Nils Homer
Nils Homer
Currently supports setting attributes on both ends using a single map.
See https://github.com/fulcrumgenomics/fgbio/pull/199 I find this personally very useful, so I'll assign this to myself.
Could also consider the same for the reference.
``` java -Xmx48G -jar /path/to/fgbio/target/scala-2.11/fgbio-0.1.2-SNAPSHOT.jar \ PickIlluminaIndices \ -n 1000000 \ -o /path/to/output.txt \ --vienna-rna-dir /path/to/ViennaRNA-2.2.5/src \ -l 10 \ -e 2 \ --allow-reverses=false \ --allow-reverse-complements=false \ --allow-palindromes=false \ --max-homopolymer=2...
The following terms need to be unified in `CallMolecularConsensusReads`, `VanillaUmiConsensusCaller`, and `VanillaUmiConsensusCallerOptions`: `errorRatePreUmi -> errorRatePreLabeling` `errorRatePostUmi -> errorRatePostLabeling` `maxBaseQuality -> maxRawBaseQuality` `baseQualityShift -> rawBaseQualityShift`
Extracted from this PR: https://github.com/fulcrumgenomics/fgbio/pull/422 FgbioMain ``` /* * The MIT License * * Copyright (c) 2016 Fulcrum Genomics LLC * * Permission is hereby granted, free of charge, to...
I could see it working like this. 1. Compute the edit distance between all pairs of barcodes. 2. Factor in `--max-mismatches` and `--min-mismatch-delta` to log if a pair of barcodes...
I've found the following useful for debugging, and so I'd like them to become debug options. The `group="debugging"` should be set on the argument annotation for the command line option....
Leaving this here for our later selves. In `fillInterior`, we could define a method and a few `var`s: ```scala val shouldUpdateBestScore: (Int, Int) => Boolean = { this.mode match {...
It has both `FgBioCommonArgs` and `FgBioTool` hard-wired in the `makeItSo` method.