Rope bwt chr index #282
Rope bwt chr index #282
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…ull chromosome indexer.
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #282 +/- ##
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+ Coverage 80.46% 80.63% +0.17%
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Files 101 102 +1
Lines 7514 7592 +78
Branches 1230 1233 +3
==========================================
+ Hits 6046 6122 +76
- Misses 992 995 +3
+ Partials 476 475 -1 ☔ View full report in Codecov by Sentry. |
| else { | ||
| Pair("-n", "phgv2-ropebwt-conda") | ||
| } | ||
| //time ../ropebwt3/ropebwt3 build -t24 -i phg_ASMs_input.fmr -bo phg_ASMs.fmr /workdir/zrm22/phgv2/ropeBWT/fullASMTests/ASMs/A188 |
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I don't know if you want your file paths in here
| */ | ||
| fun runBuildStep(inputFasta:String, indexFilePrefix:String, numThreads: Int, condaEnvPrefix:String) { | ||
| //"conda","run","-p","phgv2-conda" | ||
| val prefixArg = if(condaEnvPrefix.isNotBlank()) { |
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Could this be refactored? It looks like you are repeating this if/else block several times throughout the file.
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For example:
// example helper function
fun getPrefixArg(condaEnvPrefix: String): Pair<String, String> {
if (condaEnvPrefix.isNotBlank()) {
Pair("-p", condaEnvPrefix)
} else {
Pair("-n", "phgv2-ropebwt-conda")
}
}
// deploy into other functions
val prefixArg = getPrefixArg(condaEnvPrefix)There was a problem hiding this comment.
Yep makes sense, I updated.
| val condaEnvPrefix by option (help = "Prefix for the conda environment to use. If provided, this should be the full path to the conda environment.") | ||
| .default("") | ||
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| override fun run() { |
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Do you want to call the parameter logging?
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Yes I thought I had put that in there but missed it. It's in there now.
Description
Full Chromosome BWT3 indexing
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xin boxes that apply.CHANGE(fix or feature that would cause existing functionality to not work as expected)FEATURE(non-breaking change which adds functionality)BUGFIX(non-breaking change which fixes an issue)ENHANCEMENT(non-breaking change which improves existing functionality)NONE(if none of the other choices apply. Example, tooling, build system, CI, docs, etc.)Checklist:
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