeltzer

Relax reference name validation with ValidationStringency

6

Right now, the (default ?) reference name validation stringency of htsjdk is pretty strict, leading to errors when reference names in alignment files are ill-formated (for example, the refererence names...

maxibor

We should have a significant amount of tests

apeltzer

Hi, I want assistance with the script that I run via the Shell command: Script: java -Xmx75G -jar ~/bin/DamageProfiler.jar -i ${1}.cram -o ./${1}.damage -r ./refseq.fa Error: Picked up JAVA_TOOL_OPTIONS: -Xmx2g...

sultandromeda