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My goal is to list some Todos and potential future directions. It is a WIP issue that I will continue in the forthcoming days. Next, I need to split this into individual issues and milestones.
# Mo…
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hi, thanks for the library!
I was wondering how best to handle a particular use-case, where a single column can "expand" into multiple categorical factors. The specific context is when analyzing da…
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I think it's likely that there is a general expression pattern for how mutated a tumor is. For example, super mutated tumors may have wacky gene expression, solely because they're super mutated and no…
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I was working on another issue and discovered that the example input YAML I was using was outdated and the workflow I was running could be run with Cromwell but not `cwltool`. Before putting out a ne…
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I got the foolowing error messages for about 1/3 of my single cell wgs after running latest scansnv as of today (12/6/19). Any ideas? For those cells with errors in the log, some produced file somati…
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Data and ref2020 are sybolic links that point to folders outside the repo. There are three solutions to fix this issue.
1. Add the data to the repository.
1. Post the data to FigShare or similar a…
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@petrelharp and I had an extended convo in Slack this week about silent mutations and the complications they introduce for users. I have some strong opinions about changes we could make so that future…
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Hi i am trying to run snpgenie.pl with this command:
```
snpgenie.pl
--vcfformat=4
--minfreq=0.01
--outdir results/7_Snps/SnpGenie_Dyak_Tai18E2/NW_025048829.1
--snpreport=results/7_Snps/Dyak_…
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The problem with using MD5 checksums for blacklisting mutations (blacklisting false-positives) is that a simple change in the source code (e.g. because of a new feature) will change ALL checksums and …
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This this the code:
```
public class BusinessLogic {
public int getPrice(int amountOfThings, boolean coupon) {
if (amountOfThings >= 20 || coupon) {
retu…